BtaINT0073190 @ bosTau6
Intron Retention
Gene
ENSBTAG00000009238 | HOXC6
Description
homeobox C6 [Source:HGNC Symbol;Acc:HGNC:5128]
Coordinates
chr5:26161892-26163475:-
Coord C1 exon
chr5:26163061-26163475
Coord A exon
chr5:26162337-26163060
Coord C2 exon
chr5:26161892-26162336
Length
724 bp
Sequences
Splice sites
5' ss Seq
GTGGTGAGT
5' ss Score
8.95
3' ss Seq
TTTTGTGCCCGGATCTCTAGGGG
3' ss Score
6.81
Exon sequences
Seq C1 exon
GGTAAAGGCAAAGGGATGAATTCCTACTTCACTAACCCTTCCTTATCCTGCCACCTCGCCGGGGGCCAGGACGTCCTCCCCAACGTCGCCCTCAATTCCACCGCTTATGATCCAGTGAGGCATTTCTCGACCTATGGAGCGGCCGTGGCTCAGAACCGGATCTACTCGACTCCCTTTTATTCGCCACAGGAGAATGTCGTGTTCAGTTCCAGCCGAGGGCCGTATGACTATGGATCTAATTCCTTTTACCAGGAGAAAGACATGCTCTCAAACTGCAGACAAAACACCTTAGGACATAACACACAGACCTCAATCGCTCAGGATTTTAGTTCTGAGCAGGGCAGGACTGCGCCCCAGGACCAGAAAGCCAGTATCCAGATTTACCCCTGGATGCAGCGAATGAATTCGCACAGTG
Seq A exon
GTGAGTTTTACAGCTCCGAGATATAAATTAAATAAACTGAACTGGCTTTATGACCGGCTTCCCTAGAAGAACGGGCGGAGAGAGTTTTTTATGGCCCCATAAAAACAATCACGCTCGTCTCCTCGCCGACGCCGAGACAGGGCCCCCTCTTCTGCCCCCTCTGCTCGCCTCCTGCTTGCTTGCAGGGGCCTGGCCCCCTCGGCCCCTGACGGATTGGAGGGCTCTAAGGCGAGTTGAGGGGGCAGGAACAGGGCAGGGGATGAGGGGAGGGGGTGGGGGAGCCCCCAAAGTCGAGTCAGACTGAGGAGAAGGGAGTGGGGGGAGAATGGGACAGAGAAGTGGGGAGAAGTTTCCCAGGGGCTAGGGCGCTTGGGGAGATGGGGGAGCCCAGACCTTGAGAAATGGGGCCTCATCCCCAGTGTTTTGAGATTTTTCTGAAAAATCAGCTTTTAGTTTACAGCTTCCTGCTTGGTTCTGTCCCCCCACCCCCCACACACCTTTCTTTGGGACACACCTACCAACCGGGGAGGGGGGGGGACTGAATGAGTTTAGGATCCTGGCTGTACCCCCAGTGGGGGTGGGGACAGCAGAGGGGAGAAGGCTGGAGCCGGAGGGGCCCGTGAGTGCTGGCCAAGTTGGGAGGGTCAGGGCTGTGCTAGGCTAGATCATCTGCAGAGGATGCCTTGCTGATTGTTTGTAGTGTGTTTTGTGCCCGGATCTCTAG
Seq C2 exon
GGGTCGGCTATGGAGCGGACCGGAGGCGCGGTCGCCAGATCTACTCGAGGTACCAGACGCTGGAACTGGAGAAGGAATTTCACTTCAACCGCTACCTAACGCGGCGCCGGCGCATCGAGATCGCCAACGCGCTCTGCCTGACCGAGCGACAGATCAAAATCTGGTTCCAGAACCGCCGGATGAAGTGGAAAAAAGAGTCTAATCTCACGTCCACGCTCTCAGGGGGCGGCGGAGGGGCCGCGGCTGACAGCCTGGGCGGAAAAGAGGAAAAGCGGGAAGAGACAGAAGAGGAGAAGCAGAAAGAGTGACCAGGACTGTCCCTGCCACCCCTCTTTCTCCTGCTCCCTCGCTCCCCCCAATACCCTCCTAATCACACACTCTATATTTATCACTGGCACAATTGATGTGTTTGGACTCCCTGAGACAAAATTAGGGAGTCAAATAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000009238:ENSBTAT00000012174:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.164 A=NA C2=0.422
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=55.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Chicken
(galGal4)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCAGTGAGGCATTTCTCGACC
R:
ACCTCGAGTAGATCTGGCGAC
Band lengths:
355-1079
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]