HsaINT0037730 @ hg19
Intron Retention
Gene
ENSG00000100473 | COCH
Description
coagulation factor C homolog, cochlin (Limulus polyphemus) [Source:HGNC Symbol;Acc:2180]
Coordinates
chr14:31354600-31355518:+
Coord C1 exon
chr14:31354600-31354826
Coord A exon
chr14:31354827-31355001
Coord C2 exon
chr14:31355002-31355518
Length
175 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAAG
5' ss Score
9.06
3' ss Seq
TTATGTGTCTCCCCCATTAGGCT
3' ss Score
8.65
Exon sequences
Seq C1 exon
GAAAAGCCTTGAAGCATACTGCTCAGAAATTCTTCACGGTAGATGCTGGAGTAAGAAAAGGGATCCCCAAAGTGGTGGTGGTATTTATTGATGGTTGGCCTTCTGATGACATCGAGGAAGCAGGCATTGTGGCCAGAGAGTTTGGTGTCAATGTATTTATAGTTTCTGTGGCCAAGCCTATCCCTGAAGAACTGGGGATGGTTCAGGATGTCACATTTGTTGACAAG
Seq A exon
GTAAAGTGGTGAGGGTTATCTTCTGTTACAGTGATGGGTATTCCATTTTGGACCTCTAAGTGCAGTGCTGACTGCCTCTTATCTAGATTAACTTGAAACATTCAGGATTTTCCAGTTTTTAAGAAGAAACAACTTTTGATCCTTTTGGATATCTTTTATGTGTCTCCCCCATTAG
Seq C2 exon
GCTGTCTGTCGGAATAATGGCTTCTTCTCTTACCACATGCCCAACTGGTTTGGCACCACAAAATACGTAAAGCCTCTGGTACAGAAGCTGTGCACTCATGAACAAATGATGTGCAGCAAGACCTGTTATAACTCAGTGAACATTGCCTTTCTAATTGATGGCTCCAGCAGTGTTGGAGATAGCAATTTCCGCCTCATGCTTGAATTTGTTTCCAACATAGCCAAGACTTTTGAAATCTCGGACATTGGTGCCAAGATAGCTGCTGTACAGTTTACTTATGATCAGCGCACGGAGTTCAGTTTCACTGACTATAGCACCAAAGAGAATGTCCTAGCTGTCATCAGAAACATCCGCTATATGAGTGGTGGAACAGCTACTGGTGATGCCATTTCCTTCACTGTTAGAAATGTGTTTGGCCCTATAAGGGAGAGCCCCAACAAGAACTTCCTAGTAATTGTCACAGATGGGCAGTCCTATGATGATGTCCAAGGCCCTGCAGCTGCTGCACATGATGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000100473-COCH:NM_004086:10
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0009223=VWA=PD(47.1=94.7)
A:
NA
C2:
PF0009223=VWA=PD(3.7=3.5),PF0009223=VWA=PU(72.8=72.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCCCCAAAGTGGTGGTGGTAT
R:
GCACAGCTTCTGTACCAGAGG
Band lengths:
257-432
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)