BtaINT0073196 @ bosTau6
Intron Retention
Gene
ENSBTAG00000004314 | HOXD12
Description
Bos taurus homeobox D12 (HOXD12), mRNA. [Source:RefSeq mRNA;Acc:NM_001205871]
Coordinates
chr2:20848044-20849010:-
Coord C1 exon
chr2:20848434-20849010
Coord A exon
chr2:20848283-20848433
Coord C2 exon
chr2:20848044-20848282
Length
151 bp
Sequences
Splice sites
5' ss Seq
ACGGTAAAG
5' ss Score
7
3' ss Seq
GGGTTGGGGCTGTGTTGCAGGCC
3' ss Score
5.25
Exon sequences
Seq C1 exon
TTGGAGATGTGTGAGCGCAGTCTCTACAGAGCGGGCTATGTGGGCTCGCTTCTGAATCTGCAGTCGCCCGACTCCTTCTACTTTTCCAACCTGCGGCCGAATGGCGGCCAGTTGGCCGCACTTCCCCCTATCTCGTACCCACGCGGCGCGCTGCCCTGGGCCACCACGCCCGCCTCCTGCGCCCCAGCGCAGCCTGCTGGTGCCACCGCCTTCGGCAGCTTTCCCCAGCCCTACCTGGCTGGCTCTGGGCCTCTCGGCCTGCAGCCCCTGGGCGCCAAGGACGGATCCGAAGAACAGGCCAAGTATTATACTCCCGACGCGGCCGCGGAGCCGGAGGAGCGTGGCCGTGCGCGGCCGCCCTTCATCCCGGAGTCTAGTCTGGCCCCTGCGGCCGCTGCTCTCAAAGCGGCCAAATACGACTACACGGGTATGGGCCGCGTCGCGCCGGGCTCTTCAACCCTTCTCGAGGGGACACCCTGCTCCGCCGGTTTCAAGGACGACGCCAAAGGCCCGCTCAACTTGAACATGACAATGCAGGCGGGCGTCGCCTCCTGCCTGCGACCTTCGCTGCCCGACG
Seq A exon
GTAAAGGGTGGCCAGGCTCCCCGAGCAAAGCTCCCCGGGCCGGGGTGGGAGGTGGGGTGCTGGGGAGAGTGTGTAGAGGGAGGGAAGCCGCCAGGGGCGGGCAGGCAACTGGGAGCGGGCCGGGCTGACTTGGGTTGGGGCTGTGTTGCAG
Seq C2 exon
GCCTACCGTGGGGGGCGGCCCCGGGGAGGGCCCGAAAGAAGCGGAAACCCTACACAAAGCAGCAGATTGCGGAACTGGAGAATGAATTCCTTCTCAACGAATTCATCAACCGGCAGAAGCGCAAGGAATTGTCCAACAGGCTAAACCTCAGCGACCAGCAAGTCAAAATTTGGTTCCAGAACCGGCGTATGAAGAAGAAGCGCGTGGTGCTGCGCGAGCAGGCGCTGGCGTTGTACTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000004314:ENSBTAT00000005652:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.264 A=NA C2=0.241
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=71.2)
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:
GGCCAAATACGACTACACGGG
R:
GTTCCGCAATCTGCTGCTTTG
Band lengths:
245-396
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]