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Previous gene FasterDB identifier: 14439 - SEMA3F (Sema4, SEMAK) sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3F Next gene
Gene Close
Symbol SEMA3F
Synonyms Sema4, SEMAK
Description sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3F
EnsEMBL link ENSG00000001617
Chromosome 3 - forward strand
Chromosomal location
(UCSC link)		 50192524 - 50226507 (33984bp)
Sequence sequence
Associated transcripts AB209259 BC042914 NM_004186 U33920 U38276
Alternative 3' splice site (acceptor) Close
 Identifier   Position   Distance (bp)   Transcript 
ASS1 5 12 BC042914
NM_004186
U33920
U38276
Alternative 5' splice sites (donor) Close
 Identifier   Position   Distance (bp)   Transcript 
Intron retentions Close
 Identifier   Position   Transcript 
Exon deletions Close
 Identifier   Position   Transcript 
No data
Transcription start sites Close
 Identifier   Position   Gene coordinates   Chromosomal coordinates   Transcript 
P1 1 1 50192524 AB209259
P2 2 325 50192848 BC042914
NM_004186
P3 3 3929 50196452 U38276
Protein prediction Close
 Transcript name   Sequence 
AB209259 sequence
BC042914 sequence
NM_004186 sequence
U33920 sequence
U38276 sequence
Polyadenylation Close
 Identifier   Position   Gene coordinates of cleavage site   Chromosomal coordinates of cleavage site   Pattern   PolyA tail   Accession number   Type 
PA1 21 33131 50225654 TATAAA no AI378926 3prime_est
PA2 21 33984 50226507 AATAAA no AB209259 Cdna
PA3 21 33984 50226507 AATAAA yes BC042914 Cdna
PA4 21 33984 50226507 AATAAA yes NM_004186 Cdna

More polyadenylation sites ...

Exon skipping Close
 Identifier   Position   Transcript 
ES1 2 AB209259
ES2 3 AB209259
BC042914
NM_004186
U33920
ES3 4 AB209259
ES4 8 AB209259
U38276
Splice site strength Close
 Identifier   Site   Exon   Strength   Alternative   Sequence 
S1 5' (donor) 1 -27.46 no GGGtacgcc
S2 5' (donor) 2 10.03 no GAGgtgagt
S3 3' (acceptor) 2 -11.27 no cggaaccggttaagccgcggCCG
S4 5' (donor) 3 4.67 no CTGgttggt
S5 3' (acceptor) 3 -8.55 no cattctctgcctttccttttCTG
S6 5' (donor) 4 10.57 no AAGgtaaga
S7 3' (acceptor) 4 9.02 no atcttggttccccttcccagGTT
S8 5' (donor) 5 4.89 no ATTgtaagg
S9 3' (acceptor) 5 -23.24 no gtcctaattggtgccctgccCTC
S10 3' (acceptor) 5 11.29 yes gccctgccctccacccacagAGC
S11 5' (donor) 6 9.54 no AACgtgagt
S12 3' (acceptor) 6 11.6 no tctgacccccctctctgcagATA
S13 5' (donor) 7 9.88 no CAGgtaagc
S14 3' (acceptor) 7 7.5 no agccttccctgtggccccagGGC
S15 5' (donor) 8 8.07 no CAGgtgggc
S16 3' (acceptor) 8 10.56 no cctgttcctcgtcttctcagGCC
S17 5' (donor) 9 7.68 no TCAgtgagt
S18 3' (acceptor) 9 9.08 no agccccgctctgccttacagGAT
S19 5' (donor) 10 9.89 no ACGgtaagc
S20 3' (acceptor) 10 8.27 no acccactggcctacccacagATG
S21 5' (donor) 11 6.73 no CTGgtatgc
S22 3' (acceptor) 11 9.5 no ctgacccctgccacctgcagACC
S23 5' (donor) 12 8.93 no TCCgtgagt
S24 3' (acceptor) 12 8.79 no cctcttgccccaccccccagAAC
S25 5' (donor) 13 6.74 no TGGgtgagg
S26 3' (acceptor) 13 12.75 no ccttctccctctgtccccagAGG
S27 5' (donor) 14 10.38 no ACGgtaagg
S28 3' (acceptor) 14 7.03 no agcgcctgccatgcccacagCTC
S29 5' (donor) 15 8.63 no CAGgtaccc
S30 3' (acceptor) 15 6.73 no cactcgccacctgtccacagTGC
S31 5' (donor) 16 8.23 no AAGgtgggt
S32 3' (acceptor) 16 7.03 no ccctgcccggcccgttccagACC
S33 5' (donor) 17 9.04 no AGGgtaagc
S34 3' (acceptor) 17 10.82 no tgatctttatctttttctagGAT
S35 5' (donor) 18 4.48 no GAGgtgtgg
S36 3' (acceptor) 18 4.54 no ggccctaccctttgccccagCAA
S37 5' (donor) 19 10.13 no ATGgtgagt
S38 3' (acceptor) 19 5.4 no caggggctatcctcatccagGCG
S39 5' (donor) 20 10.03 no GAGgtgagt
S40 3' (acceptor) 20 5.34 no caacccctctcactctaaagCCA
S41 3' (acceptor) 21 13.15 no ccctctccttgcccctgcagATT
Conserved exons Close
 Gene identifier mouse   Position human  Position mouse 
7980 1 2
7980 4 3
7980 5 4
7980 6 5
7980 7 6
7980 8 7
7980 9 8
7980 10 9
7980 11 10
7980 12 11
7980 13 12
7980 14 13
7980 15 14
7980 16 15
7980 17 16
7980 18 17
7980 19 18
7980 20 19
7980 21 20
Report Close
 Exon   Number of supporting transcripts 
 Transcription initiation & first exon(s) 
1 1
2 1
3 1
 Transcription termination & last exon(s) 
21 4
 Exon skipping 
2 1
3 4
4 1
8 2
 Alternative 3' splice sites 
5 1
Splicing factors Close
 Splicing factor   Exon array   CLIP data   Exon position 
CELF1 (CUG-BP)
 
