GgaINT0090086 @ galGal4
Intron Retention
Gene
ENSGALG00000015908 | COL12A1
Description
collagen alpha-1(XII) chain precursor [Source:RefSeq peptide;Acc:NP_990352]
Coordinates
chr3:80253191-80254021:+
Coord C1 exon
chr3:80253191-80253310
Coord A exon
chr3:80253311-80253856
Coord C2 exon
chr3:80253857-80254021
Length
546 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGT
5' ss Score
9.8
3' ss Seq
CCCTCTTTGTTTCATGCTAGGAA
3' ss Score
10.29
Exon sequences
Seq C1 exon
GTCTTGCACAGTATAGCGGAGATCCCAGGACAGAATGGAATCTCAATGCTTACCGAACGAAAGAGGCTTTGTTAGAGGCAGTAACCAACTTACCATACAAAGGAGGCAATACTCTAACAG
Seq A exon
GTATGTCACACTGTGAGGATTTTCTTTATGCTTATTAAAAAAAAGTTCCAGTAGCTGACCCTAATATTGTTCAGTGAACTCAAATTCATCCATGATGAAAGGGCCTCACAGTTAACTTCGGTACATTTGGAACTGAATGTCCCTAGTACATGAACATTCATTATCAGTGTAGATCTGGATAAAGAGAGCAGGATGGAAGATTGTAAGTGCTGAAGAACCAGATGAGTTTGGGTTTATGTTGAGCATATGAAAAGAAGAAAAGGTAGTTCCATTGGTTGATGTGAAGACAAGGTGAGGACCAAGAAGGGAGGCTAAAGGGAGACAAATAGAAGGGCAATACATAGAAGGTATGATGTTAAAGACTTTCAGAGGGCTGAAATAATGTCAGTTGCTAAGTGTGATGATGAACTATAACTAGATTGAGTCCTTGAAGAATTAATCTGTGGAATGATGTTGTCAGTGTGAAATCACTGGAATGAATTACTGGCTTTTACCAGTATGTTCAAAGAGTTTATGGTTATGGTTACCCTCTTTGTTTCATGCTAG
Seq C2 exon
GAATGGCCTTGGATTTCATCTTAAAAAACAACTTTAAACAAGAAGCAGGCTTGAGGCCCAGAGCTCGCAAAATTGGTGTTCTCATTACTGATGGTAAATCACAAGACGACGTAGTGACCCCTTCAAGAAGACTCAGAGATGAGGGAGTAGAACTTTATGCAATTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000015908:ENSGALT00000025640:23
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.089
Domain overlap (PFAM):
C1:
PF0009223=VWA=FE(23.1=100)
A:
NA
C2:
PF0009223=VWA=FE(31.8=100)
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:
GCACAGTATAGCGGAGATCCC
R:
ATTGCATAAAGTTCTACTCCCTCA
Band lengths:
278-824
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]