DreINT0083310 @ danRer10
Intron Retention
Gene
ENSDARG00000028507 | itgb4
Description
integrin, beta 4 [Source:ZFIN;Acc:ZDB-GENE-030131-7209]
Coordinates
chr8:13113736-13115993:+
Coord C1 exon
chr8:13113736-13113924
Coord A exon
chr8:13113925-13115837
Coord C2 exon
chr8:13115838-13115993
Length
1913 bp
Sequences
Splice sites
5' ss Seq
CCGGTGAGA
5' ss Score
8.72
3' ss Seq
TTCTCATGCATGTTCTTCAGGGT
3' ss Score
8.53
Exon sequences
Seq C1 exon
GTGACGTAAAACGTATCGAGGTGAACAATCCTGCTCAGAACTCAGTGCTGGTTCAGGATCTCCTGCCTAACCAGTCCTACATCTTCAAAGTCAAAGCACAGAGTCGAGAGGGCTGGGGTCCTGAGAGAGAGGGCGTCATTACCATTGAGTCCAACGTCGACCCCAAGAGTCCACTGAGCCCAGTGCCCG
Seq A exon
GTGAGAGGAACACACTGCACAAACACAGTTCTTTCATCCACCTGATTTTGGAGATTTTGAGTGTTTTTTTAAGTCAAATGTAAGCCAAATCTTTTGCAACACATTACCAATTTCAATTGCAATACATGTTTTAAAGTCTATTTTCTCAAAATGCTTTTTTTGCACTAAGGCTTAAATCTGCACCTCGTGGGCTCTTGCACAGACAGTTTTATTCATATCTGTATTATGAAGGATTATAGAGATATATGTTGATATGTGATTTGCCTGATTGGACAAAAAAATATGGCTTCAGCATCAATATCCCAGTGTGCACATCCGCAATAGTCACGTCGCAGAATCTGCTACGATAAGTCTGAATTACACTACTGGTCAAAAGTTAGGGGTCAGTACAGTATACATAAAATACAGTACAAATTGTAAAATAGTGAAGTGTTATTGCACTGTAAAATAACTGTTCAAAGTAGTTTATCATTTAATTTAATAGTTTATTCCAGTGATTTTAAAGATGAATTTTCAGCTACATTACTCCAGTCTTGATGATCCTTCAGAAATCACTCTAATATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATCATTTTTATTCATTCATACATTCATGCATTTTCTTTTCAGCTTAGTCTCTTTATTAATCTGGGGTCGCCACAGCGGTATGAAATGACAACTTATTCAGCACATGTTTTACACAGCGGATGCCCTTCGGGAAACACCCATACACACTCATTCGCACACTCACATATACTACGGACCATTTTTAGCCTACCTAATTCACCTGTACCGCATGTTTTTGGACTGTGGGGGAAACCAGTGCACCCGGAGGAAATCCACGCCAACGCAGGGAGAACATGCAAACTCCACACAGAAACGCCAACTGACCCAGCCGAGGCTCGAACCAGCGACCTTCTTGCTGTGAGACGATAGCACTACCTACTGCGCAACCGCGTCTCCCTATCATTATCATTTTTATCATTATTATTAAACAGAATGAAAGAATAATTTACTTTAAAAAAATGCCTAAAAAACTGACCTCAAACTTTTGACCGCTGGTGTATATTTGACCAGGAGCCAGAGAACATATGTGATTTGTAGAGTCACTGCAAAGTCCAACCATAATAGAGTGAAAGTGTCATTAGTGTGTTTTTAAGGCCTTGGATTGTGAGCGTTTTAAGAGAGTTTGTAACATGTGGGCACAAAAAATGATGACATTTGAGGTGTAACCTTGATGAATTGTATTTAATTCTACAGTAAGGAAATACTCAGTGTTATATTTTTATTTGCACTGGAAAAAAATGCTTTTCTTACAATTTCTGTAATAAATTTTTGTATCAAACCAGAAACAATATTATTTTACTTACCCCATTGGCAGATTATTTTGCTTGTTTGAAAAATGTATTATTTTACAGAACACAACAATATTTTTACTTATTAGACTTAAAATTTTACTTAAAATTGAGATATTTGGAAAAAAAAATGTGTTCTGACTATTCAAATTCTGTACCTGAATACTGTTAGACTCCTGAGGAAAAACGTCAAATATAGCTATTCAAACCATTCGGTGAAATTGTTGAAAAATAAAATCCAATATCGTGCAACCTTAACATTTATGCAAATTGGTGCACATTAAATGAAATAGTGCCTCAATTGCATATTTAAATGTAACAATTTAGAACATTTTGACTTGTATTAGAAAAATGTTTTTAATTCCTATTGTAATCAGTCAACTGGGAAAGTGTGGTAATAACTATTATACTCTATTATACCCTGTTTACCAGCAGTGTATTGTCTTAACTGTTGTCAGCAGGGGCAGCTTTGATGAAATCTTCAACCCACTTCATCTTTAAATTATTAATAAACATGTTCTCATGCATGTTCTTCAG
Seq C2 exon
GGTCTCCGTTCACTCTCAGCACTCCCAGCGCTCCAGGACCTCTGATCTTCACAGCGTTACGTCCAGATACACTGCAGCTGAGCTGGGAGAAACCCCGAAAACCCAACGGAGACATCCTGGGATACGTGGTGACCTGCGAACAGCTGCATGGTGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000028507:ENSDART00000029308:37
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.312 A=NA C2=0.208
Domain overlap (PFAM):
C1:
PF0004116=fn3=PD(50.0=65.6)
A:
NA
C2:
PF0004116=fn3=PU(50.0=81.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACGTATCGAGGTGAACAATCCTG
R:
CTCCACCATGCAGCTGTTCG
Band lengths:
335-2248
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]