GgaINT1015670 @ galGal4
Intron Retention
Gene
ENSGALG00000009362 | ITGA6
Description
integrin alpha-6 precursor [Source:RefSeq peptide;Acc:NP_990620]
Coordinates
chr7:17228312-17229165:-
Coord C1 exon
chr7:17228955-17229165
Coord A exon
chr7:17228506-17228954
Coord C2 exon
chr7:17228312-17228505
Length
449 bp
Sequences
Splice sites
5' ss Seq
TGGGTATGG
5' ss Score
6.23
3' ss Seq
TTTTTTTCCCCTTCTTTAAGATG
3' ss Score
9.65
Exon sequences
Seq C1 exon
GTTTCTCTTTGGATTCTGGTAAAGGAATTGTCTCCCAAGATGAGATGACTTTTGTGTCTGGTGCACCAAGGGCCAACCATAGTGGAGCAGTTGTTTTACTGAAAAAGGAGAAAAATCAGAGAGCGCTTTCACTGGAGCACATGTTCGAAGGAGAAGGGCTGGCCTCTTCTTTTGGTTATGATGTGGCCGTTGTGGATCTGAACAGTGATGG
Seq A exon
GTATGGCCTTGGTTAACTCATGCTGCCTATATAGGATAGCAGACTGACTTATTTCTGCTTTGGTTTTTACTTTTGAAGTGTAAACAATCTTACATGTTTTGCTGGAGGAAATGGCGAGCGTGTCAGAAAGTCACGCCGAATGCAGTCTGTGTTCTTAATTACAGAAATGAGTTGTACTCGAATTCATAAGATTAGTGTTAACAAAGAAGAAATAATACCAAAGGAAGGCCCAGTAAGTTTCTTGTGTGTGATGGAGGGAGTGTAAAAGGCTTGCAGTCTTAGTGGATCCTCTGCCAGCTGTTTTTGCATGACTAGTTGAAAGTACTTTTTAATCACCTCTGTTCAGCAGCGGGGGTTGACTGTGACCTTGAGACTGTAGCCTTTATCAGTTACTTTTTAGAGTTCTTCAGTACGAGCACCGTTTTTTCTTTTTTTTCCCCTTCTTTAAG
Seq C2 exon
ATGGCAAGATATTGTGGTTGGAGCCCCGCAATACTTTGATAGAAGTGGAGATATCGGTGGTGCTGTGTACATCTACATTAACCAGCAAGGCAAATGGGAAGGAATAAAACCTATTCGCTTAAATGGGACCGCTGACTCAATGTTTGGTCTCGCAGTTGAAAATGTTGGGGACATTAATCAGGACGGATATCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000009362:ENSGALT00000038606:6
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=0.000
Domain overlap (PFAM):
C1:
PF135171=VCBS=PU(6.8=7.0)
A:
NA
C2:
PF135171=VCBS=FE(87.8=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTTGTGTCTGGTGCACCAAGG
R:
TCCGTCCTGATTAATGTCCCCA
Band lengths:
348-797
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]