GgaINT0047774 @ galGal3
Intron Retention
Gene
ENSGALG00000009362 | ITA6_CHICK
Description
NA
Coordinates
chr7:19103760-19105512:-
Coord C1 exon
chr7:19105385-19105512
Coord A exon
chr7:19103856-19105384
Coord C2 exon
chr7:19103760-19103855
Length
1529 bp
Sequences
Splice sites
5' ss Seq
CAGGTATTA
5' ss Score
7.26
3' ss Seq
TTTTTTTTCCCCAAATAAAGATC
3' ss Score
4.48
Exon sequences
Seq C1 exon
ATTCTTGATGGTGAAAAAACAGGCACCAATTTCTTTGGTTACTCTATTGCTGGAAACATGGACCTGGATAAAAATTCCTACCCTGATATTGCTGTTGGTTCCCTTTCAGATTCTGTATCTGTGTTCAG
Seq A exon
GTATTACATTACAGGACTGTAATTATACCAAGGTTTTCAGTTTTCTAAAAACAAACTGCTTAGAAATAACAAAATAGATGTTTGGCCTGGAGTGTATTTCTCCTGTTAGAAGCTGGAAATTCTGAGAAAAAATACCCATGAATTGATTTGTTACTCTATTCCCCGTTTCTTGTTCAGAAGCTACCTTCCGATTAGTGCAGGCTTAGAGGGTGAATGTGTGCAGTTGCTGTGGGACACTGGTGTGCATTGCTGCTGTTACATAACAATAATCCTACTTTATTGAAGGTAGAACAAAATAAAGGAAAACCTCACTTCTGGCTGAGACTCAAAAGTGCTGAGGCTGTGGTGGGGTCTATGAAACAGCACTGAAAAAGCACTGCAGCCTAGATCCTGTTTGATTTCTGTAGCACAGGCCTTAATTAAGGATGTACCAGGATGACCTTGTGGTCTTTTACAGACCAGTTTTTCTTTAATGTTACTGTTAAGCTGAATTCACTAGTAATGAGCAGGAAGAGGACTATCTCTTCCTCAGAGCAGTGAATCTTGTGTGAAGTTTGAGGCTTTGGTGATTATCAGTTCTCAAAAAGGGAGGTGTGGAACTGCCAAACTGGTTATCCTAATCTTGGTGAAAAGAAGTCTGCCCTTCAGGGAGAATTGCTTTTCCTACAATCTTTTGATGACCCTGTCTCTAAGGTGTATGGAATCTGTGTGTGTAATTGGAATGCCTTTAAATACACTGAAACAGTGTATAACAAAAGCAGCCCGTATTGCTTGTGGAAGGGAATAATCCGGGTGAAATGGACACTCAATAGATTATTAAATGCTCTACTTAGTCAAAAGAAGCTTTAATTATAAGGGCATTAAAAAACAAACAAAAAAAAACTTGTAGAAGTGAGAACTCAACCTTTATGCTTATAAACAGCAAAAAGAGTCACCCATTTAAATCTGATAAAAAGGGTGAGGTGGCTTGTTTGGACTCTAGTTTAAACAGATGCCTTTTCTTATCCCCCATGCAAAAAGGGAAAGAAAGGAAAAGTTGCAAGGCTAAATCACGACTGCAGTCTGCATGCAGAGGAGTCAGGATATAAAAGCTTTGTTTCCCATAGCCATCCAGGCTCCACATTAAAGCTGTTTTGGACATTAATTTGAATGAACTTTAGTACCTACAGTTGCTCACAAGGGCTGAATTACCATTGGTATGGGAACCATCACTTTGAATTTCCTGTGTGTGTATAAAATAACAACCATAACATTGCATTAGTGTACCCTGCTCCCTCATTAGGCATTTCCTACTCACTGTTGTAGTCAGTTATTCTGACTTGCTTAGCTTAGCATTAAATTGTTTTGTTTCTTACTATAATGAAAGCCAAATCCTGTGTTTCTTGGGGTGTCTTTGCTGCAAATCAGTGCAGGCATAGCTAAGGACATCTGGATTCATACGAATTGTTGCATTAATTTTATTTGAAACTCTTCCTTCTTCTACCCTTTCTTTTCATTCCTTGTTTTTTTTTTTTTTTCCCCAAATAAAG
Seq C2 exon
ATCTCGACCTGTCATAAGCATTACAAAAAGCATTACAGTACAGCCTGACAAACTTGACCTGAAGAAAAAGAACCCTGAAGACCCCAGTGAAATATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000009362:ENSGALT00000015247:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.023 A=NA C2=0.182
Domain overlap (PFAM):
C1:
PF0183918=FG-GAP=WD(100=72.1)
A:
NA
C2:
PF084417=Integrin_alpha2=PU(6.5=93.9)
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:
AAAAACAGGCACCAATTTCTTTG
R:
TTTCACTGGGGTCTTCAGGGT
Band lengths:
206-1735
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]