BtaINT0073191 @ bosTau6
Intron Retention
Gene
ENSBTAG00000012149 | HOXC8
Description
homeobox C8 [Source:HGNC Symbol;Acc:HGNC:5129]
Coordinates
chr5:26180271-26182515:-
Coord C1 exon
chr5:26182080-26182515
Coord A exon
chr5:26180686-26182079
Coord C2 exon
chr5:26180271-26180685
Length
1394 bp
Sequences
Splice sites
5' ss Seq
ACGGTGAGA
5' ss Score
8.94
3' ss Seq
TGGGCTTCTGTTCTGTCCAGCTC
3' ss Score
6.94
Exon sequences
Seq C1 exon
ATGAGCTCCTACTTCGTCAACCCCCTGTTCTCCAAGTACAAAGGCGGCGAGTCCCTGGAGCCGGCATATTACGACTGCCGCTTCCCGCAGAGCGTGGGCCGGAGCCATGCGCTGGTGTACGGGCCCGGCGGCTCGGCGCCCGGCTTCCAGCACGCCTCGCACCACGTCCAAGACTTCTTCCACCACGGCACCTCGGGCATCTCCAACTCGGGCTACCAGCAGAACCCGTGCTCGCTGAGCTGCCACGGAGACGCCTCCAAATTCTATGGCTACGAGGCGCTCCCCAGACAGTCCCTTTATGGGGCTCAGCAAGAGGCGAGCGTGGTGCAATATCCCGACTGTAAATCCTCCGCCAACACTAACAGTAGCGAAGGACAAGGCCACTTAAATCAAAACTCGTCTCCCAGCCTCATGTTTCCATGGATGAGACCCCACG
Seq A exon
GTGAGAAGCCTTTTCTCTTTCCCCCTTAGTCTCCCGCGCTCCGGGGTCTTCCCCCCTCCCTCGCCTCCTTTTTGTCTGCCCTCGCTCTCCCTCCTGGCTTGGGGCTCTCTCGGGCCCCACCCCCGGGCCTGAGTGGGTTTCTGGAGGTTGGGAGGTTCAGCTGGGGGTGGGGCACCGGGTTTGTCTGGGAGATTTGGGGGATTGGGGTAAAAGTGGGGGAAAAGGTGGTATCTGGGTGCAAAGGGTTAAAAAAACGTTTTCTCCACCTCTGTCAGTCAGTCTGTCTCTCTCTCTCCCCTCCTCTTTCTCTGTCTGTCTCTTTCTCTCACCGTCTCTAGTCAAAGTTGGGGAGGTGGCTGGGAAGGAGCGGGGGACCCAGTGGTTATCAGCCTTTGGAACAAGCCAGTGTCTCCATAAGGCAGAGAGCCCCAGTCCAGGACAGTGGCCAGGCTGTCTTGGGATGAAGACCCCTGCTTCCCTCCCCTGGCTGGGTCAGGGGGTGGCAGGACCCCAAGGACAGGTGATCTGCCTCTCTGGGGTACCCACCACCTCCTCTCAGAGAACTAGCCTTAGGGCCACTACCCCAACTTTGCTCTACTTCCCTCAGTTGGAGAGAAGAGAGGGAGTCAGAGAGAAGGGGAAAAAAAAAAAAAGAGTCCTGAAAAGGAGGGAGGCCATGTAGGTTAGAGGGCTCTGACGTCCAGAAGACCCTGGGGGAAGCCAAGCTGCCCCCCATCAAAGGCTTGTGGGGTCTTCCTGAGACCCTCAGGGCAGCTCAGGTCATGAGCCCCTCCAAGGGTGGCCCCTCATCGCCCAATTTCGAAGTAAAAGGGGAAGCTAGAAAGCGACAAGTTCCAGCAAGGATGGCCCGTGATTTATTTGCTGATCTCTAGTTAGCAATCAGGCCAAGCAGTGATACATTCCAGGAGATCAATTATTTTTCCTCCTTGCAAGGCATAAGGCAGAGAGATCTGAAGAGGGGCAGTGAGCAGAGCCTCACTTCTTCACCCCCAGCCCTTTTGCCTTCCTTTTGGAAAGAGACTCTGTCCCCAGCCCTTCTCACCCAATGCCCCTCTGCACTTGTAAACAAAGCTGCAGGGCCAGTTTCCTGGAACTGCAGGCCTGGGGGGACTCTGCAGTGCTCCCTTGGCCTCTTCCAGCCCCGGCTTTCCAGACAGATCCTAGTCCCTGCCCCCACCCCTACCCTACCTCCCAAGGTGAAGCTAAACCAAAACAAACCCCCCAAACTTTCCTGCCCTTGCCTGCTCTGCCTTTTATGCAGGAGGGAGGGGAACTGGGGAAACCAGAGGGGGGGATTTCAGGGGAGGAAGAGTGACAGGGGAAAGCCAAGCCCCTACCCAAACATAACCAGACTGGGCTTCTGTTCTGTCCAG
Seq C2 exon
CTCCGGGGCGGCGCAGCGGAAGGCAAACTTACAGCCGGTATCAGACCTTGGAACTAGAAAAGGAGTTTCTCTTTAATCCTTATTTGACACGAAAGCGTCGGATTGAAGTCTCTCATGCCCTGGGACTGACTGAGAGACAAGTGAAGATCTGGTTCCAGAACCGAAGGATGAAGTGGAAAAAGGAGAACAACAAGGATAAACTGCCCGGAGCCCGAGATGAGGAGAAGGTGGAGGAAGAAGGAAACGAGGAAGAGGAGAAAGAAGAGGAGGAAAAGGAAGAAAACAAGGACTGAGCAAAAAAAGAGAGACATCCCCCCCCTCCTTTAGCAACTCCCTTGAAGTTTCATTTTATGGTAGCAGATAAATTGAGAAGTTTACGACTGTCATTTGCTTTTATAGAGAATAGAATGACACT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000012149:ENSBTAT00000016117:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.253 A=NA C2=0.526
Domain overlap (PFAM):
C1:
PF095335=DUF2380=PU(74.1=56.8)
A:
NA
C2:
PF095335=DUF2380=PD(25.0=28.6),PF0004624=Homeobox=WD(100=58.2)
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:
CGTGGTGCAATATCCCGACTG
R:
TCCACCTTCTCCTCATCTCGG
Band lengths:
348-1742
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]