GgaINT0090072 @ galGal4
Intron Retention
Gene
ENSGALG00000015908 | COL12A1
Description
collagen alpha-1(XII) chain precursor [Source:RefSeq peptide;Acc:NP_990352]
Coordinates
chr3:80225992-80227012:+
Coord C1 exon
chr3:80225992-80226048
Coord A exon
chr3:80226049-80226748
Coord C2 exon
chr3:80226749-80227012
Length
700 bp
Sequences
Splice sites
5' ss Seq
AAAGTAAGA
5' ss Score
6.91
3' ss Seq
TTTTTATGTGTGTGTTTCAGAAT
3' ss Score
11.76
Exon sequences
Seq C1 exon
TTCAGACAGGTGGTCCAGGCATACCAGAAGAAAAGAAGGTTGAAGCTCAAATACAAA
Seq A exon
GTAAGATGTTTTGTCAATCAGTGCATCTTGTATTTTGTCTATCAGATGTTTTAGAGATAAGTGAGATTTATTTTCAGGGCCCTACAAAGTTAAGCTGTGTTCCTTTGTTACTTAGCAGTAAACTTAACTTTTAAAGCTGTCTAGAATTAGAGTTAGGGTAGTGTGGTTAGGTTGCGGTTGGACTTGATGATCTTTAAGGTCTTTTCTAACCTGAGAAATTCTGTGATCCTATGAAGACTCTCTTCTATCAAGAAAAGACATTGTCTTTTCAAGGCACTGCAAAAGATGCCATGCAGCTATTATGGGGAGATAAGAATGGAAAGCAGAAGTGGTAACAAAATGACATTTCTTTAGCATTAAACTTTTTCAAAAAATTTTATGTGTAAATTACCACCTGCTGTGGGATAACAGATCTTGTGAAATAGAGTGAGAGGTATCTCAAAGCTGATTTTGCAGCTGACAGTTCCCTTATGGTAATGGCAGCTAAAAGTCCCTTGTCTGTGTTCACATAGGTGAATAATGCTTCCCTAAGTAAGATAATTCCAGACAATAATATGAATCTATTAAAAATCTGTTCATTTTATCTTTTATTCATTATTTCTCTCAGATGTTTCTTACTGATTTCTAAGAATGCAATTGCTCATCTGCTAACAGTTTTTGTTTGTTTGTTTGTTTGTTTGTTTTTATGTGTGTGTTTCAG
Seq C2 exon
AATGCTCCATAAGTGCAATGACAGATTTAGTTTTCCTGGTAGATGGTTCATGGAGTGTAGGGAGAAATAACTTCAGATATATTCTGGACTTCATGGTTGCCCTTGTATCAGCTTTCGACATTGGGGAAGAAAAGACAAGAGTTGGAGTTGTTCAGTACAGTTCAGATACAAGAACAGAGTTCAATTTAAATCAGTATTTCAGAAGAAGTGATCTTCTTGATGCAATTAAAAGGATACCTTATAAAGGTGGCAACACAATGACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000015908:ENSGALT00000025640:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.150 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0009223=VWA=PU(46.2=89.9)
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:
TGGTCCAGGCATACCAGAAGA
R:
CTGTCATTGTGTTGCCACCTT
Band lengths:
311-1011
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]