BtaINT0073176 @ bosTau6
Intron Retention
Gene
ENSBTAG00000001455 | HOXA7
Description
homeobox A7 [Source:HGNC Symbol;Acc:HGNC:5108]
Coordinates
chr4:69340738-69342484:+
Coord C1 exon
chr4:69340738-69341116
Coord A exon
chr4:69341117-69342084
Coord C2 exon
chr4:69342085-69342484
Length
968 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGC
5' ss Score
9.88
3' ss Seq
GTCCATGTGTCTGCTCGCAGGGC
3' ss Score
9.36
Exon sequences
Seq C1 exon
ATGAGTTCTTCGTATTATGTGAACGCGCTTTTTAGCAAATATACGGCGGGGGCTTCTCTGTTCCAAAATGCCGAGCCGACTTCTTGCTCCTTTGCGCCCAACTCGCAGAGAAGCGGCTATGGGGCGGCCGCCGGCGCCTTCCCTTCGACTGTACCGGGCTTGTACAATGTCAACAGCCCCCTCTATCAGAACCCCTTCGCGTCTGGCTACGGCCTGGGTGCCGACGCCTACGGCAACCTGCCCTGTGCCTCTTACGACCAAAACATCCCGGGGCTCTGCAGTGACCTCGCCAAAGGCGCCTGCGACAAGGCAGACGAAGGCGCGCTGCACGGCTCGGCCGAGGCCAATTTCCGCATTTACCCCTGGATGCGGTCTTCAG
Seq A exon
GTAGGCGCAGCCGCTAGGCGGGCCGGGTGGGCGGGCGGACTGGGAGCTGGGAGCGCCGGGCTGGGGGAGCGGAGCGCGGAACGAGGCGGCTGCGAGCCGGCGGCCCCTTGACTCCTGGCGGCGCTGCCTTTCTGGTTTTAATTAGAGCCGAGGCGCCATAGCAAGGAGAGCTCCTAGCATTGTATGTAAATGAGGCTCATAAAACTTTTTATGGCCCAATTAATGGGTTCGATCCTCGTAAATTTATTTAACTCTATTTGCCTTGGAATCTCAACATTAAGTTGGTTTGTTCGCTATTCTCGTATTCTCTTTCTCCCTCCCTTTCTTCTCTCTCCCTCCTCCTTTTCCTTTCAGCCTGGCTTTTCTTCTCAAAAGCAGGGAGAGCCAAACGCTTTTGGGTCCCTTATGCGCCCCTGTGCCAGGGGCCATTTAAAGGCAGGGAGGGACGGATGGGTGGGAGTGGAGACAGAGAGCCCAGTGCCCTAGGAAGGTCTGGGGATGGGGGCGCGGGCTGCTGGGGAGGAAAGGCGCCCTTGGAGTGAGGGCCGCCGGAGAGGGTCTCCCACTTGCCTAGCTAGGCGGGGAAGCGGCTGGCTCGCCTTTGAATGGCAAAAGCGCAGCGTCTCCCACTTGCCCACACTCTATATTTACAATTTGCCTTTGTCAGGGGGAAGCAGGACATTGTGGAAGCCTAGCCGGCTGGAAAGAGCAGTTGTAAAGTTGGGATTCTGCGCCTTCCCCCCTCACAGAGCTGCCTGCGCGTCTGGCACCGCAGTCGGTGTCTTCCGCTAACACTCCCGCTCCTCCCCCAGCTCAGGTTGGGGGCGCAGGGCGGAGGGGGACTCGGACCTGGGTCAGGGCCCGGATTGAGGTGCGCGCTTCTGAATGGCAGCCGGGTTGATGCCCTGGCCTGTGTCCCTGTCGGCTTGTCTGTCCGTGTGTCCATGTGTCCATGTGTCTGCTCGCAG
Seq C2 exon
GGCCGGACCGAAAGCGGGGCCGCCAGACCTACACGCGCTACCAGACGCTGGAGCTGGAGAAGGAGTTCCACTTCAACCGCTACCTGACGCGGCGCCGCCGCATCGAGATCGCCCATGCGCTCTGCCTCACCGAGCGCCAGATCAAGATCTGGTTCCAGAACCGCCGCATGAAGTGGAAGAAAGAACATAAGGAGGAGAGTCCGGCCGCTTCCGGCGCCCCCGAGGGTGCCGCGCCCGCCGCCTCTGCAGCCGCCGCCGCCGCCGCTGCCGCGGACAAGGCCGACGACGAGGACGACGACGAGGAGGACGAGGACGACGACGAGGAGGAGGAGGAATGAGGCCCGGCTGCCCCAGACAGTTTGGAAAGCGTCTTTAGAGACTGATTTTATTTACAAAAGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000001455:ENSBTAT00000001908:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.536
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=50.4),PF0306610=Nucleoplasmin=WD(100=64.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACAGCCCCCTCTATCAGAACC
R:
CAGATCTTGATCTGGCGCTCG
Band lengths:
358-1326
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]