DreINT0049562 @ danRer10
Intron Retention
Gene
ENSDARG00000069093 | col2a1a
Description
collagen, type II, alpha 1a [Source:ZFIN;Acc:ZDB-GENE-980526-192]
Coordinates
chr8:21175942-21176456:+
Coord C1 exon
chr8:21175942-21175995
Coord A exon
chr8:21175996-21176402
Coord C2 exon
chr8:21176403-21176456
Length
407 bp
Sequences
Splice sites
5' ss Seq
GTTGTGAGT
5' ss Score
6.59
3' ss Seq
ATGATTTTGATGTGTTTTAGGGT
3' ss Score
10.15
Exon sequences
Seq C1 exon
GGTTTGCCTGGTAAAGATGGAGAGACTGGACCTTCTGGTCCTCCTGGCCCTGTT
Seq A exon
GTGAGTATTACTTTAAATTAAGTTGTCCTTACGCAGCCAGGCTAAGGTTGCTCTGTGACTGCTCGTAATTCAGTGTAAAGATATGATGCTGCCTAAATCCAGATTAAATTATACCTGCACTGACCCACCTTAGCCCCCAGTATCACAGTATACATTTGTTATTGTTGTGTAAATGCATTCATCTCACCTATATGAGAAACATAAAACATCTGTGTGGAGTTAAGAAGCATGTTTGTTCAAATTTATTCTTATCTTATTATCTAAATTAATTTATGTAATTGTACAATTAATGCAGCATTACCTTAAACATTTAGCTTCTGTAATCAATCAACAAAATTAAAAAACAGTTTACTCTAGTGTCTGAAATATTTCTGTAGTGCCTAAATTATGATTTTGATGTGTTTTAG
Seq C2 exon
GGTGCTGTTGGTGAGAGAGGAGAACAAGGTCAACCTGGTCCATCTGGCTTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000069093:ENSDART00000100234:29
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(16.4=66.7),PF0139113=Collagen=FE(26.2=100)
A:
NA
C2:
PF0139113=Collagen=FE(26.2=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]