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Previous gene FasterDB identifier: 11409 - CCDC3 (DKFZp761F241) coiled-coil domain containing 3 Next gene
Gene Close
Symbol CCDC3
Synonyms DKFZp761F241
Description coiled-coil domain containing 3
EnsEMBL link ENSG00000151468
Chromosome 10 - reverse strand
Chromosomal location
(UCSC link)		 12938627 - 13141713 (203087bp)
Sequence sequence
Associated transcripts AK311458 AK307203 AK095792 AK307304 CR618046 BC051334 NM_031455 AL136562
Alternative 3' splice site (acceptor) Close
 Identifier   Position   Distance (bp)   Transcript 
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 13141713 AK311458
P2 1 5 13141709 AK307203
P3 1 62 13141652 AK095792
P4 7 49807 13091907 AK307304
P5 11 97976 13043738 CR618046
Protein prediction Close
 Transcript name   Sequence 
AK311458 sequence
AK307203 sequence
AK095792 sequence
AK307304 sequence
CR618046 sequence
BC051334 sequence
NM_031455 sequence
AL136562 sequence
Polyadenylation Close
 Identifier   Position   Gene coordinates of cleavage site   Chromosomal coordinates of cleavage site   Pattern   PolyA tail   Accession number   Type 
PA1 10 93603 13048111 no AK311458 Full_length
PA2 13 201444 12940270 no AK307203 Full_length
PA3 13 201757 12939957 no AK307304 Full_length
PA4 13 203087 12938627 AATAAA yes BC051334 Cdna
PA5 13 203087 12938627 AATAAA yes NM_031455 Cdna
PA6 13 203087 12938627 AATAAA yes AL136562 Cdna
PA7 13 203087 12938627 AATAAA no AK095792 Full_length

More polyadenylation sites ...

