DreINT0048736 @ danRer10
Intron Retention
Gene
ENSDARG00000024032 | coch
Description
coagulation factor C homolog, cochlin (Limulus polyphemus) [Source:ZFIN;Acc:ZDB-GENE-030616-403]
Coordinates
chr17:28728972-28729941:-
Coord C1 exon
chr17:28729838-28729941
Coord A exon
chr17:28729199-28729837
Coord C2 exon
chr17:28728972-28729198
Length
639 bp
Sequences
Splice sites
5' ss Seq
CAGGTTTAA
5' ss Score
1.88
3' ss Seq
AGTTATTGGTTTTTGCACAGGTA
3' ss Score
5.57
Exon sequences
Seq C1 exon
TGAAACACCTCGAACTGAATTCTACCTGACAAACTATACGACAGCCAAAGATGTGACCTTTGCCATCAAAGAAATCCCGTACATTGGGGGCAATACCAATACAG
Seq A exon
GTTTAATAACTTCTCCTGAACTGCGTATTTCATATGAACGAATGGGTTGAACACATGAAATATTTTTGTAAGTAAATCATGCCACCCTTTAGAAGATGTAAACTGAACAAATGTAATTTATAGTGATGCACTTAAAATAAAATCCAAATAAATGAAGTATACACATGCATATATATTCTTAATTAATTTACATTTATAAAAAAATTGGTTGAGCAAATAAGTCGCTTGCTCCAAAAAAATTGTCTAGGAATCAAGTGCAATAATAAATAACTCACTCACCCATAAAAATAGTTCATTTTTGGCACATTTTGGCATGTTAATGTATCACGCAAAACTTTAAACATTTGTGCATTGAGACCCATAATATTGAACCCTTCCAGACAGACTTGTATTGTAAGTACATTACTGGAAATACAGTTTTTACATCCTCAATCCATTTCCCAACTGCTTATCTATCGCAGGAGATGTGGACTTGCTTTGCAGGTCAGTATGATTTTGATCAACACTATGCCACAGATAATGCTGACGTAGATTAAACTTATCTCTGACACTTAACTTTAGTTTGCTTTAGTTCAACTCAATGATTATTGATGCTTATGAGCAGATCTTGGCAGGCTTAAGTTATTGGTTTTTGCACAG
Seq C2 exon
GTAAGGCCATACTGCACACCGTGAGGAACTTCTTCAGTCCGGATTTTGGGGTGCGGAGAGGTTACCCACGGGTGATTGTGGTGTTTGTTGATGGGTGGCCTTCTGATAATGTGGAGGAGGCAGCAATTTTAGCCAGAGAGTCTGGCATTAACATCTTCTTTGTGTCTGTGGCCAAGCCTTCCCCTGAGGAGGCAAGTCTGGTGAGCGATCAAGACTTCATGAGAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000024032:ENSDART00000000948:9
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:
PF0009223=VWA=FE(19.8=100)
A:
NA
C2:
PF0009223=VWA=FE(42.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGAAACACCTCGAACTGAATTCT
R:
TCATGAAGTCTTGATCGCTCACC
Band lengths:
326-965
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]