GgaINT0050814 @ galGal4
Intron Retention
Gene
ENSGALG00000003923 | COL6A3
Description
collagen alpha-3(VI) chain precursor [Source:RefSeq peptide;Acc:NP_990865]
Coordinates
chr7:4783837-4785289:+
Coord C1 exon
chr7:4783837-4783982
Coord A exon
chr7:4783983-4785196
Coord C2 exon
chr7:4785197-4785289
Length
1214 bp
Sequences
Splice sites
5' ss Seq
CTCGTAAGT
5' ss Score
9.63
3' ss Seq
CCATCTGTGTTTCCTCGCAGGAT
3' ss Score
11.89
Exon sequences
Seq C1 exon
GTGTCCATGCTCTCCTCTTCGTTGGCTTGGATCGAGTGAAAAACTTTGAGGAAGTGATGCAGCTGGAGTTCGGGAGGGGTTTCACCTACAACAGGCCGCTGAGAGTTAATCTCCTGGACTTGGATTTCGAGTTGGCAGAGCAGCTC
Seq A exon
GTAAGTCACTTGGCACAGGCAGCGCTGCCTCGCAATGCTGGGGAAAAGCCAAAGGCTGGATGTGCTGCAGGTCTGGAGTGCTGCTGAATCACACCCTCTTGGCTCCAGCCGTTCCCCCTCCCTAGCTCACGTCTGCTCTTTATACAGATGCCGTAGCAAGTTAATGAAAAGCAGATCCTGGTGCTGCCCTGTCCTGTACCATTCCTGGAGTAGGGCTTCTCCAGTTCAGGCTGCAAAGGGCACAAAGCCCAGTGCGACTAGGTCAAATGGATAAGGTTAATCCACATAGCACACTAAAGGCTTGAGGGTGATGCACCGTCATGCATTGTCAGTGCTAAATCTCCTGCATAAACATAACTTTCTAGGTTTCTTCCTGGAGTTGATACAGTGCCTGTGTGTTAGACGTGTTTCTTACAAATGGCAGTTGTTTTTCTTCCAGGCAGAAGCTCATAGATTTACCTCCACTCCATGTATATATCCTCTCTCGAGCCCGTTGAGAACGAATTTGCTATCATCCCTTACATGTGCAGCTCCTCCTAGCTTCATATCTGCTCTAGATCTGTTAACCTCCTTTTCCAGCAGCTTTAATGAAATTAGGCTTAATTCGCTGTTACAACCTTGATGGGCCCTCCTCTGCAGAGCCAAGTGCAGACACTTGGAAGTGAACCTGGAAGTGAACCGTGGTTTCTGGGACAAGAGCTACTCTTCAGCCCATCCCCGTGTAGTTCCTTTGGCTAGGAAAATCCTTTCAAAATGTAAATGTGCAAAGCTGGCAGGAGGCATCTGCAGCCAGCAATGTCCTTGGCAAAGAAAAGGATTTTTTCTTTCTAGTGGATGATGCAAAACCAAGCTGTGATTTCTCTGAATCTGCATCTCCTTATTTTTTCCTCTTGCTGCGTGCTTGCAAACTGTTCTCAGCCCGTGGGTTGCTGGTGAGCTGCTCACCGCAACAGCTTTCTCCTGCCCTATTCCACAGCCTAGATTTGTTTCTTCACAGATGAGGTTGCTCTCTTCAGCAACGGGCACCGTTTTGGGGACTGGTCTCCTACTAAACGCCCCCTGTGACTTCTGCCCAAGCAGAATGTTGGTTTGACATCCCCTAAACAGGCAATCTAATCTTTCTGCCATCACACACCTCTTTCTCACACTGCTGTGGCTGTTTCCCGGTGGAGGGAACCCCAACATTCAGTTGTGCCATCTGTGTTTCCTCGCAG
Seq C2 exon
GATAACATCGCAGAAAGGACGTGCTGTGGGGTCCCTTGCAAGTGCTCAGGGCAGAGAGGGGACAGAGGTCTTCCCGGCCCCATAGGACCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000003923:ENSGALT00000006250:14
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=0.387
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0139113=Collagen=PU(25.8=51.6)
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:
TGTCCATGCTCTCCTCTTCGT
R:
CTATGGGGCCGGGAAGACC
Band lengths:
230-1444
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]