DreINT0012614 @ danRer10
Intron Retention
Gene
ENSDARG00000052496 | HMHA1 (1 of 2)
Description
histocompatibility (minor) HA-1 [Source:HGNC Symbol;Acc:HGNC:17102]
Coordinates
chr2:56557814-56560104:-
Coord C1 exon
chr2:56560053-56560104
Coord A exon
chr2:56559854-56560052
Coord C2 exon
chr2:56557814-56559853
Length
199 bp
Sequences
Splice sites
5' ss Seq
GCGGTGAGA
5' ss Score
7.4
3' ss Seq
ATGCATGTGTGTGTGCGCAGGTG
3' ss Score
8.69
Exon sequences
Seq C1 exon
GACAGTGAGACTGGAGCTCATGAAGAGCCAATCAGAGCCCATCAGGAGTGCG
Seq A exon
GTGAGACAGCACACGGTGTATATTACAGATATTAGAAGTGATAACTATTAAATAATATATATTTAAATAAACTATTAGTAATATATATATATTTGTGTGTGTGTTTTGTGTGTATGCATCTGTATATGTGTGTCTATCTGTGTGTCCCTCTCTGTTTGTGTGTATACATGTGTGCGTGCATGCATGTGTGTGTGCGCAG
Seq C2 exon
GTGATTCAGTGGGCTCGTCAGGCTCTCAGGAGCGCTCTCTGGACTCAGACTCGGATGTGGAGGATCCGGCTGCTGGTTTCAGACCCCACCGTCCACCTCTAGTTAGTCAGGAGAGCGAAACCAGCACAGAAGAAGACCAATTGAGTCCCAGAGCCAGTCTGGATCTGAGCGGCCTCGTCCCAGAAACCATCCCAGAGCAGAGCGTCCCAGAGCCTGCAGAAAACACCAGCGGCAGATCCCAGCAGTAAGAGCAGAATCCAGAGCGTACACACACACCACCGCCAGAGCTCAGTGTCATGCTTGTACAAGAAGCCTGTTCATTTGATCAAAAATACAGCACAATTGTGAATTATTACTCTTTAAAATTCTTATTGAAGGCATTTTAGTTTTTTAGTGCAAAAACATACTAGAAAATTACATTAAAGGGGTGGTTCACTACGATATCATATTTTAAACTTTAGTTCATCTGTAATGTAGCTGTGTGAACATAAACAACACCTCAGAATGCAGCAAATGAAGTGCGCATATACCTGGAGCAGTGAAGAGGCATGGCCAGAGGCGCTGTAATCTTATAACAGAGATGCTTCCTGGTGATGTGGAGTTGATCTGCGAATCACAGCACATTATGTTAGCTAACCAATCAGAGCCTCTTGATGGCGGGCCTTTTGGAGGAACTAGGAAACATGACAGTCATTTTCATGTTAGCTAATTAGCTGAATACAATCAAAGTAAGGTATATGAAAAAAATAATGTGATTTTCTACAAATGAAACATAAACACACATTACTTTGCACCCCATAAACACAACCAAGCCTTAAAAATGCACTCTGGACCACCCCTTTAATAAGACGACGTCCATCATTCATATAGTTTGAATCCTGACCCCCACATGAAAACTTAGAATAAAAAATAATAAAATGAAATTGTAATTGAATAAACAAACAAATAAAAAATAAGGATATTCAATACTTTTACAGAAAGGCAGAGAGTTTTGAGTGAGTTTTAAAAGTCTTTTTTTTGTGTGTGTGGTTTAAAAGAGCCCCTATTATTCTTTATAAAGGGTCATATTTTGGTTTTGGGCGTCTCCAACAACAGACTGATCTGCATGCAAGGTCAAAAAACACTTTCATTGTCCTATAATCAGAGATGTATAAAGTACTAGAGACCCAGACTTAAGTCAAAGTACAAGTGCTCTATCAAAAAAGTGACTTGAGTAAAAGTTGAAGTGCTCTTTAAGCACTATACTTAAGTGGAAGTACTGAAGTATCCAACATTTTTTTTCTTCAGTATTGCAAGTAGTTTATTCTAAAATGTACTACTCATGTACTTAAAATAAAAGTACTACTATTGTGTAATGTAGTTATTAAAGAAAGCAGTCAAAAGACATCATATTGTTTTGTTTATTTTAAATATCTTTTTTTGGGGCACGTGATCAAGCAGAACGAAAAGAAACATGGCTTACGATACTGTTTTTCTCTCGCGCTTGAACCACAGATCTGACTATAACAGCTTTAACACACCTTTCAAAGTTGTGCGTCACAAAAACACTCCGTAATCCACTCAAAACGCTATTGAAACCTATTTTCGGATCGCAAATTACTGGTTGTAAACAATATAAACGAAAGTTCTAAACAATCTACCGAAAGACGCTGGTCACTATGGCGCCCTCCATGCAGTAGCCAAGAAAAAGGTCTATAATTATAACGAATAGGGGTGTGAATCTACACTGGTCTCACGGTTTGATTCATTACGATTATCATGCCATCGATTCGATTTAATTCGATGTCTCGGTGCATTGACGATGCTTTCCATACATAATTAGATTTTTTCTTCACAACACATGAATTTTTTTTATTAAAATATATATTTTATTTATATAATATTTGTAATAAAATTTTGTGCTTTATCACAGCAGTTAGATATATGAACTGTGCCCTTAATTTGACCCATAATCACAGCTGAAGCCCGCGCTTTACTTTTAGCATTGGAGTATATAGAAATTGCCCAACAAAAGAAATCCATCATTTTTACAGACTCTAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000052496:ENSDART00000164461:19
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Human
(hg19)
No conservation detected
Mouse
(mm10)
No conservation detected
Mouse
(mm9)
No conservation detected
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGCCAATCAGAGCCCATCAG
R:
TGGTGTTTTCTGCAGGCTCTG
Band lengths:
256-455
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]