GgaINT0090089 @ galGal4
Intron Retention
Gene
ENSGALG00000015908 | COL12A1
Description
collagen alpha-1(XII) chain precursor [Source:RefSeq peptide;Acc:NP_990352]
Coordinates
chr3:80255011-80256445:+
Coord C1 exon
chr3:80255011-80255150
Coord A exon
chr3:80255151-80256315
Coord C2 exon
chr3:80256316-80256445
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:ENSGALT00000025640:26
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:
NA
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]