GgaINT0127637 @ galGal4
Intron Retention
Gene
ENSGALG00000002389 | ITGB4
Description
integrin, beta 4 [Source:HGNC Symbol;Acc:HGNC:6158]
Coordinates
chr18:4697081-4698829:-
Coord C1 exon
chr18:4698671-4698829
Coord A exon
chr18:4697231-4698670
Coord C2 exon
chr18:4697081-4697230
Length
1440 bp
Sequences
Splice sites
5' ss Seq
ACGGTGAGT
5' ss Score
11.45
3' ss Seq
ACCGTCCTATTTTGCTTCAGATT
3' ss Score
10.88
Exon sequences
Seq C1 exon
AACACCTGCTGAATGGCCGCATGGATTACTTCTCCGGCAGCAGCAGCACGCTGACCAGGACAGCAAACACCAGCTACCACCAGCACGTGCAGCAGGAGCACAGGGTGATGGGGAGCTCCTCACTGACCAGAGACTACTCCACCATGATGGCGGGGCACG
Seq A exon
GTGAGTATGAGGTGGTGGGGACTGCTCTTCCATTCCATGGCCACCTTCACATCCATGCCCTGCAGATCCCTTTGGGGTGAGGGCTGTGTTTGCAGCCAAAGGGGCTGACAAATCAGAGAAATCGCAGCTCATGTCCTTGGAGGTTGGACTCGATGGTCCTTATGGGTACCTTCCAACTCAGAATGGTTCTATTATTCTACCACTGGTGTGGTAGGGCTTTGGTAAGGCTGCTCTCCTTCCAGACCACTCTGGAAAAGGGTGCCCATCCCTGACTTGGGAACAGGAGTCACATCCTTGTTTCCACACTGCAAAGCTTGTGTTGTTGCCCCTTACTATGTCTAGCAGATGATTCCCTTTCAGCTCCGTGCATGTACATCAGACTGGTGTTGACAAGAGGTTGTAAAGAACTTCAGATCTGATCCTTAGAAACCTCTCTCTGTGCAGGAGTCAGCACCTGGGCTGAACCCACTCTGACATCTTCTACGGTGTTTTTCTTTTTCTTTCTTTCTCTACGCTGGTCTGTAGATTACTCAGGGAGATTCCTTCCTCCCATCCTTGAAGATGCTGGGAGGAGAATCCCACAGCCCAGGGACGTGGGTTTCAGGAGCAGGGTAAAGGTGAAGGGTTACTACCCCAGCACTGGCTGTCGGGACTCTATAATCATGACCGATGGGTCCACGGGGACTTGCAAGTACATAGGTACAGCTTTGTCCAGTGCCTCCTTCCAGTCTCGCATCCCATAACCAGCCACACCGCTGGCCCTCTGTGAGCTGCTCCCCAAAACCCTTTCTCATGGCTTTCTGTGTGCCACACTGATCTCCCTCCTCACCTGGCTCAGCCTCCATCACACCACCTTTCCATTTGCAGGAAACTTCAGCTGTGTTCCAAGCCATGTGGGCTGATTAACTCTCACCACTGCTGTCACCGTGCTCTAATGAGCTGATCACATCATCGTCCCCTTCCCCCTCATTCCTAACAAGCTACTTGTTCTCATTCTCACCCCACAGGCTTTTGGAGGACTCTTGGGGAGAACGTGGGTCCCAGCCTTGAGCAGTCCCTGGAGGTGTTGGGTTGGTTTAGCTGTAGATCAGGGCTGTGCTTGCTCTGAAGACATCCACAAAGCATTTGGCAGACTGGACAGAGAGCTGTGGGGTAAGCCACGAGGGCAACACACAGCACCAGGTCCGTGGCCAAAGGGCTGTGAAGCTTACTTTGCCTTGTCCCATGCAAGGGCGGCACCCCAAGGCCACAGGACATCCCTGTAGGTGTGCAGAGTCCCCCTGCAGACAGGCCTAGCTTGCAGAGAGGACATCTCCCCACGTTCTCCCCATGTTGTCCCTGGACCATCAGGACCATCCCACGCTTGCGTGTGCTGCTGCCTCCTCTCACCCAGCCCAGTTAAACCCAAATCCCTGCTGTGACCGTCCTATTTTGCTTCAG
Seq C2 exon
ATTCCAGGTTTCCACTGGGTGTCCCTGACATCCCCACGAGGTTGGTGTTCTCTGCTCTGGGACCCACCTCGCTGAAGGTGAGCTGGCAGGAGCCGCGCTGCGAGAAGGAGGTGCAGGGCTACAGCGTGCAGTACCAGCTGCTCAATGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000002389:ENSGALT00000003760:33
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.642 A=NA C2=0.078
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004116=fn3=PU(48.8=80.4)
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:
GCTGAATGGCCGCATGGATTA
R:
CTCCATTGAGCAGCTGGTACTG
Band lengths:
302-1742
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]