BtaINT0073200 @ bosTau6
Intron Retention
Gene
ENSBTAG00000039581 | HOXD4
Description
Bos taurus homeobox D4 (HOXD4), mRNA. [Source:RefSeq mRNA;Acc:NM_001101087]
Coordinates
chr2:20794855-20797028:-
Coord C1 exon
chr2:20796024-20797028
Coord A exon
chr2:20795480-20796023
Coord C2 exon
chr2:20794855-20795479
Length
544 bp
Sequences
Splice sites
5' ss Seq
CCGGTAAGG
5' ss Score
10.19
3' ss Seq
CGATCTGTTTTGTCTCTCAGTGA
3' ss Score
9.11
Exon sequences
Seq C1 exon
GGTGACCCTGATGAAGACAAAGCCGGCGGGATTCGGCCTTTGTATGGCAGAGTCCCCATGCTCCCGCGGGCTGGGTGGGCGGGAGTCCTGCCTGCCTGGGGTTCTCTGTCCAACTCAGGAGTCACCTCCTCCACCCACCTTTTGATGCCCTGCACCTTGATAAATATGGGAAATTCATTCCCTCTTGAACTGTGCGCATTTTGGGGGGCTGATTGCAGTCCGGGTGCATGGAGAGGGCAGTGGAGGTTAGCAAAGTCAGTGGCAGACAAAAGCTGGGGTTACCAGTGGGGAATGAGGGTGCTGGGATTAGAACTCCACTAACATCTGGTGGGAGCCCTCAAAGGTGCCACGGTGAGTCACTTGATTACACGTATGTTATTTAGTTAAATTTGTGAAAATTATGAGATGCTCACCAGCCCGGTGATAAACTCACTCCCTCGCTATTGGCTGGCCTGGTCACATGGCCGCCAACTTTATTCAGTTGACAGCAAGTAGGAGGGCCCTATGGAAGAAGAAAAAAAGACAACACGAGAAAAATTAGTATTTTCTACCTTCTGAAATTAATGGCCATGAGTTCGTATATGGTGAACTCCAAGTATGTGGACCCCAAGTTTCCTCCGTGCGAGGAGTATTTGCAGGGCGGCTACCTAGGCGAGCAGGGCGCTGACTACTACGGCGGCGGCGGTAGCGCGCAGGGGACTGACTTCCAGCCCCCGGGGCTCTACCCACGGCCCGACTTCGGTGAGCAGACCTTCGGAGGCGGCGGCCCCGGGCCCGGCCCGTCTCTGCCCACGCGGGGTCACGGGCCAGAACCCGGCGGCCCCGGCGGCCACTACGGTGCTTCCGGAGAGCCATGCCCGGCTCCCTCCGCGCCCCCGCCCGCACCCCTGCCAGGCGCCCGGGCCTGTAGCCAGCCGGGAGGCCCCAAGCAGCCGCCCCCCGGGACTGCCCTCAAGCAGCCGGCAGTGGTCTACCCGTGGATGAAGAAGGTGCACGTGAATTCCG
Seq A exon
GTAAGGACGGGCACAGGACCGCTCAGTCTCCACCCTGGCCCGGCGGCCTGAGCCCCTAGAGGGGGTGCGAGTGGGTGGGGGCGTGTGGGGTTTCAATGGGCGCCGCAATTACTCTCTCCATAAATTTTTATAGCCAAGGGAGCAAGCTGGGACCATGTGGCTGGCTGCTTGGCTGTGGGCGCAAAAAGGGGTGGAGATGGGGGTGGGGTGGGGGAGGACTCCATTTTCAGAGTGGAGGGAACGCGGTGGAGGAGAGGGGATTTCCAAAATGCCTGGGAATTCTGGAGCTGGCGGCAGGCTGGGGAGATGGGGGTACGTTTGGGGATCCCTGCCTGCGAGCCCAGGGGAGCAGGTGGGTGCGAGGGGGTGGGAGGGAAGGAGCGTGTGCGCTGGGGAAAGAGGGCGGGCGGGAGGCAGGGAGTAGTGGGCCAGGAGGGAGCGCAGGGAGGGCCCGGCCTCGGGGCGCGCCAGGAAGTGAGTGCCGGTGGCCAGGGGCCTACCCCGAGGTCGGAGCTGACCTTGTGCGATCTGTTTTGTCTCTCAG
Seq C2 exon
TGAACCCCAACTACACCGGCGGGGAGCCCAAGAGGTCCCGGACGGCCTACACCCGGCAGCAAGTCCTAGAACTGGAAAAAGAATTTCATTTTAACAGGTATCTGACGCGGCGCCGTCGGATTGAAATCGCTCACACCCTGTGTCTTTCCGAGCGCCAGATCAAGATCTGGTTCCAGAACCGGAGGATGAAGTGGAAAAAAGACCACAAGCTGCCCAACACCAAAGGCAGGTCCTCCTCGTCCTCGTCCTCGTCCTCCTGCTCCTCCTCAACTGCCCCCGGCCAGCATTTGCAGCCGCTGGCCAAGGACCACCACACGGACCTGACGACCTTATAGAAGTGGGGACCCTGGGCCCACCCCTCCCTGAGCTCCTGGCTGAGCCGAAGCTGCGGGGGCAGGCCGGGCCTGCTGTCACCTCCCTGGGCTCTAAGGTACTGTGGGGTGGACCTGGGACACACGCAGGCCTCCCTCGGACTAAGGTTAGCATCCTGCCCGAGGGCAGCCCCCTCCCTGGATCGGGGATGGGGGTGGGAGGGGGCGGGATTCTCTCTCTAAGTATATTATCAAATGGCAGGAGCTACTGAGAACATAAAACCTTGGCGAGTCATTAAACTCCTGAAAATCTC
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000039581:ENSBTAT00000028606:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.764 A=NA C2=0.631
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=50.9),PF105004=SR-25=WD(100=67.9)
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:
AGAAGGTGCACGTGAATTCCG
R:
ATAAGGTCGTCAGGTCCGTGT
Band lengths:
354-898
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]