DreINT0049439 @ danRer10
Intron Retention
Gene
ENSDARG00000020007 | col1a2
Description
collagen, type I, alpha 2 [Source:ZFIN;Acc:ZDB-GENE-030131-8415]
Coordinates
chr19:41403779-41404716:+
Coord C1 exon
chr19:41403779-41403877
Coord A exon
chr19:41403878-41404662
Coord C2 exon
chr19:41404663-41404716
Length
785 bp
Sequences
Splice sites
5' ss Seq
GGTGTAAGT
5' ss Score
8.07
3' ss Seq
TGAACTGTTTTTATGCTCAGGGT
3' ss Score
7.16
Exon sequences
Seq C1 exon
GGTCTTCCTGGAATTGCTGGTGCCCCTGGTTTCCCTGGCCCTAGAGGAGGCCCTGGCCCACAGGGACCTAGTGGAGCTTCTGGTCCAAGAGGTCTTGGT
Seq A exon
GTAAGTACATCTGCTTAATCCTAACTGCTGCATTCACAACGTACTTATTATTGATGAAACATTAGCTGATATTTTAGGCCTTTAATAAAAAATAAGGCTGGAATGTTTTATAGAAACTATTACAGATTTTGACATTAGGTCAAAGATGAGATTTTTTTTCAGGTGTTGCATCAAATTAAACTTGCATCAACTTTCAAAAACATTTTATTAATATTAAATGAAACTGTCAAATGTGACAAATGATGTAGTACAATTGAATGTCAGAAAATGAGTGAAATAATGTTGCTTCTTTAGAGGTTGATGTAAAAATGAAAATTAAAACATAATGACAGACACATGCTAAAAAAATAAGGAATAAGTGATCATACTAAATTTTGTAATGTTAAAAAAATGACAATAAGAAATAAAGACATTAACAAAACTCATTCTATAAATAAACAAATACATAAATGATTCAAATAAAGCCCTATTACAATTGTTTTGATGCTTAAAAACTTGATTTCTGTCATTGACTTATGAAAGAAAATGTAGATTTAATTTAAATTTTCTATGTCTATGCAGTCATTTGTTTAAACAATATTTCAAAATAATAATTTGTTAATCATAAAGAGGAAGAAAAGTATCTACTAATTGGATAATTCATCAGATGCTACTAAATTATTACTTAAATATGTTCAGTATCCATTTTGTTCATTTGTTTTTGTTTTGTTTTTTTCTATTCATATATTGTCAGATTTATACATTTCCTAATCTAAGTTTAACCTTTGAACTGTTTTTATGCTCAG
Seq C2 exon
GGTGACCCCGGACCTGTTGGAGTGAAGGGAGATTCTGGTGTGAAGGGAGAGCCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000020007:ENSDART00000144544:17
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=PD(14.7=33.3),PF0139113=Collagen=FE(48.5=100)
A:
NA
C2:
PF0139113=Collagen=FE(25.8=100),PF0139113=Collagen=PU(7.8=27.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]