DAZAP1
 
ELAVL1 (HuR) Yes Yes
 
ESRP1/2 (ESRP) Yes
 
FUS Yes
 
HNRNPA1 Yes
 
HNRNPA2B1 Yes
 
HNRNPAB
 
HNRNPC Yes
 
HNRNPF/HNRNPH1 Yes Yes
 
HNRNPL Yes
 
HNRNPL_2
 
HNRNPM Yes
 
HNRNPU Yes
 
MBNL
 
NOVA1
 
PTBP1/2 (PTB) Yes Yes
 
QKI
 
RBFOX2 (FOX2) Yes
 
RBM4 Yes
 
SFRS3 (SRP20)
 
SFRS6 (SRP55)
 
SFRS7 (9G8)
 
SRSF1 (SF2ASF)
 
SRSF2 (SC35)
 
SRSF5 (SRP40)
 
TDP43
 
TIA1/TIAL1 Yes
 
TRA2A
 
TRA2B
 
YBX1 (YB1)
 
Expression Close
 Exon position   Tissues   Cell lines   Cancer cell lines 
1 Expression Expression Expression
2 Expression Expression Expression
3 Expression Expression Expression
4 Expression Expression Expression
5 Expression Expression Expression
6 Expression Expression Expression
7 Expression Expression Expression
8 Expression Expression Expression
9 Expression Expression Expression
10 Expression Expression Expression
11 Expression Expression Expression
12 Expression Expression Expression
13 Expression Expression Expression
14 Expression Expression Expression
15 Expression Expression Expression
16 Expression Expression Expression
17 Expression Expression Expression
18 Expression Expression Expression
19 Expression Expression Expression
20 Expression Expression Expression
21 Expression Expression Expression
Exon-Intron Close
 Position   Type   Gene coordinates   Chromosomal coordinates   Length   Sequence   Features 
1 Exon 1 - 58 50192524 - 50192581 58 sequence download
1 Intron 59 - 324 50192582 - 50192847 266 sequence -
2 Exon 325 - 474 50192848 - 50192997 150 sequence download
2 Intron 475 - 3928 50192998 - 50196451 3454 sequence -
3 Exon 3929 - 4198 50196452 - 50196721 270 sequence download
3 Intron 4199 - 4484 50196722 - 50197007 286 sequence -
4 Exon 4485 - 4644 50197008 - 50197167 160 sequence download
4 Intron 4645 - 18690 50197168 - 50211213 14046 sequence -
5 Exon 18691 - 18863 50211214 - 50211386 173 sequence download
5 Intron 18864 - 18961 50211387 - 50211484 98 sequence -
6 Exon 18962 - 19024 50211485 - 50211547 63 sequence download
6 Intron 19025 - 19140 50211548 - 50211663 116 sequence -
7 Exon 19141 - 19260 50211664 - 50211783 120 sequence download
7 Intron 19261 - 20005 50211784 - 50212528 745 sequence -
8 Exon 20006 - 20098 50212529 - 50212621 93 sequence download
8 Intron 20099 - 21677 50212622 - 50214200 1579 sequence -
9 Exon 21678 - 21771 50214201 - 50214294 94 sequence download
9 Intron 21772 - 27193 50214295 - 50219716 5422 sequence -
10 Exon 27194 - 27313 50219717 - 50219836 120 sequence download
10 Intron 27314 - 27553 50219837 - 50220076 240 sequence -
11 Exon 27554 - 27693 50220077 - 50220216 140 sequence download
11 Intron 27694 - 27813 50220217 - 50220336 120 sequence -
12 Exon 27814 - 27928 50220337 - 50220451 115 sequence download
12 Intron 27929 - 28095 50220452 - 50220618 167 sequence -
13 Exon 28096 - 28165 50220619 - 50220688 70 sequence download
13 Intron 28166 - 28329 50220689 - 50220852 164 sequence -
14 Exon 28330 - 28474 50220853 - 50220997 145 sequence download
