DreINT0049680 @ danRer10
Intron Retention
Gene
ENSDARG00000104110 | col4a2
Description
collagen, type IV, alpha 2 [Source:ZFIN;Acc:ZDB-GENE-070725-3]
Coordinates
chr9:8897128-8899687:+
Coord C1 exon
chr9:8897128-8897319
Coord A exon
chr9:8897320-8899400
Coord C2 exon
chr9:8899401-8899687
Length
2081 bp
Sequences
Splice sites
5' ss Seq
TGGGTAAGT
5' ss Score
10.24
3' ss Seq
GATTCTGTTTTGTTCTGCAGGTC
3' ss Score
11.01
Exon sequences
Seq C1 exon
GGACTCGAGGACGACCTGGTATGCCCGGTCCTCTTGGAATGGCTGGCCGCAGTGTGAACGTTGGCTATCTGCTGGTGAAGCACAGTCAGTCTGAGGAGATCCCCATGTGTCCTCAGGGCATGTCCTTGTTATGGATGGGTTACAGTCTTCTGTACTTCGAGGGCCAGGAAAAGGCCCACAACCAAGACCTGG
Seq A exon
GTAAGTGCTGGACATCAATCACGAGATGTCAGTAAGAGATGCAGAACTGTAGAACCGAATGTTAATTTCAGATTAAATGCATATCATATATATCATTGTGTTTTCCACAAATATATTAATTAGGCAGAACTGTTTTCAACATGGAGAATGGTAATAAATGTTTCATGAGCAACATCTTACAATGGTTTCTGATGGATCATGATGCTGATCCTAAAGGTTTCTTTCCAAAACATCTTACTAACTCCTAGGGATGGCTGACGTAAAACCGACATTTCAACAGTGTCTAGATCCAGAAGAGCAAGTGTTTTGAAATAAGCACAGTACTATGGAACCAGATTAGTCTCAAAAGAAATTCACACAAAAGACACGATGTACACATGCGTAGCCAAATTCACGTGCATAAAACCAAATTAACGTGCGTAAAATATTTATTTATATTCACAAAAAAAATTCACATGCACAAATTAAAAATACATTTTCATAAAGTACGTTTCACAAATGCAAAACACCATTTGCAAATGTATAAGAGTGTACAAAAGGTTTTGAATGTTTAAAACTTGTGAGTTCATCCTGAATGAGAATGTGCAAATCCTCTTTCACGTACGACTCCCCCTGGATACGTGTGTGTGTATTTGTGAGACTTTCCTGCCAGAGTCAGGACTACTCGTACCTTTCAGCCAATCAGATGAGAGCTGTTTTCAATGAAACCAACTCTGCGCTTCTTTTGTGCAGACTGTTCCTCTCCAGCATGGCGAACGGAGAAAGCAGCAGTTGCACTTTTTTAAAATTTATTTATATATTTGACCATATCCTCACTCTTTTTATCCATTATTTTGCCGCAGCTCCGCTTTTCTTATTTATTGTCTCGCAGCCCTATGAGCAACATGTATCCTTCAGGGTAATCATAAGTATCATTCCGGCCAGGCCAGCATTGCAGTGCCATTGTGGTCCAGTGGTCAGCACGTTGGGTTACCATGCCCTTAGACCTGTGAATTTCTTTTGAGACTAATCTGGTTCCATACTGTACAGTATTAATGTTCAAACTATTTATAATGATTAAAATGGCTGACAGTAATAAATATTTTTAATAATAGGAATTATTAATCTTCCTCGTCATTATGGTGGTACTTGGAGACAGATTTTTTTTACTTAATGAAAAAAGTTTGAGAACCACTGATTTAAAGGAATAGTTCACCATAAAATGAATACTTACTCATACTCCAGTGCTTTTAAAGGCCCTGGTAAACTTTAAAAGAAATTGAAAATAGTACTGAAAGGACATCATTTCAAACAAAATCCTCTTTTTAGTTTGTTTTGGCTGGATTTTCTTCGAAATGAGCAAAAAGAAATTCAGTAAGGCTGATTGATTGAATGCTGCTTTGTATGGAAACAGAATACTGTCACTCAGTCTTTTTGCAGAACGAACAAGATTTTACGTATACCAGAGCCTTAAACCCTGAGTATCTTTTTTCTGTTTGAACACAAAAGAAGATAGTTTGAAGAATGTTGGAGATAGGGTTTTCTAGTGGGAAAAAAATGCCATGGATGTCAATGGCTACCAATCTCCAACATTCTTCATTTTTCAATACATTCTTTCATTCTTTCATTCTTTCATCTTCATTTTTAGGTGAACTGTCAATTTAAAATTGTATAAAATTCATTAATTTTCCTTCGGCTTAGTCCCTTTATTAATCAGGGGTTGCCACAGCGGAATGAACTGCCAACTTATCCAGCATATGTTTCACACAGCAGATACCCTTCCAGCTGCAACCCAGCACTGGGAAAAACCCATACACACTAATTCACACACATACACTGCGGATAATTTAGCTCAGGGTTGGTCACCCCTGTTTTAGCTTATCCAATTCAACTTTAGCATGTGTTTTTGGACTTGTAGGAGCACCCAGAGGAAACCCACACCAACACAGTGAGAACATGCAAATTCCACACAGAAATGCCAACTGACAAAGCCAGGACTCAAACCAGAGACCTTCTTGCTGTGAGATGGCAGTGCTAACCACTGAGCCACTCAAAAGAGTACAAATATAAACGTCCTCATATGATTCTGTTTTGTTCTGCAG
Seq C2 exon
GTCTAGCCGGATCATGCCTCCCCCGTTTTAACACCATGCCCTTTCTGTACTGTAATCCGGGAGACATATGCTACTACGCCAGCCGCAATGACAAATCCTATTGGCTGTCCACAACCCAGCCGATTCCCATGATGCCCGTAGAGGAGTCTGAAATAAAGCCGTACATCAGCCGCTGCTCTGTGTGTGAAGCTCCATCTGTGGCCATCGCCGTACACAGTCAAGATACAACCATTCCAAACTGCCCAGTCGGCTGGAGAAGCCTCTGGATTGGCTATTCCTTCCTCATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000104110:ENSDART00000160004:20
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.215 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(37.3=33.8),PF0141314=C4=PU(39.8=66.2)
A:
NA
C2:
PF0141314=C4=PD(59.3=66.7),PF0141314=C4=PU(26.3=31.2)
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]