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Previous gene FasterDB identifier: 9765 - Ccdc3 (ENSMUSG00000026676) coiled-coil domain containing 3 Gene Next gene
Gene Close
Symbol Ccdc3
Synonyms ENSMUSG00000026676
Description coiled-coil domain containing 3 Gene
EnsEMBL link ENSMUSG00000026676
Chromosome 2 - forward strand
Chromosomal location
(UCSC link)		 5058795 - 5151910 (93116bp)
Sequence sequence
Associated transcripts AK172247 BC058616 NM_028804 AK009833
Alternative 3' splice site (acceptor) Close
 Identifier   Position   Distance (bp)   Transcript 
ASS1 3 106 AK172247
Alternative 5' splice sites (donor) Close
 Identifier   Position   Distance (bp)   Transcript 
ASS1 1 -380 AK172247
Intron retentions Close
 Identifier   Position   Transcript 
Exon deletions Close
 Identifier   Position   Transcript 
ED1 3 AK172247
Transcription start sites Close
 Identifier   Position   Gene coordinates   Chromosomal coordinates   Transcript 
P1 1 1 5058795 AK172247
P2 1 184 5058978 AK009833
Protein prediction Close
 Transcript name   Sequence 
AK172247 sequence
BC058616 sequence
NM_028804 sequence
AK009833 sequence
Polyadenylation Close
 Identifier   Position   Gene coordinates of cleavage site   Chromosomal coordinates of cleavage site   Pattern   PolyA tail   Accession number   Type 
PA1 3 93116 5151910 yes BC058616 Cdna
PA2 3 93116 5151910 yes NM_028804 Cdna
PA3 3 93116 5151910 no AK172247 Full_length
PA4 3 93116 5151910 no AK009833 Full_length

More polyadenylation sites ...

Exon skipping Close
 Identifier   Position   Transcript 
ES1 2 AK172247
Splice site strength Close
 Identifier   Site   Exon   Strength   Alternative   Sequence 
S1 5' (donor) 1 9.6 no AAGgtgagc
S2 5' (donor) 1 -16.49 yes GCCgccggc
S3 5' (donor) 2 9.16 no AGGgtaagg
S4 3' (acceptor) 2 10.74 no ctttgacccttccccttcagGAT
S5 3' (acceptor) 3 9.34 no tgtactgtttctgccctcagCTC
S6 3' (acceptor) 3 -24.5 yes gcggaacaggcagctccgagAGC
Conserved exons Close
 Gene identifier human   Position mouse  Position human 
11409 1 11
11409 2 12
Report Close
 Exon   Number of supporting transcripts 
 Transcription initiation & first exon(s) 
1 2
 Transcription termination & last exon(s) 
3 4
 Exon skipping 
2 1
 Alternative 3' splice sites 
3 1
 Alternative 5' splice sites 
1 1
 Exon deletions 
3 1
Splicing factors Close
 Splicing factor   Exon array   CLIP data   Exon position 
CELF1 (CUG-BP)
 
DAZAP1
 
ELAVL1 (HuR)
 
ESRP1/2 Yes
 
FUS Yes
 
HNRNPA1
 
HNRNPA2B1
 
HNRNPAB
 
HNRNPC
 
HNRNPF-H
 
HNRNPL Yes
 
HNRNPL_2
 
HNRNPM
 
HNRNPU
 
MBNL3KO/MBNL3WT/MBNL3C2C12 Yes
 
Nova/Nova1 Yes
 
PTBP1/2 Yes
 
QKI
 
RBFOX2
 
RBM4 Yes
 
SFRS3 (SRP20)
 
SFRS6 (SRP55)
 
SFRS7 (9G8)
 
SRSF1 Yes
 
SRSF2 Yes
 
SRSF5 (SRP40)
 