14 Intron 28475 - 29501 50220998 - 50222024 1027 sequence -
15 Exon 29502 - 29724 50222025 - 50222247 223 sequence download
15 Intron 29725 - 30352 50222248 - 50222875 628 sequence -
16 Exon 30353 - 30441 50222876 - 50222964 89 sequence download
16 Intron 30442 - 30575 50222965 - 50223098 134 sequence -
17 Exon 30576 - 30617 50223099 - 50223140 42 sequence download
17 Intron 30618 - 30798 50223141 - 50223321 181 sequence -
18 Exon 30799 - 30956 50223322 - 50223479 158 sequence download
18 Intron 30957 - 31190 50223480 - 50223713 234 sequence -
19 Exon 31191 - 31258 50223714 - 50223781 68 sequence download
19 Intron 31259 - 31522 50223782 - 50224045 264 sequence -
20 Exon 31523 - 31656 50224046 - 50224179 134 sequence download
20 Intron 31657 - 32614 50224180 - 50225137 958 sequence -
21 Exon 32615 - 33984 50225138 - 50226507 1370 sequence download
Close  5' untranslated regions 
 UTR 1   UTR 2   UTR 3 
 Supporting GenBank
accession identifers 		 BC042914
NM_004186
U33920
 U38276
 AB209259
 Length  198 900 544
 Number of ATGs in frame  0 4 2
 Total number of ATGs  1 13 8
 Number of GTGs in frame  2 13 8
 Total number of GTGs  4 31 13
 Number of CTGs in frame  1 6 5
 Total number of CTGs  2 16 10
 Number of micro ORFs in frame  0 2 1
 Total number of micro ORFs  1 2 1
 GC percentage  79 58 59
 Number of pyrimidine tracks  2 12 3
Close 3' untranslated regions 
 UTR 1   UTR 2   UTR 3 
 Supporting GenBank
accession identifers 		 BC042914
U38276
U33920
 AB209259
 NM_004186
 Length  963 961 959
 Number of ATGs in frame  5 5 3
 Total number of ATGs  11 11 11
 Number of GTGs in frame  5 18 10
 Total number of GTGs  33 33 33
 Number of CTGs in frame  3 5 8
 Total number of CTGs  14 14 14
 GC percentage  57 57 57
 Number of pyrimidine tracks  5 5 5
miRNAs Close
 Identifier    Name    Gene coordinates   Chromosomal coordinates   Prediction algorithm 
Group 1
M1 hsa-miR-328 33049 - 33056 50225572 - 50225579 pictar
Group 2
M1 hsa-miR-431 33131 - 33150 50225654 - 50225673 miranda
M2 hsa-miR-1207-5p 33132 - 33138 50225655 - 50225661 pita
M3 hsa-miR-486-3p 33134 - 33140 50225657 - 50225663 pita
M4 hsa-miR-200c 33134 - 33156 50225657 - 50225679 miranda
M5 hsa-miR-429 33135 - 33156 50225658 - 50225679 miranda
M6 hsa-miR-200b 33135 - 33156 50225658 - 50225679 miranda
M7 hsa-miR-511 33144 - 33150 50225667 - 50225673 pita
M8 hsa-miR-429 33148 - 33155 50225671 - 50225678 pita
M9 hsa-miR-200c 33149 - 33156 50225672 - 50225679 pictar
M10 hsa-miR-200c 33149 - 33156 50225672 - 50225679 targetscan
M11 hsa-miR-200b 33149 - 33156 50225672 - 50225679 pictar
M12 hsa-miR-429 33149 - 33156 50225672 - 50225679 targetscan
M13 hsa-miR-200b 33149 - 33155 50225672 - 50225678 pita
M14 hsa-miR-200c 33149 - 33155 50225672 - 50225678 pita
M15 hsa-miR-200b 33149 - 33156 50225672 - 50225679 targetscan
M16 hsa-let-7d 33177 - 33184 50225700 - 50225707 pictar
M17 hsa-let-7a 33177 - 33184 50225700 - 50225707 pictar
