DreINT0078470 @ danRer10
Intron Retention
Gene
ENSDARG00000062049 | hmha1b
Description
histocompatibility (minor) HA-1 b [Source:ZFIN;Acc:ZDB-GENE-071213-2]
Coordinates
chr22:17597586-17599581:-
Coord C1 exon
chr22:17599444-17599581
Coord A exon
chr22:17597777-17599443
Coord C2 exon
chr22:17597586-17597776
Length
1667 bp
Sequences
Splice sites
5' ss Seq
TCTGTAAGG
5' ss Score
4.7
3' ss Seq
AAAAAAAAAACTTTTTCCAGGCC
3' ss Score
4.27
Exon sequences
Seq C1 exon
GCTGAGGAAGCGGAGGCCACATACCGGACCTGCATTGCAGACGCTATCACTCAACACCAGGAGCTAGAGCACATGAAAGTCACTGTCCTGCGGGGGATTCAAGAGGTCATCAAGCAGACCGACCAGACCATTCGATCT
Seq A exon
GTAAGGGACAATTTTCTTTCTTTTTACAAAAAAAAAACACAGATTAACCCTTTGACTGCCTGCTTTACCAAATGGTTGACCATATTTTGACTGTTTTAAATAATGACTGTTAAATTCATTCAAAGAACGGCTGTTTTAAATAATTGCTCTTACACAGCATTGTTGGGTTACAAAATAAAAATCACACAAACATAATCCTGTTGCACTAATACACTTGATTTTGGTTTTATTGTTAAAAAAAACAACAACAAAAAAACAAGAAAACATGTTAAATGATAATCAGGAATATAAAAAATATATGATTTGGCATTTAAAAATGTTTTAATTTGGAATATTTTTTAAAATAAATGACTCTTACACTTCATATTTTCAGATTTTTTTATAGTACATCGATTAAGTCCGGTACTTTCACCATAAACCGACATATCAGTCCTTTGGTAGAGGTTGATATTTTAGAAATTAGGGGAGATGTGTTGAAAAAAAAAACATTGAGTGTGTTAACTAGCGACATTAGGAGTTAAGAAATGCAATTCAACCTTTTTTTTTCTTTTTGAGGTAGTTAAAGGGTTAATGTAAAATGCACAGAATTTTCATATTTTTATTTAAATATAAAAAAATTATTACATATTTTTAAATATATTTTGTAAATATTGTAAAATCAAAGGTAATATTTTCCAAATATATTACATATATTTAAAAAGTGCTATGGATTTTTAAAATTGAGAAATACATGAATGGAAAATCTGAAAACACAACAAATATTTAAGTAAAAATATATTAATTAGTGGTGGGCCGTTATCCATGTTACTGTGCTGCTTTAACGCGTGACTCTTATTGTGTGATTAAAAAAATGTTGCCGTTAATCTATTCTCAAAGTTGGGTTTGGGAGCTGGGTCTATTCTACACAAGCTGTGATGACTTTCACCTTGATATTTTAGCGCGGATGTATACCTGACCAGTGAGCAAATCAGCAGGTTGCCTGACTTTAACTGCAGTTCGGTAGTTTCACATTTAATCATGAACATTTAATTCATGCCACCGTGACAAACTGGGGTATTAGATGCAAATACGAAGTAAGGACTGGTCAGAGTGTTAGGGAATTTAATATGATGCACGCCAAATGGATAGAAAAAAAGTTTTGCGTTTTGTGTGTGTGTGTGCGTGCGCGGTCCTTTACTGACAGCCGTGTATGTATCTTGTCGGAAAATATGACAAAGTCCTACATGACGGTAATAGTTTGATCACAGTGTTTACTTCAATAATGCCACTAATATCTGCATACTCCACATCTTAATTCCATTTCTGTTTAGATCAGTGCATGAATTTGCATGATTAGTAGCATTAATTAGTATTACATTTGTTAGTAATGATAATATAATATTAAAAAGTTTTCTAAGATGTTAAATAAAACCAACGTGTAATAAATAATCAAATGAATGAATATATTAAAGAAATACTTCTTTAAATTAGTACACGTTTCCAAAGTGCAAACTCCACTTTAAACTCTGATCAGAATATCTGTGCTTGTTTACATGCTTAAGCAATGGCCCAGTCTTGCATTTCTTGGACTTAATAGAAACAAATAAATGCTGAAACACAGCCAGAAAATCTAAATCCAGCTTGAGCGGGTTTTAACTGTGAGCTCTGAAAAAAAAAACTTTTTCCAG
Seq C2 exon
GCCACCATCTCCTACTACCAGATCATGCACATGCAGACGGTCGCGCTGCCGGTCCACTACCAGACTCTGTGCGAGAGCAGTAAACAGTACGACCCGGGACAGCAGTACGGCACGCACGTCAAAGACCTTCAGATGAGCGAAGAACCTGAAACGCATTATGAGTTTGAGGCCTACTCTGCCTCCTCTGTCCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000062049:ENSDART00000132565:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.065 A=NA C2=0.656
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGGAAGCGGAGGCCACATA
R:
TGGACAGAGGAGGCAGAGTAG
Band lengths:
326-1993
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]