DreINT0012606 @ danRer10
Intron Retention
Gene
ENSDARG00000052496 | HMHA1 (1 of 2)
Description
histocompatibility (minor) HA-1 [Source:HGNC Symbol;Acc:HGNC:17102]
Coordinates
chr2:56574754-56576124:-
Coord C1 exon
chr2:56575997-56576124
Coord A exon
chr2:56574856-56575996
Coord C2 exon
chr2:56574754-56574855
Length
1141 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGT
5' ss Score
11
3' ss Seq
GTGCTGTTTTGTCTCTGTAGTTC
3' ss Score
8.92
Exon sequences
Seq C1 exon
GCAGTTACTTCGTACCCGGAACAACAGCCTGTCCAATGACCAGCGACAAAACAGCTGTGAGGCTCCTACCACCCCTGAGGAGGCGGGGTTTGGAGAAGGAACTGTGGTTAAGCAAAGACGAGGTCAAG
Seq A exon
GTAAGTTACAGACAACTAATAGACAGAAACAGATGTTTTATAGAGAACACACACAACACAACACAGTCTTACCCTATAAATTAACCTGAACTAAGTGTAACAGAAGCCAATTTTTTGATGATTGCATATAGTGTTGTGCAATATAACCATTTATATACGGTATGGACAAAATAAAAAGTCTAATGTTTAATATTATTATGCTTAATTGTTTATATTGTTTTGTCATGAAATGCATTATTTACATTAATACTTTTTTATAATTAACATACATGCAATATTAAATTATGGGATGCAGACAGAAACATGAAGAGCATCATGAGAAAGTTGCAATCTAGAAAGTACGGTGTTAACATTTTGCATGTTATATAGGGATATTTTTATTTTTATGTTGAATCTGTTATCATTCGTTTTTGAAAAGTGTTTAATATTTTATTATTATTTATTTTATATTTCTACATTTTCTTATAAAAGTGAGAATTATGATCACTTATAAATGAGTATATGCTTCAAAATGTAAAAAAAAATATATATGTATAAATTTATAAATTTAAATATATAAATTTATATGTAGTTAATAAATATCATTGATTTAATTGACAGAAATGGTACTATATCATAATAACCATTGATATATACAGTATATTGATAATCGGTAACACTTTACAGTAAGGTTGTATTAGTTGATGTAAGTTAATGCATTTACTAACATGAACAAACAACAAACAACACATTTATTACAGTATTTGCTCATGTTAGTCAATGAAAATACAGTCATTCATTGTTAGTTCATGTTAACTCACAGTGCATTAACTAATGTTAACAAGCATGAATTTGGATGTTAATAATGCATTAGTAAATGTTGAACAACAATTAATAAATGATGTACAATTATGTTTATGTTAGTAAATACATTAACTAATGAAACCTTATTGTAAAGTGTGACCTGATAATCAATGATATATATATATATATATATATATATATATATATATATATATATATATATATATATTGTTATCAGGATATGAGACGTATGTCTTATATTGTGAAATTAGATTATTTTTTTACATCATTGCCCAGCCCTATTTGCATGCACAATAAAATAAATAGTGAAGAAGTGTGTGCTGTTTTGTCTCTGTAG
Seq C2 exon
TTCGGGATCACCATCAGGCTCATAAGTCCTGGCCCTCCACACTGAGTGACACTGACAGTGTTGGTCCTGGAAGTGGACTGGGCTCTCCCACCAACAGCACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000052496:ENSDART00000164461:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
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 Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCAGTTACTTCGTACCCGGAA
R:
CAGTGCTGTTGGTGGGAGAG
Band lengths:
230-1371
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]