DreINT0012616 @ danRer10
Intron Retention
Gene
ENSDARG00000052496 | HMHA1 (1 of 2)
Description
histocompatibility (minor) HA-1 [Source:HGNC Symbol;Acc:HGNC:17102]
Coordinates
chr2:56592698-56595749:-
Coord C1 exon
chr2:56595674-56595749
Coord A exon
chr2:56592830-56595673
Coord C2 exon
chr2:56592698-56592829
Length
2844 bp
Sequences
Splice sites
5' ss Seq
GCAGTGAGT
5' ss Score
7.39
3' ss Seq
TTGTTGTTGCGTGTCCGCAGTCA
3' ss Score
9.48
Exon sequences
Seq C1 exon
TCGATGGAGGATCTGTACAGGTTGTCTTCAGGTCAGGGCCCTGAAGGAGGAGGAAAATACGACCAGCAGGACTGCA
Seq A exon
GTGAGTCAATTGCTCATTATGTTGCCTTTATTTATTTTAATATGCTTCTAGTTTCAGTTTTACTTAATAATGTAGGAACATCCTGGGGTGCGTTTCCTAAACAACAACGTAAATCGCGACTGAATTATCATAGTACGATGCATTGTATGAGGAAAGAACAATGTAGTGACGAGTGTTTCCCAAAGCTGTAGTTCAGGGGTGTCCAAACTCGGTCCTGGAGGGTCGGTGTCCTGCATATTTTAGTACCAACCCCAATTAAACACACCTTAACCAGCTAATCAAGGTCTTTCTAGGTATACTAGACTTCCAGGCAGGTGTATTAGAGGAAGTTGGAGCTAAACTATGCAGGGCACCAGCCCTCCAGGACTGAGTTTGGACATGCCTGCCATAGTTGCTTTGATGCAGATCCATCAGTAGAAACACGTTAGTTAACGTATAACATCCATAATGATGCTTTAAACAAGGGTGTGTGTGTAGGGGGGTGGGGGGTAGTTAATTAACTACATGTTAATTAATTTTTGTGCAAATTATATTGTTTTACACGCCCTTAACAAAAATTCAATAATAGTTTTGGTAAAAAAACATGCACTCGCTTTCCATGTTAGGTAACGTTTTACAAACTAATTTCGAGAGGAGCACATGATATGATTGACTACAGCTGATCCTCATCGCTAATCATTAGCCAGCCTATTAAATCATTCCAGAATTACTATAAATATTCTGCCTAAACTTCATTCCATATCTTCGTTTTGAAAACCCCCCTTCTCTATCCTTCCCTTCTCCCTCCTCCACAATTCTATGTTCGGGTGACACGGAGGCTCAGTGGCTGGTGCTGCTGCCTCACAGCGGGAGGGCCAATGGTTCAAGTTCTAATCGAGCCAGTCGGCACTCCCTGTGTGAAGTTTGCATGTTCTCCTCGTGTTCACGTTGGTTTTTCCTCGGGTGCTCCGGTTTCCTCCTACAGTCTAAAACCTATTGTAGTTGTAATAACAGTAACACGCACTTAACGCATACATACTGAATCAATTAGAACCACCGTATTAACCAAATTATAGGTAAGAAACGAACTGGGGGCTCTCAAAAAATACCTGATCTCGTATCCCTCCTAATGCTCATTGACCAGACGCGGGGACCTTGGGCTCATCTATCTCCGAGCTCAGGGTTCTCTCCCGGGACAGCATGCCAAACCTGCTATTACAGTCAAGCATTATCTAAATGTGAATTCTTGAATTGAAATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNATATATATATATATATATATATATATAAATCGTTAATAGTTGTAATTTACAGTAGGCTATTTATTAATAAATGACAAAAATCCGGCGAAGCAGTGGCGCAGTAGGTAGTGCTGTCGCCTCACAGCAAGAAGGTCGCTGATTCGAACCTCGGCTCAGTTGACGTTTCTGTGTGGAGTTTGCCTGTTCTCCCTGCCTTCGCGTGGGTTTCCTCCGGGTGCTCTGGTTTCCCCCACAGTCCAAAGACATGCGGTACAGGTGAATTGGGTAGGCTTAATTGTCCGTAGTGTACGAGTGTGTGTGTGGATGTTTCCCAGAGATGGGTTGCGGCTGGAAGGGCACCCGCTGCGTAAAAACTTGCTGGATAAGTTGGTGGTTCATTCTGCTGTGGGAACCCCGGATTAATAAAGGGACTAAGCCGACAAGAAAATGAATAAATGAATGAATGAATGAAAAAATCCTACTTACTTATGATAACAATTATACATCATATAGGCCTACAGTACAGATAGATTTCTTAATAAATAACCTATAAAACCATTAATGAATGCTAGACTGCTTTTAAATAACAGGTCACCTATAGCTTTCGTCATGAGGCACGGCTGCGTTCAAAATGGCATGAATGATTTCAAAGTGCACTGCGAAGTGAGCACAATTGTCAATATGAAGATAGCTAAAACTGAACTGTAAAAACACTTTAAAAGCAAATTACACATCAGAGAGATGACCTTAATGCCTTTTTTTCAAGTTTAAATGTTGGAAACCTCTAAATGAACAGGGCATAGGGAGGATAACTGGGAATAGAGCACAACCAGGAATTATGCGTCTAACTACAGCTCCAGAGGTGTAGTTGCAAGCATACAAGTTTACAGTTTGCGAATGTTTGTTGGAACGATAGATTTGGGAAACGCCAAATCCACAAATTAGGTTTGTAATGGCGGAACTTGTAACCTTATTTGACTAATGATGGTTTTTGGAAACGCATCCCTGGTTAGTATACATTACTTATGTTAACCATTTTCAACACGTGTATTGTTCAATTAAGCCTGACTAATGCTTGGGGTCCTGGTAAATCAGGGGTCACCAATCCTGGTCATGGAGGGCAGGTGTCCCTGCAGGGTTTAGCTCCATTTTGCCTCAACACACCCGCCTGGATGTTTCAAGTATACCTAGTAAGACTTTGATTAGCTTGTTCAGGTGTGTTTGGTTAGGGTTGGAGCTAAAATCTGCAGGACACCGGACTTCAAGAAACAAGTTTGGTGACCACTGTGGTAAATAATCATTTTTTAAATTTAATTGTTTGTTTTTTATACCAAACTCCATATAATTTTCAAAATTTATTTATTATTTTTCTACTTTTATTTGTTTGGCCTCTATTTTAATGGCTTAAAAAAATCTAAATAAAAATCTGTTGGTTTGTTGTTGCGTGTCCGCAG
Seq C2 exon
TCAGTCCTCAGGAGGTGGATATTCTCCTGCAGCGCAGTGAAGGCGGCGTCGACTCGGCTCTGAGTTACTCCAAATCCATCGCCAAATACATGAAGGACATCATCAGCTACGTCGACAAGAGAATTGCTCTCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000052496:ENSDART00000164461:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.765 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0061118=FCH=PU(29.8=80.0)
Main Inclusion Isoform:
NA
Associated events
Conservation
Cow
(bosTau6)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]