BtaINT0073172 @ bosTau6
Intron Retention
Gene
ENSBTAG00000008138 | HOXA2
Description
Bos taurus homeobox A2 (HOXA2), mRNA. [Source:RefSeq mRNA;Acc:NM_001075854]
Coordinates
chr4:69394241-69396203:+
Coord C1 exon
chr4:69394241-69394803
Coord A exon
chr4:69394804-69395438
Coord C2 exon
chr4:69395439-69396203
Length
635 bp
Sequences
Splice sites
5' ss Seq
AAGGTCAGT
5' ss Score
8.68
3' ss Seq
GTTGGTTTCCCTTTCCTCAGAAT
3' ss Score
7.76
Exon sequences
Seq C1 exon
AGTTTAATAGTAGCGCGGTCCCCATACGGCTGTAATCAGTGAATTAGAAAAAAAACACCCCAGCAGCGATCTTCTATGATAGATTTTTTTCCCCCTCTGCGCTCGCCTTTTTCCTGGGCCTTGCCCCCCCAAACCCCTCCAGAAGAGGGAACTTTTTCTCCGAGGGGGCTCCAAGGAGAAGGCCATGAATTACGAATTTGAGCGAGAGATTGGTTTTATCAATAGCCAGCCGTCGCTCGCTGAGTGCCTGACATCTTTTCCCCCTGTCGCTGATACATTTCAAAGTTCATCAATCAAGACCTCGACGCTTTCACACTCGACACTGATTCCTCCTCCTTTTGAGCAGACCATTCCCAGCCTGAACCCGGGCAGTCACCCTCGCCACGGCGCTGGCGGCCGCCCCAAGCCGAGCCCCGCGGGCAGCCGCGGCAGCCCAGTGCCCGCCGGCGCCCTGCAGCCGCCCGAGTACCCCTGGATGAAGGAGAAGAAGGCGGCCAAGAAAACCGTGCTGCCGCCCGCCTCGGCCGCCTCCGCCACCGGCCCTGCCTGCCTCAGCCACAAAG
Seq A exon
GTCAGTCCAAAGACTTGGCCCCAGGTCCTGGGACCCTCTTCCCCTTCTGGGTTGCCCTGAGAGCGGTTATGGGGGAGGGGAGCGTGGGCTGGGAGAGAAGGGGGAGAGGGAGAGATGCTTGGCTGCTTTCCCTTCCCCTGTGGGCTCAGGAGTGGGTTTGATGTGGAGACAAGGGATCCACAATGAGACATATATATATTTTTAAGAAGGGGGTGGGGGAACTTTCCCTAACTTGTGTAATGTGGGATGATTTATTTGAGTTGGAACTGACCTCCTCTTGTCTAGTTGTCCTAGAGTTTGGCTTTTTGACAGTAATGAAGAGTGATAGATCGCTCTTGCTCAGCTAAGCAGCTGATGCATTAATTATAAATTGTGGTGTGGCTAATATAAAGTTTGCTCCCGGATGGAGAGGTTGGGGGGAGCTACAGGCAGGAATCTGATGGAGGTGGAAGAGATGGGGTCTCCCCAGGCTAGGCTCCCAGGAAGGGCAGCACAATAGCTTTACTGCATCCAGGGGCGGCCATTTTGTTGCAGTTGATCTTTTCTGCTATATTTATTCTCCAGTGGAATAACCCCGCTCGGACCCCTCCACCTCCAACTGTGCGTGTGTCTCTTGTTGGTTTCCCTTTCCTCAG
Seq C2 exon
AATCCCTGGAAATCGCCGATGGCAGCGGCGGGGGCTCTCGGCGCCTGAGAACTGCTTACACCAACACGCAGCTTTTAGAGCTGGAAAAAGAATTTCATTTCAACAAGTACCTTTGCAGACCCCGAAGGGTGGAAATTGCAGCGCTGCTGGACTTGACTGAGAGACAAGTGAAAGTGTGGTTTCAGAACCGGAGGATGAAGCACAAGAGGCAGACCCAGTGCAAGGAGAACCAAAACAGCGAAGGAAAATTTAAAAGCCTCGAAGACTCTGAGAAAGTGGACGAGGACGAGGAAGAGAAGTCGCTCTTTGAGCAAGCCCTCAGCGTCTCCGGGGCCCTTCTGGAGAGGGAAGGTTACACTTTTCAGCAAAATGCCCTCTCTCAGCAGCAGGCTTCCAATGGACACAATGGCGACTCCCAAAGTTTCCCAGTTTCGCCTTTAACCAGCAATGAGAAAAATCTGAAACATTTTCAGCACCAGTCACCCACTGTTCCTAACTGCTTGTCAACAATGGGCCAGAACTGTGGCTCTGGCCTAAACAATGACAGTCCCGAGGCCCTCGAGGTCCCCTCTTTGCAGGACTTTAATGTTTTTTCCACAGATTCCTGCCTGCAGCTTTCAGATGCAGTCTCGCCCAGTTTGCCGGGTTCCCTCGACAGTCCAGTAGATATTTCAGCTGACAGCTTTGACTTTTTTACAGACACACTCACCACAATTGACTTGCAGCATCTGAATTACTAAAAACATTAAAGCAAAACAAAGCATC
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000008138:ENSBTAT00000010699:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.732 A=NA C2=0.516
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=23.1)
Main Inclusion Isoform:
NA

Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAGACCATTCCCAGCCTGAAC
R:
CTTCGGGGTCTGCAAAGGTAC
Band lengths:
347-982
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]