DreINT0048727 @ danRer10
Intron Retention
Gene
ENSDARG00000024032 | coch
Description
coagulation factor C homolog, cochlin (Limulus polyphemus) [Source:ZFIN;Acc:ZDB-GENE-030616-403]
Coordinates
chr17:28728354-28729198:-
Coord C1 exon
chr17:28728972-28729198
Coord A exon
chr17:28728868-28728971
Coord C2 exon
chr17:28728354-28728867
Length
104 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGA
5' ss Score
8.68
3' ss Seq
TGCTGTCATGTACCTTACAGGCA
3' ss Score
8.16
Exon sequences
Seq C1 exon
GTAAGGCCATACTGCACACCGTGAGGAACTTCTTCAGTCCGGATTTTGGGGTGCGGAGAGGTTACCCACGGGTGATTGTGGTGTTTGTTGATGGGTGGCCTTCTGATAATGTGGAGGAGGCAGCAATTTTAGCCAGAGAGTCTGGCATTAACATCTTCTTTGTGTCTGTGGCCAAGCCTTCCCCTGAGGAGGCAAGTCTGGTGAGCGATCAAGACTTCATGAGAAAG
Seq A exon
GTGAGATGTTTCACATTTGAACTCATTGAAAAAACACACCACAAATCATTAGTGTGAACCTCTGACTCTCCCGAAATCCTTTTATGCTGTCATGTACCTTACAG
Seq C2 exon
GCAGTGTGCAAGGACAATGAGTTCTTCACCTTCACCATGCCCAGTTGGTTCAGCACCAACAAGTTTGTAAAGCCACTAGCTCAAAAGCTTTGCTCCATCGATCAGATGCTTTGCAGCAAGACGTGCTACAACTCAGTGGATCTGGGCTTCCTGATCGATGGCTCCAGCAGTGTAGGTGACGGGAACTTCCGGCTGGTGCTGGACCTCCTTGTCTCTATCGCACGTAGCTTTGATATCTCCGACATTGGATCTCGCATTGGTGCTATCCAGTTTACCTATGACCAAAGGATGGAGTTCAACTTCAATGACCATGTCTTGAAAGATAATGCTCTAAGGGCCCTGCAGAAGATCCCATATATGAGCGGGGGAACAGCCACTGGAGATGCCATTAACTTTGCTGTGCGGAGTCTCTTTAAACCCCGCTCAAGCTCCAACAGGAAGTTTCTCATCATCATCACTGATGGACAATCTTACGATGATGTGAGAGTTCCAGCTATGGCTGCCCAAAGAGAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000024032:ENSDART00000000948:10
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(42.4=100)
A:
NA
C2:
PF0009223=VWA=PD(11.3=11.6),PF0009223=VWA=PU(73.5=72.7)
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:
GCAAGTCTGGTGAGCGATCAA
R:
AGAGACAAGGAGGTCCAGCAC
Band lengths:
252-356
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]