DreINT0049455 @ danRer10
Intron Retention
Gene
ENSDARG00000020007 | col1a2
Description
collagen, type I, alpha 2 [Source:ZFIN;Acc:ZDB-GENE-030131-8415]
Coordinates
chr19:41409065-41410431:+
Coord C1 exon
chr19:41409065-41409118
Coord A exon
chr19:41409119-41410377
Coord C2 exon
chr19:41410378-41410431
Length
1259 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGAG
5' ss Score
6.38
3' ss Seq
CAATCTGTGTCTTCTTCCAGGGT
3' ss Score
10.22
Exon sequences
Seq C1 exon
GGTGCTCCTGGACCCAGTGGACCCCCTGGACCTGCTGGTGCTAATGGTGACAAG
Seq A exon
GTAGAGTATTATCTTAGCTTTTATTTCAAATCAATGATGATATTTGTTGATATTATGGTATATTATACAAATCTAACATTTACAGCAGCCCAAAACTACTATTTATTTAAAGCTCAACATTAAAAATTAAAATAATGATGTTATAATTGAGATAATTAAAATGAAGAGCATTTAAGATGATTAAGGGCTATACCAAAGTTTTTACCTTTTCGTGGGGCAAGTAGTTTGCTTCTTTGACTGGATGTTTAAAGAAACCCCTGCTGACTGTTACAAAATGGCCAGATATATGGAATCATTGCTGCCTTCCGGAAATAACATTCCATCTTTTATGAACACTAGAGTAATGTTTAAGCCAGTGGTTCTCAAACTGTGGTACGTGTACCACTAGTGGTACGCAGGCTTCCTTCTAGTGGTACGTGGAGGAATGAAATATGTCATGTATATGCTACATATATTTCAAAATTTATCAAAAAGCATTTATATATTATACCATATATGACATATAGCCTATATTTCTGAGGTAATCTGCCACTTTTTTAAACTGTGCAGAGTTGTAGCTGCTTTACTGGCCCTACTACGCTACTGTATTTCAATACTGCTCATTTTGGTGGTACTTGGAGAGACAATTTTTTTCTAAGGTGGTACTTGATGAAAAAAGTTTGGTAACCACTGGTTTAAGCCATTACCCAGTTCGATTCCATTTCATTTCTTTGTATTTTATCATTATTAGTAATCTCTGGAAAAAACAATGGTGACTGACGATTCGTACTAGACGCTCAACAGCGATTACACGTTGCAACATTTATTAAAATGTGCCATACATTTATACAGAAACTTGTTCTCCATACGTTTTACATCTGTTTGTGGATTTCTTCTTAGAACTCTGTTCTATGAAACTTTTCAATATGTTGAAACAAATTGGATGTTTTTTTGTTTTGATATGTGCCAACATTTTAAACCATTCAAAAATTTTTAAAGCCATTTTATTCAACATTTGTTATAATTGAGCTTTATTGATATGCATTAAGCCTTAAATAATTATTTTAAATTCTTTAGAAAAAATAAAATAAATGTAAAATAGTGTAAAACTTGCTTAATATGTTAAGCTAAAATTCCTTTAGACTTTTTAATTTTTTTATTTATTTTTTTGCAACTAAAAAAGTAACCTTCAAATAAATAACTTGCAAGACTCTCAAAAGAACTTTCTTCAAGTAGCTTTAAAGATCATTCTGACGCAACCAATCTGTGTCTTCTTCCAG
Seq C2 exon
GGTGAGACTGGCTCCTTTGGTCCTCCTGGACCTGCTGGTCCTCGTGGTGCCCCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000020007:ENSDART00000144544:32
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(20.5=100),PF0139113=Collagen=FE(19.1=100)
A:
NA
C2:
PF0139113=Collagen=PD(12.0=55.6),PF0139113=Collagen=FE(19.1=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]