M18 hsa-miR-98 33177 - 33184 50225700 - 50225707 pictar
M19 hsa-let-7g 33177 - 33184 50225700 - 50225707 pictar
M20 hsa-let-7f 33177 - 33184 50225700 - 50225707 pictar
M21 hsa-let-7e 33177 - 33184 50225700 - 50225707 pictar
M22 hsa-let-7i 33178 - 33185 50225701 - 50225708 pictar
M23 hsa-let-7c 33178 - 33185 50225701 - 50225708 pictar
M24 hsa-let-7b 33178 - 33185 50225701 - 50225708 pictar
M25 hsa-miR-328 33253 - 33260 50225776 - 50225783 pictar
M26 hsa-miR-328 33271 - 33278 50225794 - 50225801 pictar
M27 hsa-miR-328 33276 - 33283 50225799 - 50225806 pictar
M28 hsa-let-7g 33314 - 33321 50225837 - 50225844 pictar
M29 hsa-let-7f 33314 - 33321 50225837 - 50225844 pictar
M30 hsa-let-7e 33314 - 33321 50225837 - 50225844 pictar
M31 hsa-let-7d 33314 - 33321 50225837 - 50225844 pictar
M32 hsa-miR-98 33314 - 33321 50225837 - 50225844 pictar
M33 hsa-let-7c 33314 - 33321 50225837 - 50225844 pictar
M34 hsa-let-7i 33314 - 33321 50225837 - 50225844 pictar
M35 hsa-let-7b 33314 - 33321 50225837 - 50225844 pictar
M36 hsa-miR-328 33501 - 33508 50226024 - 50226031 pictar
M37 hsa-miR-31 33607 - 33614 50226130 - 50226137 pictar
M38 hsa-miR-328 33619 - 33626 50226142 - 50226149 pictar
M39 hsa-miR-328 33655 - 33662 50226178 - 50226185 pictar
M40 hsa-miR-328 33665 - 33672 50226188 - 50226195 pictar
M41 hsa-let-7d 33679 - 33686 50226202 - 50226209 pictar
M42 hsa-miR-98 33679 - 33686 50226202 - 50226209 pictar
M43 hsa-let-7c 33679 - 33686 50226202 - 50226209 pictar
M44 hsa-let-7i 33679 - 33686 50226202 - 50226209 pictar
M45 hsa-let-7b 33679 - 33686 50226202 - 50226209 pictar
M46 hsa-let-7g 33679 - 33686 50226202 - 50226209 pictar
M47 hsa-let-7a 33679 - 33686 50226202 - 50226209 pictar
M48 hsa-let-7f 33679 - 33686 50226202 - 50226209 pictar
M49 hsa-let-7e 33679 - 33686 50226202 - 50226209 pictar
M50 hsa-miR-328 33736 - 33743 50226259 - 50226266 pictar
M51 hsa-miR-328 33741 - 33748 50226264 - 50226271 pictar
M52 hsa-miR-328 33805 - 33812 50226328 - 50226335 pictar
M53 hsa-miR-328 33880 - 33887 50226403 - 50226410 pictar
M54 hsa-miR-612 33923 - 33930 50226446 - 50226453 pita
M55 hsa-miR-1285 33924 - 33930 50226447 - 50226453 pita
M56 hsa-miR-661 33926 - 33932 50226449 - 50226455 pita
M57 hsa-miR-31 33953 - 33960 50226476 - 50226483 pictar
M58 hsa-miR-199a-5p 33965 - 33972 50226488 - 50226495 pita
M59 hsa-miR-199b-5p 33965 - 33972 50226488 - 50226495 pita
M60 hsa-miR-199a-5p 33966 - 33973 50226489 - 50226496 targetscan
M61 hsa-miR-199b-5p 33966 - 33973 50226489 - 50226496 targetscan
M62 hsa-miR-575 33968 - 33974 50226491 - 50226497 pita
Protein features Close
 Category   Feature identifier   Feature name   Exons   Start on gene   End on gene 
Receptor EXONT:007890 Plexin-like fold 18,19 30850 31242
Binding EXONT:002928 Sema domain 4,5,6,7,8,9,10,11,12,13,14,15,16,17,18 4614 30864
Binding EXONT:002929 WD40/YVTN repeat-like-containing domain 4,5,6,7,8,9,10,11,12,13,14,15,16,17,18 4620 30852
Binding EXONT:004886 Immunoglobulin-like domain 20,21 31564 32737