Exon skipping Close
 Identifier   Position   Transcript 
ES1 2 AK311458
AK307203
ES2 3 AK311458
AK307203
ES3 4 AK311458
AK095792
ES4 5 AK307203
ES5 6 AK307203
AK095792
ES6 7 AK307203
ES7 8 AK311458
AK307203
AK095792
ES8 9 AK307203
AK095792
AK307304
ES9 10 AK307203
AK095792
AK307304
ES10 11 AK307203
AK095792
AK307304
ES11 12 AK307203
AK307304
Splice site strength Close
 Identifier   Site   Exon   Strength   Alternative   Sequence 
S1 5' (donor) 1 9.45 no AAGgtagga
S2 5' (donor) 2 2.46 no GGAgtgagc
S3 3' (acceptor) 2 4.03 no caaaacctaatctgaaacagGAA
S4 5' (donor) 3 11.37 no GCGgtaagt
S5 3' (acceptor) 3 1.49 no tatctactgggataatccagGCA
S6 5' (donor) 4 10.03 no GAGgtgagt
S7 3' (acceptor) 4 6.08 no tactgtttaaaaccctatagGTG
S8 5' (donor) 5 10.47 no AAGgtgagt
S9 3' (acceptor) 5 4.75 no tctgtttcttgcaatcctagTAA
S10 5' (donor) 6 6 no CCGgtaaaa
S11 3' (acceptor) 6 8.89 no tgtgtctgtgcatcttccagCTC
S12 5' (donor) 7 10.74 no AACgtaagt
S13 3' (acceptor) 7 9.72 no gtgtttcttcccgtcctcagCTA
S14 5' (donor) 8 8.1 no GAGgtaaca
S15 3' (acceptor) 8 5.64 no taattttaatcccttctcagCTG
S16 5' (donor) 9 11 no AAGgtaagt
S17 3' (acceptor) 9 9.64 no gtggtttctcctctttctagAAA
S18 5' (donor) 10 -4.91 no CATggatga
S19 3' (acceptor) 10 7.89 no ctatcacatttattctgcagAGA
S20 5' (donor) 11 9.6 no CAGgtgagc
S21 3' (acceptor) 11 -15.23 no ccagtccccgggacccttttAAA
S22 5' (donor) 12 9.21 no AGGgtaaga
S23 3' (acceptor) 12 10.38 no gcctttttttcctccattagGAT
S24 3' (acceptor) 13 10.38 no cacgctgtctctgcctccagCTC
Conserved exons Close
 Gene identifier mouse   Position human  Position mouse 
9765 11 1
9765 12 2
Report Close
 Exon   Number of supporting transcripts 
 Transcription initiation & first exon(s) 
1 3
7 1
11 1
 Transcription termination & last exon(s) 
10 1
13 6
 Exon skipping 
2 2
3 2
4 2
5 1
6 2
7 1
8 3
9 3
10 3
11 3
12 2
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
Exon-Intron Close
 Position   Type   Gene coordinates   Chromosomal coordinates   Length   Sequence   Features 
1 Exon 1 - 208 13141506-13141713 208 sequence download
1 Intron 209 - 404 13141310-13141505 196 sequence -
2 Exon 405 - 630 13141084-13141309 226 sequence download
2 Intron 631 - 1111 13140603-13141083 481 sequence -
3 Exon 1112 - 1189 13140525-13140602 78 sequence download
3 Intron 1190 - 1236 13140478-13140524 47 sequence -
4 Exon 1237 - 1508 13140206-13140477 272 sequence download
4 Intron 1509 - 25613 13116101-13140205 24105 sequence -
5 Exon 25614 - 25846 13115868-13116100 233 sequence download
5 Intron 25847 - 26350 13115364-13115867 504 sequence -
6 Exon 26351 - 26484 13115230-13115363 134 sequence download
6 Intron 26485 - 49772 13091942-13115229 23288 sequence -
7 Exon 49773 - 50040 13091674-13091941 268 sequence download
7 Intron 50041 - 50949 13090765-13091673 909 sequence -
8 Exon 50950 - 51028 13090686-13090764 79 sequence download
8 Intron 51029 - 92608 13049106-13090685 41580 sequence -
9 Exon 92609 - 92683 13049031-13049105 75 sequence download
9 Intron 92684 - 93552 13048162-13049030 869 sequence -
10 Exon 93553 - 93603 13048111-13048161 51 sequence download
10 Intron 93604 - 97975 13043739-13048110 4372 sequence -
11 Exon 97976 - 98517 13043197-13043738 542 sequence download
11 Intron 98518 - 101201 13040513-13043196 2684 sequence -
12 Exon 101202 - 101376 13040338-13040512 175 sequence download
12 Intron 101377 - 201034 12940680-13040337 99658 sequence -
13 Exon 201035 - 203087 12938627-12940679 2053 sequence download
Close  5' untranslated regions 
 UTR 1   UTR 2   UTR 3   UTR 4 
 Supporting GenBank
accession identifers 		 CR618046
BC051334
NM_031455
AL136562
 AK095792
 AK307203
 AK307304
 Length  168 953 478 316
 Number of ATGs in frame  0 5 0 2
 Total number of ATGs  1 10 6 3
 Number of GTGs in frame  0 14 6 2
 Total number of GTGs  1 35 11 10
 Number of CTGs in frame  0 5 2 4
 Total number of CTGs  4 16 8 6
 Number of micro ORFs in frame  0 4 0 2
 Total number of micro ORFs  1 8 5 3
 GC percentage  83 50 50 50
 Number of pyrimidine tracks  1 4 2 3
Close 3' untranslated regions 
 UTR 1   UTR 2   UTR 3 
 Supporting GenBank
accession identifers 		 AL136562
CR618046
AK307304
AK307203
 BC051334
NM_031455
 AK095792
 Length  1789 1788 1787
 Number of ATGs in frame  14 14 9
 Total number of ATGs  23 23 22
 Number of GTGs in frame  15 15 12
 Total number of GTGs  62 62 62
 Number of CTGs in frame  8 8 7
 Total number of CTGs  30 30 31
 GC percentage  50 50 51
 Number of pyrimidine tracks  16 16 16
miRNAs Close
 Identifier    Name    Gene coordinates   Chromosomal coordinates   Prediction algorithm 
Group 1
M1 hsa-miR-211 201774 - 201781 12939933 - 12939940 pictar
M2 hsa-miR-204 201774 - 201781 12939933 - 12939940 pictar
M3 hsa-miR-211 201894 - 201901 12939813 - 12939820 pictar
M4 hsa-miR-204 201894 - 201901 12939813 - 12939820 pictar
M5 hsa-miR-138 201940 - 201962 12939752 - 12939774 miranda
M6 hsa-miR-376c 202110 - 202131 12939583 - 12939604 miranda
M7 hsa-miR-204 202235 - 202242 12939472 - 12939479 pictar
M8 hsa-miR-211 202235 - 202242 12939472 - 12939479 pictar
M9 hsa-miR-142-3p 202389 - 202413 12939301 - 12939325 miranda
M10 hsa-miR-136 202408 - 202431 12939283 - 12939306 miranda
M11 hsa-miR-211 202967 - 202974 12938740 - 12938747 pictar
M12 hsa-miR-204 202967 - 202974 12938740 - 12938747 pictar
Protein features Close
 Category   Feature identifier   Feature name   Exons   Start on gene   End on gene 
Localization EXONT:000019 Signal_peptide 11 98144 98206
Localization EXONT:000064 Nuclear_localization_signal 13 201119 201196
Localization EXONT:000064 Nuclear_localization_signal 13 201263 201286
Structure EXONT:000035 Coiled_coil 13 201047 201238
Structure EXONT:000074 Intrinsically_unstructured_polypeptide_region 13 201095 201112
Structure EXONT:000074 Intrinsically_unstructured_polypeptide_region 13 201137 201196
PTM EXONT:000992 N4-(N-acetylamino)glucosyl-L-asparagine 11 98441 98443
Gene CCDC3
Gene CCDC3 Gene CCDC3
Gene CCDC3 Gene CCDC3
Gene CCDC3 Gene CCDC3
Gene CCDC3 Gene CCDC3
Gene CCDC3 Gene CCDC3
Gene CCDC3 Gene CCDC3
Gene CCDC3 Gene CCDC3
Gene CCDC3 Gene CCDC3

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Exon 1Exon 2Exon 3Exon 4Exon 5Exon 6Exon 7Exon 8Exon 9Exon 10Exon 11Exon 12Exon 1Exon 2Exon 3Exon 4Exon 5Exon 6Exon 7Exon 8Exon 9Exon 10Exon 11Exon 12Exon 13Extended region