TIA1/TIAL1
 
TRA2A
 
TRA2B
 
YBX1
 
Expression Close
 Exon position   Tissues   Cell lines 
1 Expression Expression
2 Expression Expression
3 Expression Expression
Exon-Intron Close
 Position   Type   Gene coordinates   Chromosomal coordinates   Length   Sequence   Features 
1 Exon 1 - 559 5058795 - 5059353 559 sequence download
1 Intron 560 - 3482 5059354 - 5062276 2923 sequence -
2 Exon 3483 - 3657 5062277 - 5062451 175 sequence download
2 Intron 3658 - 91167 5062452 - 5149961 87510 sequence -
3 Exon 91168 - 93116 5149962 - 5151910 1949 sequence download
Close  5' untranslated regions 
 UTR 1 
 Supporting GenBank
accession identifers 		 BC058616
NM_028804
 Length  158
 Number of ATGs in frame  1
 Total number of ATGs  1
 Number of GTGs in frame  0
 Total number of GTGs  1
 Number of CTGs in frame  1
 Total number of CTGs  2
 Number of micro ORFs in frame  1
 Total number of micro ORFs  1
 GC percentage  80
 Number of pyrimidine tracks  0
Close 3' untranslated regions 
 UTR 1 
 Supporting GenBank
accession identifers 		 BC058616
NM_028804
AK009833
 Length  1676
 Number of ATGs in frame  7
 Total number of ATGs  36
 Number of GTGs in frame  15
 Total number of GTGs  42
 Number of CTGs in frame  11
 Total number of CTGs  29
 GC percentage  47
 Number of pyrimidine tracks  15
miRNAs Close
 Identifier    Name    Gene coordinates   Chromosomal coordinates   Prediction algorithm 
Group 1
M1 mmu-miR-211 91806 - 91813 5150600 - 5150607 pictar
M2 mmu-miR-204 91806 - 91813 5150600 - 5150607 pictar
M3 mmu-miR-211 92003 - 92010 5150797 - 5150804 pictar
M4 mmu-miR-204 92003 - 92010 5150797 - 5150804 pictar
M5 mmu-miR-22 92010 - 92033 5150804 - 5150827 miranda
M6 mmu-miR-145 92153 - 92175 5150947 - 5150969 miranda
M7 mmu-miR-211 92334 - 92341 5151128 - 5151135 pictar
M8 mmu-miR-204 92334 - 92341 5151128 - 5151135 pictar
M9 mmu-miR-542-3p 92713 - 92735 5151507 - 5151529 miranda
M10 mmu-miR-211 92847 - 92854 5151641 - 5151648 pictar
M11 mmu-miR-204 92847 - 92854 5151641 - 5151648 pictar
M12 mmu-miR-204 92998 - 93005 5151792 - 5151799 pictar
M13 mmu-miR-211 92998 - 93005 5151792 - 5151799 pictar
Protein features Close
 Category   Feature identifier   Feature name   Exons   Start on gene   End on gene 
Localization EXONT:000016 Peroxisome targeting signal 1 575 583
Structure EXONT:000027 Polypeptide_repeat 1 236 247
Structure EXONT:000074 Intrinsically_unstructured_polypeptide_region 1 326 352
Structure EXONT:000027 Polypeptide_repeat 1 404 415
Structure EXONT:000027 Polypeptide_repeat 1 461 472
Structure EXONT:000027 Polypeptide_repeat 1 491 502
Structure EXONT:000027 Polypeptide_repeat 1 521 532
Structure EXONT:000027 Polypeptide_repeat 1 551 562
PTM EXONT:000161 O-phospho-L-serine 1 170 172
PTM EXONT:000161 O-phospho-L-serine 1 212 214
PTM EXONT:000161 O-phospho-L-serine 1 290 292
PTM EXONT:000161 O-phospho-L-serine 1 302 304
PTM EXONT:000161 O-phospho-L-serine 1 320 322
PTM EXONT:000161 O-phospho-L-serine 1 332 334
PTM EXONT:000161 O-phospho-L-serine 1 350 352
PTM EXONT:000161 O-phospho-L-serine 1 362 364
Gene Ccdc3

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Exon 1Exon 2Exon 1Exon 2Exon 3Extended region