DreINT0049676 @ danRer10
Intron Retention
Gene
ENSDARG00000104110 | col4a2
Description
collagen, type IV, alpha 2 [Source:ZFIN;Acc:ZDB-GENE-070725-3]
Coordinates
chr9:8891781-8894112:+
Coord C1 exon
chr9:8891781-8891879
Coord A exon
chr9:8891880-8893965
Coord C2 exon
chr9:8893966-8894112
Length
2086 bp
Sequences
Splice sites
5' ss Seq
CAGGTGATT
5' ss Score
5.95
3' ss Seq
ACTATGCCTTTGTTTTTCAGGTT
3' ss Score
11.1
Exon sequences
Seq C1 exon
GTGATAAAGGAGAGCCAGGGATGATGGGATTTCCAGGAAGACGTGGTTTTCAAGGTGACAGGGGCCCTTTTGGACCTAAAGGAGATACCGGACCCCCAG
Seq A exon
GTGATTAGTTAAAATCATTAAATAATTTGTCCGAACAACACCTAATCTAGAATAAAACATATAGCATTATTCCCAAAAACATTTTATTTAAATAAAATATTTGTGTTTTGGTATCCCAGTGTGGAAGATCTTGTATATGATATTTGTGAACCATTTTTGCTTATATATTTCATATTTTGTCAGTGTCTGGTATCTGACGGGCAGATTTCTTTTTAGTAAACAGATCTTAATAAGTTAGCTGATGCATATATATATATGCATATATACTATGTTGTGTATATATATATATATATATATATATATACAACAGTTCTGTCTGGTTCTCAAATCTGATTGGCTGATAGCCGTGCGATATTCTGCAATATCAGAACTCCTACAGCCTCTTTACCCTTTGTGTATTAGTCCGCCCACATAGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTTAGTATAATAGGTATGACTGTCTATCAGAACACATATTTGTGTCTATTTTTATTTTTGCCCAGTTTTTGGGTTCATCTAATTGGTCAACTGCCTTTAAAATGACAATGATGAGTGGAGCTGCATGTAATAGTTTAAATTAATTTAGTTTCTTTTTTTTTTTTTGATTTGGCATCAAAACATAGTAAGACACTCCAAGATACACAAGTCGAATGGTCATGTGTGTCAGTCAACCTCATTTACTTATGGCCCGTTTCCAATGAGTGGTACAGTACGGTACGGGCCGGTACCGGTCACCTTTATCAAGCATACGACAGAAAGTTTCAGACAATGTAATTTTTACGCGAGGAAATGTCACAGTAAAGCCGTATGGGTCGTTCACATATCATATGAGAAGTACTTCTCACAAAACAAATGCTTTACACACATAAATACTACTGTACTGTACTACTGTAACATCTGCATATATGTTAAATAAATAATGCAACATATATGAACACAAACAAACCCTCACTCTCTGAAATGTTACCAAGTATAGAAAAACTACACACAGCATACATTTAGTCCTTATTTGAATTCAAAAACAACACAAAATATAGCCCACAGTCAAAGCAAACCTCTCATCTGTGTCTGTAATCTTCAGCAGCACATGTAACCTCTTGTTAGAAAGTAATTCCGTCATTCCCAGTTCATAATAGTCCAAAAGGCGATGATGAGCATGGCAGTTTGTTGTTGTTTTATGTTGCAGAAGCACCATTTGCTGCAGTTTTTCTGGCTTCTCCTTTGATTTTTCACGCTTCGCTCTCGCGTTTGTTTATTTCAGAAAGGATCGGATATTAGAAGTGCTGTAATGATTACGAGCACGTTATTAATATGAGCTCAAGACGTTTATCATTTCAAATGTAGATGCGCGGCAACCTCTCTGAAGAAAGTGAAACTGCGCGCACTTTTAGACGGCCTCGTAAAACAAAAACAGGACACGGCAGATTTCATTCTTCTTGGCTTTGTGGCTGTTCATCAAGATGACGACAAGGTTTGTTTGAGCTTGGATAGACCATGGCTTGTGATTATATGTATATATTATTACAGTGTAATGTCTCAGCTGTGTTTTAAAAAATGCCGCTTCCTTTGTTTTCATTCACCTACTTCTGCGAGCGACGTATTTCTGTAAACCAAAAGCGTTCAGCTATGCGTCTAGCTTTTTTCGTGCTAGGTACCTTTGCAAAGGGTCACCAAAAAGTGGTACAGTACGGTTTGCTTTTAGGTACCCTTTTACTAAGGAAACAGCCATAAAAGCGTACCAAATCGTACCGTTCCACTCAGTGGAAACAAGCCAGTAGAAAAACAATGGAACATTTGAAATGTTAGAGCATTCTGTGTGAAAGGCTTCTCAAGAGTTTTGAGAATTGATCTGAATGCTGACACCATGTCCTACAGTTGAACGGCTTTATGATTGAGTTTTGATTCATCATTTATTCTGCGTTAACATTGCTATTCTCCCATTTTGTATTGTAAATCAACTCTACATAAATGAGTGCCATTAGCCTGCACATCATCTATACTATGCCTTTGTTTTTCAG
Seq C2 exon
GTTTTCCTGGATTACCTGGGGCTAAAGGATATCCACCAGTTCCACAGAAACTTCCAGGGGAGCAAGGGCCGCCTGGTCAGATGGGTATTCAGGGACCATCGGGGCGCAATGGAAACCCAGGCCCTGCGGGACCTCCTGGTGATTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000104110:ENSDART00000160004:17
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(9.0=20.6),PF0139113=Collagen=FE(50.0=100)
A:
NA
C2:
PF0139113=Collagen=PD(24.6=32.0),PF0139113=Collagen=PU(57.4=70.0),PF0139113=Collagen=PU(4.8=6.0)
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]