BtaINT0073169 @ bosTau6
Intron Retention
Gene
ENSBTAG00000040082 | HOXA10
Description
homeobox protein Hox-A10 [Source:RefSeq peptide;Acc:NP_001098487]
Coordinates
chr4:69323238-69326738:+
Coord C1 exon
chr4:69323238-69323997
Coord A exon
chr4:69323998-69325208
Coord C2 exon
chr4:69325209-69326738
Length
1211 bp
Sequences
Splice sites
5' ss Seq
TGGGTAAGC
5' ss Score
8.84
3' ss Seq
TTTATTCTCTCAAATGCCAGGCA
3' ss Score
5.61
Exon sequences
Seq C1 exon
GCCGACCTGCCCTATGGGCTGCAGAGCTGCGGGATCTTCCCGGCTCTGGGAGGCAAGCGCAATGAGGCGGCGTCGCCGGGCGGCGGTGGTGGCAGCGGGGGCCTGGGTCCCGGGGCGCACGGCTACGTGCCGGCGCCTATAGACCTGTGGCTGGAAGCGCCCCGGTCGTGCCGTATGGAGCAGCCCGAAGGGCCGCCGCCGCCTCAGCAGCCCCAGCCGCCGCCCCCACCGCAACCACCCCAGCCCCCGCCACAGGCCACCTCGTGCTCTTTCGCGCAGAACATCAAAGAGGAGAGCTCCTACTGCCTCTACGACTCGGCTGACAAATGCCCCAAAGGCTCGTCCGCCGCTGCCGAGCTGGCCCCCTTCCCGCGGGGCCCGCCGCCCGACGGCTGCACCCTGGGTACCTCCAGCGGGGTGCCAGTGCCCGGCTACTTCCGTCTCTCTCAGGCCTATGGCACCACCAAGGGCTACGGCGGCGGCGGTGGCGGCGCGCCGCAGCTCGGCGCCGGCCCGTTCCCGGCTCAGCCCCCGGGGCGCGGCTTCGACCCGCCACCCGCGCTCGCCTCCAGTTCGGTGGATGCAGCCCGGAAGGAGCGAGCCCTCGATTCGCCGCCGCCCCCCACGCTGGCTTGCGGTGGCGGCGGCGGCGGGGGCTCGCAGGGCGACGAGGAGGCGCACGCGTCGTCCTCGGCCGCGGAGGAGCTCTCCCCGGCCCCTTCCGAGAGCAGCAAAGCCTCGCCCGAGAAGGACTCCCTGG
Seq A exon
GTAAGCAGGGCGCGCTGAAGGGCTCCGCAATCAGGCGGGCTGGCAGACAGGCAGACCCAGAGAAGGGAAGGAGCAGAGAGCCAGGAGTCCGCACAGCAGCCGGCCGGCCTTGGCCCGAGCTGCAGGCAGGCTGACCTTGTGAACTTGCTTTTTTAATATTTGGGCGTGGGGACTCAGTAAAAAAATTCATGTCCCGGCTTAGCGCCCCACACCGCGACGTTCTCTGCTCTCGCCTCCCCTCACTCCGACTGGAGCCGAGGACACCGGCGAGCAACTCCCCTCTTGTGCATGCCCTTCTCCGTGCCCCAGAGCACCCAAAACCGAGTCTGGGCCCAGCCTGCGAGGCGCGGCCCACGCGGGGGGGAGGGGGAGGGAGGGAAAGTGGCTCGCCCGCAGATAGCGCGGATGTTTGTAAGGCATCCAAAATAAGCAGCCGCCAGCACCAATAAATAAGCCCATTAACCGGCGAAGTTCGAGTTTACGATCCCCCTTGCTTTTTTCAAACTTGCTTGAGGGGCGGGAATCCTCGTTGCGGGGAGAAGAAAAGGCAGATCCGTCCCGGACGCCTGGGCCCTGATCTGAGAGTCAGAGAGGGGTCATTTCGCTTCCCCTGGAACTCGAAACCGCCCAGACTGCACGTCCCTGGCTCCTCGAGAGACGTGAGGGAGGGCCCTTGACCCCAATCAGTTTTTTGTGCCTTTTCTAGCTCCCAGCTATGCCCTTCTCCCTCTCCTCAACAGGCCTTGGGTAACCACGGGGCTGGAGTGAGACACAGCCACGTTGCCTACCCCCCCCCCCCCACTTCCAAGTGAGCACCCCTGTCCTCCCAGCCTGGGGGTTGCAGGAAATGCTTGTCTGCCTTGGGGCGAGAGGCAAAAAAAAGGCGTTAAGTTCAAGATATACAGCCTGCCCTCCCAGTCCGTTCCTTCTGCAAGCGCATGGCAGCTTTGTGCTAAAACAGGTGTTTAGGGGGAAAAGTGGAGGAAAATGTAAGAGAGTAGGTGTAGATAGGAGGCCCACTCGATTTTACACATAACTTTTGGAGGAACTGCTCTCCCTGGGCAAACTAAAAGGGGCGGAGGGCGGAGGGATAACTCTCTCTGGGTGACTTAGGGCATCCCTCATACTGTAGAAACGACCCGAATTCCCCTCTGCGTGCAGCCCGCATGGCCTCGATTTAACCTTCCCCTCTTTATTCTCTCAAATGCCAG
