GgaINT0090089 @ galGal3
Intron Retention
Gene
ENSGALG00000015908 | COL12A1
Description
NA
Coordinates
chr3:83590992-83592426:+
Coord C1 exon
chr3:83590992-83591131
Coord A exon
chr3:83591132-83592296
Coord C2 exon
chr3:83592297-83592426
Length
1165 bp
Sequences
Splice sites
5' ss Seq
CAGGTTAGT
5' ss Score
8.02
3' ss Seq
ATTCCTTCTCTTTTATGTAGTTT
3' ss Score
7.03
Exon sequences
Seq C1 exon
GTGATTTGCCACCTCCTTCTAACCTAGTTATTTCAGAGGTAACACCTCATTCTTTCAGACTGAGATGGAGTCCACCTCCAGAAAGTGTTGACAGATATCGAGTTGAATATTACCCTACCACTGGAGGTCCCCCTAAACAG
Seq A exon
GTTAGTGCCAAATGTTCATCTCTCATGTCCATAATAAGATGGGACTTCTATATCACATGGCAGTCATTTAGAATGTCATTCTGAAGTCTTTGCTTATTAGAGTCTGTGTGTGGTATAGCTGTAAATAAAAAAAGACTTCAAGGGCAAGAATATCACGCTTCAATAAATGATCAATAAAATTACATGAAGGAGCATAAAAATGGCTTTATTAATCATTAATCTAGAAGTAAAATGTATTTATTAAGAAGAGTTTATTGAGACTTCCAGTTTTATGCTCATATTCCAGTATAATATGTAGGTTTAAGTAAATCTATAGTAAAATTTTTTTTTACTGTGCTCCCAGGTTGGCTTACTGTTCTTTTAATCCATTTTCTTGTTAATAGATAAAAAAGATGATGATGATATGAGTTGTGATATGTAGTGCTTAGCTAACACTGTGTGATGGTACTTTGGAGGATCTGTTTAGGCACAGATTCAACTGTTTAATGTACTGGACCAAACTCACCATATGATTATTATTTCTCTATACAGCCAGTAAGAGACAAGCCTTGATGCAAAATTGGTCTTCATTCTCTTCAACCAGTCAGAATAGTATTTAGGAGAATGAAGTTAGGCATCTCCATGTGTCTAGCTCTGAATGTGTATGTCGCTTTTAAATCTTAACTCAAATTTGACTTGTGAAGAGTTTGGACTTTGTAAAACATGACCATAGGATTTGGACTGTGATTTGGTTTGGAGCAGCCATTCCAGTGTACAGGGACTTTACAGGGTTTTTCCGGCAAGGTGGTGTTAATGGCATGTGCTGTAACCACCTTGATTATCCTGGATGTTTAAAATACTTTTCCAAAGTGGGAGCATCTATCAATGGCATTTTATGTTGCTGAGTGATATGAAAATGAATGCCATGAGTTAAAGCAGTGCATGTTAGATATATCCATCCCTGTTGAAAACAAGTATCTGCTTGAGTTATCTCTACAGCTTGCTTTGCAATAGTAATGGTATACTGTGAGGTGAAAGGTGTAGAAGATTAAGACCATAGCTATTTTTTAGTTCTGTACCAATGACTTCTAAAGTTTCACGTGGAATTATTAATTTTTTTTTTTTAGAGACAAGTTTACAAACATGTTTTTTGTACTGTTGTTAACATTCCTTCTCTTTTATGTAG
Seq C2 exon
TTTTATGTAAGTAGGATGGAAACTACAACAGTTTTGAAAGATCTGACACCTGAAACAGAATACATTGTTAACGTGTTTTCTGTGGTAGAAGACGAAAGCAGTGAACCTCTAATCGGCAGGGAAATAACTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000015908:ENSGALT00000037087:22
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.277 A=NA C2=0.045
Domain overlap (PFAM):
C1:
PF0004116=fn3=PU(53.8=91.5)
A:
NA
C2:
PF0004116=fn3=PD(43.8=79.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGATTTGCCACCTCCTTCTA
R:
AAGTTATTTCCCTGCCGATTAGAGG
Band lengths:
270-1435
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]