DreINT0048730 @ danRer10
Intron Retention
Gene
ENSDARG00000024032 | coch
Description
coagulation factor C homolog, cochlin (Limulus polyphemus) [Source:ZFIN;Acc:ZDB-GENE-030616-403]
Coordinates
chr17:28731283-28732014:-
Coord C1 exon
chr17:28731970-28732014
Coord A exon
chr17:28731440-28731969
Coord C2 exon
chr17:28731283-28731439
Length
530 bp
Sequences
Splice sites
5' ss Seq
ATGGTCAGT
5' ss Score
6.57
3' ss Seq
AGTTTGATATTTGGTTTTAGTTG
3' ss Score
5.12
Exon sequences
Seq C1 exon
GTATTCTCTCTTTGAGCTGGTGCACTTCTGGATCTGAATTAAATG
Seq A exon
GTCAGTTTTTACAATCACTTCAGTGTATATCTTGTCATATTAAATATTGCTATAAAGTTGCAGCACATTTTTGTAAACTCTGACTTTCTTGTTTTTAATTGGGCTGATCAATAGCTAGGAGACATTTTTTATATAACAATTTAATTTATAGTTTTATTCATCCATTTTTTATAATTCATAAGTAGCTGAAAGATCTTTTAAAATACAATTATGTATGTAAAATGTAAAATACATTAAGTTTAAAATGTTTATTAGATTTGCTTCGTTTTTTAAAACCTTTTAAAATCTATTTAAGTGAAAAAAGTATTTTATTTATGTTTTCAGTAGCACAGACATATTTTAAATATATAATTTACTTTATTTATTATTAAGGATTTATTTTACTAATTAATTAATAAATTTTTATCAGAAAAAGAACACACTTTATGACAAATTTTCCAGTCAAATGAATTTTTATCAGTATTTAAGAGACTTTTTAAAAACCTATTTATTGTTTATATGTTTGCTTTAAGTTTGATATTTGGTTTTAG
Seq C2 exon
TTGCAACGCCGATTAGCTGTGGGACTCGTGCGGTGGATCTGTCAGACACACATCTGCTGGTGCTCTGTCCAGCAAACTGCTCTCTGTGGAGCCTCTCAGTGTTTGGTTCTGGAGTTTATGCCTCTATTTCCAGCATATGCGGAGCAGCCATTCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000024032:ENSDART00000000948:3
Average complexity
IR
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:
NO
A:
NA
C2:
PF0381514=LCCL=PU(53.3=90.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATTCTCTCTTTGAGCTGGTGCA
R:
GTGAATGGCTGCTCCGCATAT
Band lengths:
198-728
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]