Seq C2 exon
GCAATTCCAAAGGCGAAAACGCAGCCAACTGGCTCACTGCAAAGAGCGGCCGGAAGAAGCGCTGCCCCTACACCAAGCACCAGACGCTGGAGCTGGAGAAGGAGTTTCTGTTCAACATGTACCTTACTCGAGAGCGGCGCCTAGAGATCAGCCGCAGCGTCCACCTCACGGACAGACAAGTTAAAATCTGGTTTCAGAACCGCAGGATGAAACTGAAGAAAATGAACCGAGAAAACCGGATCCGGGAGCTCACAGCCAACTTTAATTTTTCCTGATGAAGCTCCAGGCAATGTGGTTCATTTCGTCCAGAGAACCGTTCTCCTCCCTCTTGTCTTCGGCTCTGCCCAGGAACTCGCACCTGTGCGGGAGCCCCCCCATTCTTCCCTCCCACACTCGCCATCTCGCTGGCCGTTACATCTGTGCAGGGCTGGTTTGTTCTGACTTTTTGTTTCTTTGTCTGTTTGCTTGGTGCTGGTTTATTTGTTGTTTTCTGGGGGAAAAAGCCATATCGCGCTAAAATTCTATAGAGAATGCTGTCCTAAGTGTCAAGTGGTGACTGGGATGGTTTGCTGTCTCGGGGTTCCACTGCTTGAAATGGCCTCTGTCCTCCGGGTGCAGCTGGTTTCCTGCGGGGCCAGCAACCTAGCCGGAAGGCGGAGGTCCCATTGTAGGCAGCTGAGGTGTCTGGCCTGAGGTCAATGGTGCAAGGAGCCGCCACCGGGCTTGCCTGCCTGGAGTGCAGGGCTGTCTTTAATCAGGGGGCACAGGCCCCTGGGTTTCTTTTCTCTTTTTTTCCTTGGCAAAGAGAAGGGCTTGCAGAAATGTACATGCAGGTTGGCAAAAGGGTTGACTTTGGCTGATTGGTAAAATTGAGAAAATCAGAAAGATTCATTTTTCCTTCCCCTGTAAGATAGCTCAGCTTTAAAAGAAGAAGAAATGACCAGGAGAAGGAAACGTCTCTTCCAGTTTGTGTAAGGTCTTGCATTGTGGGACTAAATTATTTCAGTTACTTTGAATTTCCATGTCCTTCTGGCTGTAGATAAATAATAGAATGTAGTTTTGTTTATACATGCAGGTTTAGTGCATTTTTTGTCATTAAATAATTGTTACCACTGGTAACATAAGACAAGCACACCACAATTCTCCCTAGTCTGCAGAGGTTCCCCCCCTTTCCCCCCCTTTTCTTTCCAAAATTCACAGAAGCCGAGGAGGGCTGGAGCAAGCGGAATAGACTAGAGAAGGGAGACATTGCTGGGTTTCCTTTATACTGTGAAGTTACATGCATAAAAGGGTCAAACCTGTAGGTGCAGAAAAAGAAAAAACTATAAAATACAAATCTGTATAAATGTCTATTATTATGAAAAATTGCCAATCTTGTTTTATGCAAATGCATTCTATCATTATTATAAATGTTAGTTCTAGTTCTATTTACTTCTAATCTTAAATCAGAATAAATTAATATTGTAATGCTGCTGTGCGTGGAAAAAAAAGATGTTTATGTTCTTATAGAAGAATAAAAGCTGTGGAATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000040082:ENSBTAT00000063132:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.841 A=NA C2=0.363
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=62.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCCTTCCGAGAGCAGCAAAG
R:
GAACCACATTGCCTGGAGCTT
Band lengths:
342-1553
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]