GgaINT0047776 @ galGal3
Intron Retention
Gene
ENSGALG00000009362 | ITA6_CHICK
Description
NA
Coordinates
chr7:19102023-19103358:-
Coord C1 exon
chr7:19103297-19103358
Coord A exon
chr7:19102181-19103296
Coord C2 exon
chr7:19102023-19102180
Length
1116 bp
Sequences
Splice sites
5' ss Seq
TAAGTAAGT
5' ss Score
8.07
3' ss Seq
TACTTTATTTCTTCATATAGAGA
3' ss Score
5.7
Exon sequences
Seq C1 exon
GATGGATGTGAAAGCATGTTTTCAATATACTGCAAACCCTCGTAATTTAAATCCAAGAATAA
Seq A exon
GTAAGTTTTAAAGAGAAATAATTTTAATCTTTGTCGTGTGTTTGTGTGTGTGTATGTATATATAAAACTTGGTATCATGGAAGGATAGTACTTAAAATATAATGATTCATCTCAAACTATGACAGATTTAAACTGTGACTTAGTACTAAGGACAGTCAGCTATGCAGTATTTGTATTTGGAGCAGCACATAGTGTCTGGTGTGTTCTGAAGTTCTGTTGGTAAAAGACTCAACTGGAACTCTGTAGGTGACATAACTGCCAGTGAGCAAATGGCTGGGAGTCTGTATCATAAATGTAGTTAAAAATGTAAAGCATCAGTTTCTTATATATCCTGTTTTTTTTTCTCTTTAAGTTGTTACAATGCTGCTGTTATTAAACTTCTGAAAATTCTGTAGGATTTTGAGAGGAAATAAGAAGAATTTTAAGCCCTAACCTCCCCTTCCTCCTGTGGTGGTTGGGTTTTTGAGTTAAGTCTAAAATCCATAGAGATACTTGAATAGGGTGTTGGTCCCTTCAGCAGCTTCTAGCATTCGGAGGCTGCTCACATGCACACTCCTAAAGACTGGCAAATTAGCTTGGTGAGCACGGAGATGGTTAAAAGATGGACAAAATTCACATCTGTCAAACCATGGTATTCCCTGCCTCAGCAGACATAGCTAGAAAGCTCGAGAGTACCGCTTTCAGTATTAAACTGAACAATGTACCTTGACCTCAAAATCCTGCTGGCTGCTTTGCTGAGGTGCTACCTGGGACAAGACAGAAAGCAAGGAATCATGTCAGAGCGTTTACGGTTTCTTATCTCAGCCCTCTACTGGCTGTACAGCATCAATTACAACTGCTCCAGCCAGCTCTAAATATTGGTAAAGTAACAGGAATTTACTGACTAAACGTAGGATTTTGTTTGGAAGTTCCCATTGGATACATGTCCCCTCAGCTACAGAGGGAAAAAACAACAGATGAAGAAGGTTTTGTAAATAACGGAAAGAATTAGTGAAGCCTACCGCTAGGTGAAACTATTCTAGAATGTTGCTGTAAAATCATACTTGATTTTTTTTTTCCTTTTTAACCATGGCAAGGTTTCTTCCTTATAGCAAACTACTTTATTTCTTCATATAG
Seq C2 exon
AGATCAACTATACATTTGAAGCAGAAAATGAGAGGAGACAATTAGGCCTGCCATCTAGGGTACGGTTTAAAGACTATCTATCTGATCAGTTCACTGCAAGTACCACCCTAATAGGGCAGAACTCAAAACGGTGCGTGACAGCCAAGCTTGTTCTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000009362:ENSGALT00000015247:10
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:
PF084417=Integrin_alpha2=FE(4.4=100)
A:
NA
C2:
PF084417=Integrin_alpha2=FE(10.9=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGATGTGAAAGCATGTTTTCA
R:
AGAACAAGCTTGGCTGTCACG
Band lengths:
214-1330
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]