BtaINT0073186 @ bosTau6
Intron Retention
Gene
ENSBTAG00000006879 | HOXC11
Description
Bos taurus homeobox C11 (HOXC11), mRNA. [Source:RefSeq mRNA;Acc:NM_001192873]
Coordinates
chr5:26215737-26218209:-
Coord C1 exon
chr5:26217426-26218209
Coord A exon
chr5:26216152-26217425
Coord C2 exon
chr5:26215737-26216151
Length
1274 bp
Sequences
Splice sites
5' ss Seq
CCAGTAGGT
5' ss Score
5.41
3' ss Seq
CCCCCTCCCCTCCCCTCCAGACG
3' ss Score
11.73
Exon sequences
Seq C1 exon
GAGAGAGACTAAGACGGATAACGCGTCATCTCGCCTTCCCAAATTTTACCCCCTCGCTAGACCTGGTCCAAAACCTCCATCTGGAGCCGGCAGAAGAGAACGATGTTTAACTCGGTCAACCTGGGCAACTTCTGCTCGCCGTCGCGCAAGGAGAGGGGCGCCGATTTCGGCGAGCGAGGGAGCTGCGCTTCCAACCTCTATCTGCCCAGTTGCACTTACTACGTGCCTGAGTTCTCCACGGTCTCCTCCTTCCTGCCCCAGGCCCCCTCTCGTCAGATCTCCTATCCCTACCCGGCCCAAGTGCCCCCGGTCCGAGAGGTCTCCTACGGCCTGGAGCCCTCCGGCAAGTGGCACCCCCGGAACAGCTACTCCTCCTGCTATGCGGCGGCCGACGAGCTCATGCACCGGGAGTGCCTGCCTCCTTCCACCGTCACCGAGATCCTCATGAAAAACGAAGGCTCCTACGGCGGCCACCACCACCCCAGCGCCCCGCACGCCGCCCCCGCCGGCTTCTACTCCTCAGTCAACAAGAACAGTGTCCTGCCCCAAGCCTTTGACCGCTTCTTCGACAACGCCTACTGCGGCGGCGGCGACCCCCCCGCCGAGCCCCCCTGCCCGGGCAAGGGTGAGGCCAAAGGGGAGCCTGAGGCGCCCCCAGCCTCGGGACTGGCGTCCCGGGCTGAGGCGGGGGCCGAGGCCGAGGCCGAAGAGGAGAACACGAATCCCAGCTCGTCCGGTTCAGCCCACTCGGCGGCCAAGGAGCCGGCCAAGGGAGCCGCCCCCA
Seq A exon
GTAGGTAGCAGCGGCCGGGAAGCAGGCGGGCAGGAGGGAGGGAGCTAGAGAGGGAGGGCGAGCGAGGGTAGGGGGGAGGCGAGGGGAGCGGGGACGGCCTCGTGTTTTGGGTCAGTCCAATTTTATGTGGAGTTTTATAAGCATTCAAAGGATTTTATTATAACCTACAAAGCCCTCTCTCCCAACGACTCGACTTTTTACGATGGAGAAGGGGTGGGGAGGGAGGGAAAAGGGCTCTTTGGAAAAGCCGGGTGAACCCCCCTCTCCGTTATCTCCTTCGGTCTGTGAAATTTTTAAAAGCGCCACCATCGCGGGCAATATTAACTTTGATCGTGAACTTAGAGGAGCATTTAAGGAAGGATGGGGAGCCCCGCGGCCGGGGTTGGGGGTGGGAGGGAGGGGAGGGGTGGAGGGGGAGAAAGGGGAGGGCAAGGGAAAGACAGGGAGAAACTCCGAGAGGGGGAGTGGTGGAAGAGAGAGGCATTGGAGCAGAGCTGGAGCCCGGGGAGTCCAGCCAGGGCCGCTCTGCTTCTTTTAAAAAAACTATTTTTTGAAATGTTCAAACTCTGTGTTGGCGGGTCCCTGAGCAGGGCTCGGAGCGACCCGAGGGTCAGCGGCGACAGGGGGTGGGGGCGAGGCGGGCTCAGGGCTCCCCTCTGCTCCAGGCCTGGGGCTTGGCGTTTCCCTGCGGCCCGCGGCCTCCGCGCCGGCCTGCCCAGGCCGCGGGGAAGGAGCGGCCCGCCGGGCGTCCCGGGGCGCCAGGGCCCCCGGAAGCGGCTGTCGGGTGTCTCTGGTGCCTGCTCTCTTGCTTCCTCCCCGCATCCCAGTGACTCTCGCCGGATCGCACTTCTTTGCGCCTGTTCTCCGCGGTCCCCCCACATTTCTGGGGGTGGGGAGTGGGGGTGGGTTTTTAGAGCCACCCGGAGGGCAGAGGTGCGCGGCTGAGCGGGCGGGGGGCCTTGGGGACGCACTTGGCCGCGGCTGGCGCGCATCTCCCGAAGACCCCGCCACAGCCACGGCCCTCGCCGGAGGGGAGGGGGCACGGGCCCCCGCGGTGGCCCGGGACGTGGGACGCGCTTGCCGCCCAGGCTGGGGGTCGCGGCTCGGCCCAGCGCCGCGCTTGCGGGAGGAGACCCGGCCGGCCTGGTGGGAGGGCTGCCCGGCGGTGGGGCCGGCAGAGGGGCCCGCCGAGCGCTCCGGGGGGCTGGGGTCGCCAGGGTCTCACGTGTCTCTCTCCCCCTCTCCTCGCACTTGCCCCCTCCCCTCCCCTCCAG
Seq C2 exon
ACGCCCCCCGCACCCGCAAGAAGCGCTGCCCTTATTCGAAATTCCAGATCCGGGAACTGGAGCGAGAGTTTTTCTTCAACGTGTATATCAACAAAGAGAAGCGGCTGCAGCTGTCTCGGATGCTGAACCTGACGGACCGACAAGTGAAAATTTGGTTTCAGAACAGAAGGATGAAAGAAAAAAAACTAAGCAGAGACCGGCTGCAGTATTTCTCGGGAAATCCTCTGCTGTAACCGCAGACTGGGCCCTTTTGAGGGGAGGGGGGAAAGGGGAAAATTATTTTATTTTATTTTTATTTTTTATTTTCTAACTCGCCTACTTTCCGCGGGTGGAAAACTGGACTGTGGCCAGGGCTGGCCCCCACTGCCGTTTCCCGCACGTCTTTCTGGACAACCTCCTTCACCTTGGTCTGACT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000006879:ENSBTAT00000009028:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.408 A=NA C2=0.195
Domain overlap (PFAM):
C1:
PF120453=DUF3528=WD(100=62.7)
A:
NA
C2:
PF0004624=Homeobox=WD(100=73.1)
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:
TTCTTCGACAACGCCTACTGC
R:
TCAGGTTCAGCATCCGAGACA
Band lengths:
355-1629
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]