DreINT0082985 @ danRer10
Intron Retention
Gene
ENSDARG00000012824 | itga3b
Description
integrin, alpha 3b [Source:ZFIN;Acc:ZDB-GENE-050411-55]
Coordinates
chr12:5581239-5583228:-
Coord C1 exon
chr12:5583124-5583228
Coord A exon
chr12:5581444-5583123
Coord C2 exon
chr12:5581239-5581443
Length
1680 bp
Sequences
Splice sites
5' ss Seq
TAGGTGTGT
5' ss Score
4.3
3' ss Seq
GTCCTCATGTCTGTGTTCAGGTT
3' ss Score
9.47
Exon sequences
Seq C1 exon
GCACCGTCCATATGAAGTGCAGAGACACAGACTCCGATTATGCTGGCGATGCCAATGATAGAAGCTTTGGTAAACTGGGTGAGGACAAGTTCAACATCTACATAG
Seq A exon
GTGTGTACTTTATCTTTTGATTTTGACTTGTATGTTGCTAAGTTATGTTTATTTATAAACTATTTTCTAGAGGATCACATGTTTATGATTGCTTGCGGCTGGTCCTTCATTATTCAATTTATGATTCACTAATCCTAAACCACTATAAATACCCTAAGTTCCATATAACGAAGAATCCCCCTTCCACCCCTGCTCCTCCTCCTTTCCTAGATGGGTGGCACAGTGGCCCAGTGGTTAGCACTGTTGCCTCACAGCAAGAACATCACTTGTTCTAGTCCTTATGAAGCCAGCTGACGTTTCTGTGTGGAGCTTACATGCTCTCCCCGTGCTCACGTGGGTTTCCACCAGGTTCCCCGGTTTCCTCCCCCTGTCCAAAAAACATGCAACTTAAGTTAATTGACTAATCCAAATCAGCACCATAGACATGCTCCTAGTAAGTAGTTATCTCTTAAGAGCAATCACTATCTGTTCATTAGCTACTACAGCAGGGGAGTTCTCAAATCTACCTGAGCTCAAACTCGCCTTGCAAACGGGAGGGAGCCCCGGGCTCGAGGATCTTATGAGCTCAGGGATCTCTCCCGGGTCAGCATGCCAAACAAGCTTTACAATCAATCATCAGCTAAGTGTGAACTCTTAAATGTAATTTTTAAAAATAAAGCTGCTTGTGTTTTTTTTCCCCTGTTCTTTCAATAATCTGTATTAATAATAATAATAATCAGACTGGTTATGTTCATTTCATAAGTAATTTTAATGTGAATGAAAGTTTCTCGCATATCAGTGAATTTTTTTTTCTTCAAATTTTTTTTTTTTTTACTGTATGTAATTTTTTATGTTTTTGTTTAACTTTGTTGTTGAGCTAATTCTGTCACCCTAATCTAGATGAATGTATTTTATGTGTTTATTTCGGCTATATATTTAATTGAATTATACAATTGTCAAATCATCTATTCTCTAGATAGAATCAGTTGTCTATCAAAATATTTCTGTGCATTACTTTCAGTTTTTCTTTTACTGCTAGTGTTGTTAACTGATAAATAAAATTACAATAACATTATCAGTATTTTTCAAAAATTGATTGTTTTAAATTGTTGTCATTTATCTGTAATATTACTATAATTTTATTCAATAATTGCATTGCACTGCATCACATTTTTTGTATATAAAGTTGGTCAAAATTATTAACCCTCCTGTGAATTTCTTTTTTAAATATTTCTCAAATGATGTTTAACAGAGCAAGGAAATTTTCACAGTAATTCCTATATTTTTCTTCTGATTAATATGCGTATTTGTTTTATTTGAGCTAGAATAAAAGCAGTTTTTAATTTTTTAAAACCATTTTATGGTCAATATTATTTAAATGTCACTTTAAGCTGAAAACTAGTATCTTGAAAAATATCTAGTCAATTTTTATGTAGTCATCATGACAAAGATAAATGAAATTAGTTATTATGTTTAGAAATGTGTTGAAAAAATCTTTCTGTTAAACAGAAATTAGGGATAAATATTTAGGAGGGCTAACAATTTGGTCTTTAACTGTATAAATCATTTGTCTTCTTTCTCAAAAGTGTCTCTTGACTGTAACTGAACTTATTAGTAGCTGGACTGGCTTCAGTTTCAGTGTTCTGCATGTGGGCTGTTGGTTGCACACAGATGATTGACTGTCCTCATGTCTGTGTTCAG
Seq C2 exon
GTTACTCTGTGCTGGAGGACATAAAGTTACTGGATCGCTCTGTGTTCACTGTGGTGATGGGGGCTCCCAGAGATGAATTCAAGGGTTCAGTGATCCTGGCCGACAAACAAGACTTGATACTCAAGCAGCTGATGACGATCACAGGGGAACAAATAGGGTCGTACTTTGGCAGCTGCTTGGCAGTAACAGACCTCAACAATGACGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000012824:ENSDART00000105884:5
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:
NO
A:
NA
C2:
PF135171=VCBS=PU(6.8=7.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCACCGTCCATATGAAGTGCA
R:
TCGTCATTGTTGAGGTCTGTT
Band lengths:
310-1990
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]