DreINT0049448 @ danRer10
Intron Retention
Gene
ENSDARG00000020007 | col1a2
Description
collagen, type I, alpha 2 [Source:ZFIN;Acc:ZDB-GENE-030131-8415]
Coordinates
chr19:41407358-41408107:+
Coord C1 exon
chr19:41407358-41407411
Coord A exon
chr19:41407412-41408053
Coord C2 exon
chr19:41408054-41408107
Length
642 bp
Sequences
Splice sites
5' ss Seq
CAGGTCAGT
5' ss Score
8.94
3' ss Seq
ATATTATTTGACCTTAACAGGGT
3' ss Score
7.75
Exon sequences
Seq C1 exon
GGTGCCCCTGGTGAGAAAGGAGAGCAGGGACCCTCTGGTGCTCCTGGTTTCCAG
Seq A exon
GTCAGTGTCACATCATGCTTGTTTATACTTTCACATACCTTTGCAGTTCATGTACATGCATCACTCAAACTGAAAGTACTGAATAAAATTAATAAAAGAAGCATCTATTAACCTTTGTAGTAAGTTGTACACCCAAAACCCCATCGGTAGGGCTCAAAATTCAATCCAATGGACAACACAGTGGATTAAAATTCTGTCTAAGTACCTTGAGGTTTTATTTCTGGGACAGTTAATATGAAGAATTCCAGAATAGAAAAATCACCACTTTGGTGTACTCATTGCTGCCCTGTTGAAAAATCGTAACAAACCTGTATAAGAAGCTGGTGCAACTGGTACATGCTGGTAAATTGATCTGGCATGGTGATGATTAAACAAGCAAGTAGTCATGCTATTCTCAAAGTAAAACTAAGCTTAGTATTCCTACTCCTATAAAGCAACATGCTTCCTTTACTGGTCACAACTTGCAGAACATACTGTAATGCTGGTGACCAACAATGCTAGACTTTTAACAGGGTGGGAATCACCGCCACGTGAGAATTGTTCAAAATAAAAATCTTGCATGCATTATACCTGCTTACATTGTGAGTAATGTCTGCTTACATACAAGTCTTTACAACTATTTATATTATTTGACCTTAACAG
Seq C2 exon
GGTCTTCCTGGCCCCGCTGGACCTGTTGGTGAGGCTGGCAAGCCTGGTGATAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000020007:ENSDART00000144544:26
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(18.7=100)
A:
NA
C2:
PF0139113=Collagen=FE(18.7=100)
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]