BtaINT0073198 @ bosTau6
Intron Retention
Gene
ENSBTAG00000004835 | HOXD3
Description
homeobox D3 [Source:HGNC Symbol;Acc:HGNC:5137]
Coordinates
chr2:20779266-20780505:-
Coord C1 exon
chr2:20780457-20780505
Coord A exon
chr2:20779896-20780456
Coord C2 exon
chr2:20779266-20779895
Length
561 bp
Sequences
Splice sites
5' ss Seq
CAGGTGGGG
5' ss Score
6.92
3' ss Seq
CTCACTTTTCTTCTTTGCAGGTT
3' ss Score
12.13
Exon sequences
Seq C1 exon
GAGTGGACTATCTGGTTCTCTGTGGAAGATGCTGTGATTTTGAAACCAG
Seq A exon
GTGGGGGAGATACTTTTTTTTTTTTAGACTGCCAGCTGTTCTGAGGGTTAACAGACTTTTCTTTTGCCCATCACATCCCTGGGATGACCTATGATTAACTGATTGATCCATTCATTCATTCACTCATTCAACATGCATTTACTGCACTTAACTGCATGTGGTGCATTGGGCTGGATGTTAGGAATATGTAGGTGAATAAGACACAGTGCCTACCTGCAGAAAGCTCAAAGTCTAGTGAGAAACTCAGTCATTAAAATGTATAGGCCATAAGTGCTTTTCTATGCAGTTTCAAAGGCTAAACTGACAATCTTGGAGAAAGAAAATTGTATCTGGGAAAAAAAAATTAACCCCTTCCCTTGGGTGAAGGGGAGTCTTTTCTTGTGGTTTATGAGAAATTCCTTCTGACACTTCCAAGGGTTCAAATAAATTGAACTTCATAAAAATCCCAGATCCTCCTACTATGAAGTGGGTGGGAAGCAGAGAGCCTGGGCTAGTCCTTCTGTATTGATTGGTCTTGCCAATGACAGTCCCTCTGGGACCTCTCACTTTTCTTCTTTGCAG
Seq C2 exon
GTTATCTGGAGCCTGGGGCTGCCCCAGCTCTCTCAGGATTTGGCAGACATTGGAGGTGGTGGTGAAGGAGACAGTGGTGGTCAATGTTATTTGAGCAGGGTCAGCAGGCCCCGGAGGTTCCTGAGTACACGATGCAGAAGGCTGCTTACTATGAGAACCCAGGACTCTTCGGAGGCTATGGCTACAGCAAAGCTGCTGACACTTACGGCTATAGTGCCCCTCATCAGCCTTATCCACCCCCTGCTGCTGCCAACTCCATGGACACTGATTACCCAGGCTCTGCCTGCTCCATCCAGAGCTCTGCGCCTCTCCGAGCCCCAGCCCATAAGGCGGCTGAACTCAATGGAAGCTGCATGAGGCCTGGCACTGGGAACAGCCAAGGTGGGGGTGGTGGCAGCCAGCCTCCAGGTCTGAACTCAGAGCAGCAGCCACCACAGCCCCCTCCACCGCCACCGCCACCAGCCCTGCCCCCATCCTCTCCCACCAACCCTGGAGGTGGAGTACCTGCCAAGAAGGCCAAAGGTGGGCCCAATGCTTCTGGCTCCTCAGCCACCATCAGCAAGCAGATCTTTCCCTGGATGAAAGAGTCCCGCCAGAACTCCAAGCAGAAGAACAGCTGTGCCACTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000004835:ENSBTAT00000006353:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=0.896
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGACTATCTGGTTCTCTGTGGA
R:
CTCTGGATGGAGCAGGCAGAG
Band lengths:
344-905
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]