DreINT0083072 @ danRer10
Intron Retention
Gene
ENSDARG00000069946 | itga6b
Description
integrin, alpha 6b [Source:ZFIN;Acc:ZDB-GENE-050320-5]
Coordinates
chr1:30232585-30234567:+
Coord C1 exon
chr1:30232585-30232846
Coord A exon
chr1:30232847-30234435
Coord C2 exon
chr1:30234436-30234567
Length
1589 bp
Sequences
Splice sites
5' ss Seq
AAGGTATTA
5' ss Score
7.04
3' ss Seq
CACCGGTGTGTGGAAATCAGGAA
3' ss Score
3.47
Exon sequences
Seq C1 exon
GTCTGTGCACATCGATACCAGCGGCGCTTATTTGTTGGCTCAGTTCAGGAACTGCGTGACTTGACAGGTCGGTGCTATGTACTTAGTGAGGATGTGACGATTAATGAGATCTCAGATGAAGATGGAGGGGATTGGATGTTCTGCAATGGGAGAAACAGAGGGCACGAGCGGTTTGGATCATGCCAGCAGGGCATGTCCGCCACATTCACAAAGGACTATCACTATCTGGTGTTTGGAGCACCAGGCGCTTACAACTGGAAAG
Seq A exon
GTATTAAAGGAAGAGCTTGTATTATTTAAACTTTTGTTAAAATTTGAATAGTATTTGATGCTTTTTTGCAAGGTCAAAAAATACTTTTATTGTCTTATGATGTGCATTTCTTTTACCGAATTATCCTAGCGACTCCCATATGATTCGTTCAGTGATTCATTTGTTCCCAAAACCCCTCCTTAGTGCGATGCCAGTCTGCGCTGATAGGTCCGATGACCCAGTCTGTTGCGATTGGTCGACTGCTTTCAGCGTGAGGCAGAGAGAAATGCCCACCATGGCTTATCAACAATTTTGAAGTAGAGTGCAGAGTGTATGTGTGAGCCCAATGTAGGAGTGCATTAAAACAATGCAGTAAACACCAGCATATTGCTATATTCTTAACCATAAGTAAAAACAGTGACACACATTTAGTATTAATCCACACAGCGGCAAAAGCTGAGCTATTTGGAAACTTGACTGCCACACGTGTGTTGGAACAGCTGATTGTGGCTTTAGCAATGGCAAACCACAGTAGATTGTGAGCTCACAAATGCATTTAAATCCATAAATAAAGCGTCACGTTTTCAACGTGGTTTTAGACGCGATATGAGAATATAAAGTGTTAACCAGATACATTACAAGTGGCTACAAGTAACAAAACACAATTTAATACATAATTTGCAAGCTAGAGAAAACAAGGAGGCAACCATTTTAATCGCACTTAAGTTACTTACACTCAATGGACGAAAAAATTATCCATGAACTGTGTATTGTAAAGTTCCTGTCAAGTTCTGCAAAGTCCCATACATCAATAGTCTTTTTGAAGCACGAGTCAGAAAAATGACGGGAACACAGCACAAGGATGGGGCTATAATGCTGAGGTATTTTTGCTAAAATAAACTTCACTAAAATAGACTCTTCACAGCCTCATCTTTGCGTAGGGAAAAATAACACCAACTTTCCCTCACACTTCAGAGCACAGCGTCTTTGCAACATGATTCAACCAGGATCTGCTACAATATTTGTTTTCTTTCCACTGTGTTTGTGGGCAGGGCTGGGTTTTAAATTTTTCAACAAATGGGCGCGGCTTGAGTTCTGTATTGACACAGCTAAAGATTTGTTACCCTGACATTTCATTTAACCCACTATGAGTAGACTGTTTTATAGATTTAAGCCTTGTCTGGACATTTCACTTCACTTAGAGCTGTGTCACGCACTGCATGGAAGGTCATTTTCAAAAACCCATAATATGGGCTCTTTAATGTAGTTTTGAAATCAAGGTGACCTCTAGGTTAGAAAGTCATGTTTGATCAATCATGATCAAGTATTCCAGAGAGCCATGTATTAATATTATATAATGTAATTTTAAGTAAAAACCCCGCTTCAAATAATTTCTAAATGAAACGCCCCAACTCATTATTCCCTACATCACTTCATGACATGTCATTTCAGCTTTTCTTTGTTGCATCATTGCATCTGACGTGTTGTACTTTATCTCCCTTTTCCACACGTTTGCATCTTTGTCTCCATCTTTACATCCATTCTACACCCTCAACCCTTCCACCTATTCCTTTGCTTGTTCACTTAATCCACCGGTGTGTGGAAATCAG
Seq C2 exon
GAATTGTGCGGTTGGAGCAGAAGAACACCTCTCTGTTTGATAAGGATATCTTTGATGACGGCCCATATGAAGTTGGAGATGAAAACCGACTTGATGCAGAACTGGTCCCTGTTCCTGCTAACAGTTATTTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000069946:ENSDART00000102210:4
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:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TACCAGCGGCGCTTATTTGTT
R:
CCAGTTCTGCATCAAGTCGGT
Band lengths:
352-1941
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]