DreINT0049953 @ danRer10
Intron Retention
Gene
ENSDARG00000012593 | col5a1
Description
procollagen, type V, alpha 1 [Source:ZFIN;Acc:ZDB-GENE-041105-6]
Coordinates
chr21:6771314-6771678:+
Coord C1 exon
chr21:6771314-6771367
Coord A exon
chr21:6771368-6771570
Coord C2 exon
chr21:6771571-6771678
Length
203 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGA
5' ss Score
10.57
3' ss Seq
AATCACGAGGGTTCTTTCAGGGT
3' ss Score
0.28
Exon sequences
Seq C1 exon
GGTCCTCCTGGACTGCCTGGACTGAAAGGAGATCTTGGTATCAAAGGTGAAAAG
Seq A exon
GTAAGAGAAGCAAATTTTTTTTTGATTCTCATTAAGCACACTTGGATGTTGTCTAGATACTGTAGGTAACTCACTCATTGTTTGGAAATGAGCTGTCATAATGACTATATATGCTCTGTATGTTAGTTAAACTCTGGCTGAATTATTGGTTTTGAAAGCAGTTGTTCATCAGATCAGTTTAATAATCACGAGGGTTCTTTCAG
Seq C2 exon
GGTCATCCTGGTCTCATCGGACTTATTGGACCTCCAGGAGAACAGGGAGAGAAGGGAGACCGAGGCTTGCCAGGTCCACAGGGAACTTCAGGACCTAAAGGAGACAAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000012593:ENSDART00000139598:56
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(22.0=100),PF0139113=Collagen=PU(25.4=89.5)
A:
NA
C2:
PF0139113=Collagen=PD(4.9=10.8),PF0139113=Collagen=FE(53.7=100),PF0139113=Collagen=PU(8.1=13.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGGACTGCCTGGACTGAAAG
R:
TCCTTTAGGTCCTGAAGTTCCCT
Band lengths:
149-352
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]