Localization EXONT:000019 Signal_peptide 4 4533 4586
Localization EXONT:000064 Nuclear_localization_signal 9 21720 21737
Localization EXONT:000064 Nuclear_localization_signal 15 29634 29651
Localization EXONT:000067 Nuclear_export_signal 16,17 30397 30578
Localization EXONT:000064 Nuclear_localization_signal 21 32981 32998
Structure EXONT:000074 Intrinsically_unstructured_polypeptide_region 8 20012 20077
Structure EXONT:000074 Intrinsically_unstructured_polypeptide_region 15 29502 29528
Structure EXONT:007890 Plexin-like fold 18,19 30850 31242
Structure EXONT:000074 Intrinsically_unstructured_polypeptide_region 18,19 30949 31230
Structure EXONT:000074 Intrinsically_unstructured_polypeptide_region 21 32789 32863
Structure EXONT:000024 Compositionally_biased_region_of_peptide 21 32939 33004
PTM EXONT:000992 N4-(N-acetylamino)glucosyl-L-asparagine 5 18747 18749
PTM EXONT:000121 L-cystine (cross-link) 6,7 18998 19149
PTM EXONT:000935 Cysteinylation (disulfide with free L-cysteine) 6,7 18998 19149
PTM EXONT:000992 N4-(N-acetylamino)glucosyl-L-asparagine 7 19180 19182
PTM EXONT:000164 O4'-phospho-L-tyrosine 7 19195 19197
PTM EXONT:000121 L-cystine (cross-link) 7 19201 19230
PTM EXONT:000935 Cysteinylation (disulfide with free L-cysteine) 7 19201 19230
PTM EXONT:000164 O4'-phospho-L-tyrosine 7 19234 19236
PTM EXONT:000180 N-acetylated L-lysine 9 21720 21722
PTM EXONT:000192 N6-acetyl-L-lysine 9 21720 21722
PTM EXONT:000180 N-acetylated L-lysine 9 21726 21728
PTM EXONT:000192 N6-acetyl-L-lysine 9 21726 21728
PTM EXONT:000121 L-cystine (cross-link) 11,12,13,14,15 27688 29504
PTM EXONT:000935 Cysteinylation (disulfide with free L-cysteine) 11,12,13,14,15 27688 29504
PTM EXONT:000180 N-acetylated L-lysine 15 29541 29543
PTM EXONT:000192 N6-acetyl-L-lysine 15 29541 29543
PTM EXONT:000161 O-phospho-L-serine 15 29577 29579
PTM EXONT:000164 O4'-phospho-L-tyrosine 15 29592 29594
PTM EXONT:000164 O4'-phospho-L-tyrosine 15 29700 29702
PTM EXONT:000162 O-phospho-L-threonine 15 29721 29723
PTM EXONT:000121 L-cystine (cross-link) 18 30853 30909
PTM EXONT:000935 Cysteinylation (disulfide with free L-cysteine) 18 30853 30909
PTM EXONT:000121 L-cystine (cross-link) 21 32699 32905
PTM EXONT:000935 Cysteinylation (disulfide with free L-cysteine) 21 32699 32905
Unclassified EXONT:003680 Immunoglobulin subtype 20,21 31540 32758
Unclassified EXONT:002625 Immunoglobulin-like fold 20,21 31558 32764
Gene SEMA3F
Gene SEMA3F Gene SEMA3F
Gene SEMA3F Gene SEMA3F
Gene SEMA3F Gene SEMA3F
Gene SEMA3F Gene SEMA3F
Gene SEMA3F Gene SEMA3F
Gene SEMA3F Gene SEMA3F
Gene SEMA3F Gene SEMA3F
Gene SEMA3F Gene SEMA3F

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Exon 1Exon 2Exon 3Exon 4Exon 5Exon 6Exon 7Exon 8Exon 9Exon 10Exon 11Exon 12Exon 13Exon 14Exon 15Exon 16Exon 17Exon 18Exon 19Exon 20Exon 1Exon 2Exon 3Exon 4Exon 5Exon 6Exon 7Exon 8Exon 9Exon 10Exon 11Exon 12Exon 13Exon 14Exon 15Exon 16Exon 17Exon 18Exon 19Exon 20Exon 21Extended region