BtaINT0072780 @ bosTau6
Intron Retention
Gene
ENSBTAG00000020772 | HMHA1
Description
histocompatibility (minor) HA-1 [Source:HGNC Symbol;Acc:HGNC:17102]
Coordinates
chr7:45182657-45185085:+
Coord C1 exon
chr7:45182657-45182794
Coord A exon
chr7:45182795-45184754
Coord C2 exon
chr7:45184755-45185085
Length
1960 bp
Sequences
Splice sites
5' ss Seq
GAGGTCAGT
5' ss Score
7.7
3' ss Seq
AGCTCCCCCTACCCTCCCAGGAG
3' ss Score
6.79
Exon sequences
Seq C1 exon
ATGAGTGGTGGGCAGAGGATCCTCAAGGGCCTTCTGGGATGGGTTAGTGGATGGACCCGGGCCTGGAGAACTGGGTTTGCCGTGAGGGGCTGTGGCCTGCGTGCCCTGTGCCCGGGAGATCCACCCCTCCCACCTGAG
Seq A exon
GTCAGTGGGGGCCAATAGTGGGGAAGGTGTAGGGGATGAGAGGGTGAGACTCCAGAAGGGGAGGGGAGGAAGACTGGGGGAGGGGAAAAGGCTCAGATTAGGGGGGTTCCAAGAGAAGAGGTGGTTATGGGGGAGAGGGTACAGGGAGTGCTATACACATTGCCAACACCCCAGGTCTGGGGGCCAAGCCAGGGAGGGAGGAGGTGGCATGGTGGCCTCAGCAGTTAGCGTTAGGGTTAACCTGTTCTGCTGAGTGTCCCCAGAATGTAGAATCAGGGGTGGGGGTGGGAGATGGATGGAGGGAAGGCAACCCACTATACCATGCACTGTTCCCTGGGGTCTTCACGGGGAGTTGCCAAAGGGTGGAAGGCGGCCACACAGAGGAGCGGTGGGAGGACTGGAAGGCAGGTGCCTGTGTCCAGGGTACCCATTGCATCAGTGGAGCTGGGTGGCTTCTGAGCATATGTCAAAGTCTGTGTCCCCACATGTCCGTCGTGTTCAGGTATCTGCACTCTTGGGTGCATCTGGGTGTGGCTGAGTGGGGGTGAGCATCTCTGCAATCGCTGTGTCCCTGCAGGGATCGTGCCTGGGGCATCAGTGTCTTGCCTGGGGCATTGCCGCCAGGCAGGGCACCTCAGCAAACATGCACACGCAGAGCTCAGGAAAGCGGAAGCTGGGGGTGGGGCCTGGGACCCCACCTTTGAGCCCACTGTGCAGAGGGGCAGGCTGAGGCTGAAGCTGGGGAGGGTCAGGGGCGGGTCTGAGTCACCGCCTCCGGAGGCCTTTTCCTGTGGGGGGAAGCGCCCGCCAATGAGGGCTGTGCCTGTCACGTGAGCCTGACAGCTGAGGAGGGGGTGGCCAGCGGCAATGTGGTCCCGAGGCCACCAACACCAGGAGCTGTGGTACTGAGACCCCTGGCCTACCTCCCCCAGCCAGGCCCCCTTGGGCTTCTCGGGCCTGGCCCCGCCATGTTCTCCAGGAAGAAGAGAGAGCTCATGAAAACCCCGTCTATCTCGAAAAAGAACAGGGCGGGAAGCCCCTGCCCACAGCCCTCGGGGGTGAGTGAGCCTCTAAGGGGAGCACGGGGCGGGCGGGGACCTTAGAGCGACAGCTGGGCAGCACCAGGGCAGGAGGACACCCTGTGATCAGGCCCAGCAGGGCAGGGCCGGGCAGTGACATGCTGGGCCAGTGGCGGGGGGTACGAGCCAGCTACAGCCCCCACCAGGCTGGACTGCAGGGGCTTCGCAGGATGGGCTGGGATCCTCGCATTCAGCTTACGGTAGGAGCCCTTGGGACGGCCATGCACCCTCCCACCCTGTCCAGTGCCGGCTGTGGGGTCCAGGAGTGGTGGGGTGGGTACCAGGGTATGGGTACATTGGGCCTGGACTCCTTCAGGTGGGGGCTCAGGGAATTTGGGGTCTCCAGGCACCGTTAGATGTGAGAGCTATAGCCAGGCTGTTAGGCAGAAGGTTTATAAGGGAGCAGACTGTGGAAGGAGACCCACGGGGGCAGGCCTGGTGCAAGCCTGGGGGCATCTACAGGGCCTGCGGTGTCTGTGGGCTCAGGAGTCTGCTGGACCCTCAGAGGACAGGAACTGAGGAGGTGTCTACCAATGAGTAGGCATCTGCAGTGGCCTCTACTGAGACAGCTCAGGAGACCCCAGCCCTACCCCTCTCCCTTCCCCCTTACCCCCCTCCCTTCCTTACCTCCGGAAGTGGGGCGCCCCTCCCCCACCCCGGCTGTGGTTTGGGCAGAGACGTTGTTTGTGAAAGCTCCAGGAGAGGACGTTGGGTAACAGGTGTGGGAGGGGCCCAACACCAAATCTCAGCCCTCTGACCTGTGGCCTCTGACCCCTATGGGGTCAGGCTGAAGACCCTCCAGAGCCCCACTTCACTTCCAGGGAAACTGAGGCAGGGCCCAATGGGAGCACCTGCTTTACCAGCTCCCCCTACCCTCCCAG
Seq C2 exon
GAGCTGCCTAGGAGAGACGGGGCTGATGCAGTGTCCCTGGGGCCCAGCCTAGAACCCCCAAGTGTGGCCTCGAATGCTAAGGCCACAGGCACTCTCAAGAGGCCAACCAGCCTGAGCCGCCATGCCAGCGCTGCTGGCTTCCCTCTGTCGGGGGCCAGCACTTGGACGCTGGGCCGCAGCCATCGCAGCCCACTGTCTGCGGCCAGCCCGGCCGAGGCACCCATCCAGGGACCCTGCCCAGACACCGTGGAGGACATCTCCCACCTGCTGGCTGACGTGGCCCGCTTTGCCGAGGGTCTTGAGAAACTGAAGGAGTGTGTTCTGCATGATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000020772:ENSBTAT00000027682:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.196 A=NA C2=0.523
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGAACTGGGTTTGCCGTGAG
R:
AGCAGGTGGGAGATGTCCTC
Band lengths:
342-2302
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]