DreINT0078469 @ danRer10
Intron Retention
Gene
ENSDARG00000062049 | hmha1b
Description
histocompatibility (minor) HA-1 b [Source:ZFIN;Acc:ZDB-GENE-071213-2]
Coordinates
chr22:17599444-17601647:-
Coord C1 exon
chr22:17601480-17601647
Coord A exon
chr22:17599582-17601479
Coord C2 exon
chr22:17599444-17599581
Length
1898 bp
Sequences
Splice sites
5' ss Seq
AAGGTCAGA
5' ss Score
6.8
3' ss Seq
GGTGTCTGTGTTTGTGTCAGGCT
3' ss Score
6.66
Exon sequences
Seq C1 exon
ATGGAGTGTGACGTGAACCTACGCAGGGCTAAACAGGTCTACATGACCCGCTGTGAAGAATATGATAAAGCCAGGACAGCGGCGAACAGGGCCGAGGAGGAGGGCGGCAGTGCCACCACCAAAACACTGGACAAGAAGAAACGACTGGAGGAAGAGGCCAGAAACAAG
Seq A exon
GTCAGAGTCTGGTGATTGCACTGACACTTTATTAGCTATAGAATATGACCTACAGATTTGTTTGCTTATTTTTTGTTTGTCTCAAGACACAACACAAATTTGTTCTTCCATTGCTGTAGCTAATCTGCTTCCAGTTTCAACAGGGTCAGAGATGAGCTTATGCAGACCTCAGTTGTGATTAGGTGCCGTTTGAGCCTTTTAACTCAAGAACTTTTTTGCATTGAACTCCTGCTTTTAAGATATTTTCTCTGTTTTAGATCATTCTTTGTAAACAGAGTAGGCATGGATGATGTCACCATTTGCGATTATATCTGTAAAATTTTTCCACACTATAAGAATTAGCATTAGTGTGATAAGTGGTAAAAACTACAGCAACACATGTTCAAGACAGTTTTGCATCCATATGATCAGTGCTGGGTAAGTTACTTCAAAAAAGTCATTAATTTCTGATTACTAATTACATCATTAAAATGTCATTTAATAGACTTTTCTAGTTTACTTTATTTGACTGTGTAAAATACTACATAAACCTCATATAAATCTCAACACACCAACAATAGAAATTGCCATCTTTTAATTATTTAAATGCGAGTTTTAGATTTAGAAAGGGCCTTTTAGATTTGTTTAAAACATGTTATAAAAATGTTTAACATCATATGTATCAAAACACCAAACATTTTAAAGTAATGATGCCATATTTCACACATGCTATGTATTGTTATTAATTTCTTAAGTGTTCAATCATCTTGATTAAATGTTCACCTTTAGTTGAAATTATAATTGTAAAAGTATAATTTTCTTTTCTGAATTATATCTGTCAACATGTAACCCAATGAAGTGAAAGCAGCCATTTTTATATTCGTTTCAATGTGCTTTCAAGCCAAAAGAAAGCGAAAGCATAATTCTCTTGATCAGCTCTTGCAATTATATCATATTTGAGATCGTGTCTTTGGTGCTACTTTCACTTTTCATAGAAAGAAAGGTCAAAATATATACAGGGAAATACCTAAACAGAGTGATAGCGGGAAAGAATGGTAAAATACAGGAGAATCAGGTTTGCCGGGTATGCTCTGAACTGATTTATCCAGAACTGTTAAGTATATTTACTGTGTTTAGGGCAAGTACATTACATAAAATTGAAAAATAATGCCTGTATCAGTGAAGAAGAAATGGAATTACAGTAATAGTCAGTTTGAGTCTGTTGACAAACATAGAGATTTACTTATTTACAAAACCTGTGGAGAAATTATGCCAAGGTATCATTAATCCTGGATCAGGTCGTATCCTGAGCTGATGCTGTGGTGGTCATGGAGAAATGGAGTGCATGAAACTGATTCCTGAAAGACCACAGTGACAAACAAGTCCCCGCATTGATCCTGTGGGTCAGCTTGACCACAAAAAAGGAAAAAATGTCCTAAAATGTTGAGGTGAAAAAATGCCTCACCGCAGTGTTCAGCGTGCTGGTTTCGCTGTCCCTATAGGTATAGTCAGTGCATGGTCTGAAGCAGCTTTCACACTGAACTCTGAAAGCGCTGCGCTATGAAACCTATTCACTTCAAGGTACCGACTAAAGCACGAGCAGCAGAGTGAACTGTTGACTAGCTTCCATGCTCAACTTTGCCAGAGTTTTCAATATTACACTCTGTGGATATTTCGCTTATGAACACTTATACTTATCTATGCATGAATTACACATGCTCACCACAAAAGCAAAGTCTGTTAAAATAACACACAGACAGGACATTTGTATTGCAGTATACTTGTGCTGTCATGGCAACACTGGTAAAATGATGCTTCTCGACTCATTTACTGTCGGTAGCATTTTATTGTCAATTAAATGTTGAGTGTAAATGCTTCTGGAGGAGATTTGGATGAAACGGTGTCTGTGTTTGTGTCAG
Seq C2 exon
GCTGAGGAAGCGGAGGCCACATACCGGACCTGCATTGCAGACGCTATCACTCAACACCAGGAGCTAGAGCACATGAAAGTCACTGTCCTGCGGGGGATTCAAGAGGTCATCAAGCAGACCGACCAGACCATTCGATCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000062049:ENSDART00000132565:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.589 A=NA C2=0.065
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:
GAGTGTGACGTGAACCTACGC
R:
AGATCGAATGGTCTGGTCGGT
Band lengths:
303-2201
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]