BtaINT0073194 @ bosTau6
Intron Retention
Gene
ENSBTAG00000015840 | HOXD1
Description
homeobox D1 [Source:HGNC Symbol;Acc:HGNC:5132]
Coordinates
chr2:20759890-20761196:-
Coord C1 exon
chr2:20760563-20761196
Coord A exon
chr2:20760225-20760562
Coord C2 exon
chr2:20759890-20760224
Length
338 bp
Sequences
Splice sites
5' ss Seq
AAAGTAAGT
5' ss Score
9.72
3' ss Seq
GCCCTGTCTTTACATTGCAGGCA
3' ss Score
9.87
Exon sequences
Seq C1 exon
ATGAGCTCCTACCTCGACTACGTGTCGTGCGGCCGGGACGGCGGCGACTTGCTGAGCTTCGCATCCAAGTTCTGTCGCGCCGACGCCCGGCCCGTGGTCCTGCAGCCCGCCTTCCCCCTGGGCAGCGGCGACGGCGCGTTCGTTAGCTGCCTGCCCCTGGCCGCGGCGCGAGCGGTGCCCTCGCCCCCGGCCGCCCCGGCGCAGCCTCCGGGGCCTGCCGCGCCCGCGTACGCGCCGTGCCCCCTAGAGGGGGCCTACGAGCCAGGCGCCGCACCTGTCCAGGCCGGGGGCGAGGACTACGGTCTCCCGGGGTCCGCGCCCGCGTACGATTTACCGTGCGCGCTCGGGCGGCCGGCAGACGACAGCGGGGCGCACGTCCATTACGCCACCTCGGCTGTCTTCTCTGGAGGCGGCTCCTTCCTCCTCAGTGGCCAGGTGGATTACGCGGCCTTCGGCGAGCCGGGCCCCTTTTCGGCGTGTCTCAAAGAGCCGACCGACGGCCACTCTGGGGCCTTTCAGACCGCGTCCCCCGCTCCCGGCGTCTACCCCAAGTGTGCGTCCCCAGCCTCCGGCCTCCCTGCCGCCTTCAGCACGTTCGAGTGGATGAAAGTGAAGAGGAACGCCCCGAAGAAAA
Seq A exon
GTAAGTACTTGGGCCTTGGACGGACGGACGCGACTGGGGTTGGGGATCGAGCCTGCCCAGCGGAACTGAGCCGAGGGTGCGCTGCAGCGGTCCCCGTGGACGGCGGTTTGGGTCTTATGGGGAACACGCGGCCCCAGGCATTATTAAACCAGGAGAATTGCATTGAGCGTGCCCCGAATGCCAGGGGTTGAGAAAATTGCGGGAAGGAGCGCTCCGTGAAGCTTTTCTTTTGGCACAGGGCCGTTCAGTAACTGATTCTAGTGTGGCCCCAAAGCTCTCCCAAGTCGCGTCTCCGTGTCATCTCGCCACGCTGACAACGCCCTGTCTTTACATTGCAG
Seq C2 exon
GCAAATTCGCGGAGTATGGAGCCGCCACCCCCTCCAGCGCGATCCGCACGAATTTCAGCACCAAGCAACTGACAGAACTGGAGAAGGAGTTTCATTTTAATAAGTACTTAACTCGGGCCCGACGCATCGAGATAGCCAACTCATTGCAACTGAATGACACCCAAGTCAAAATCTGGTTCCAGAACCGCAGGATGAAACAGAAGAAAAGGGAACGGGAAGGGCTTCTGCCATCGGCCACCCCCGTGGCTTCCTTCCAGCTTCCCATCTCAGGAACGAGCCCTGCCAAGTCTGGCAAGAACCCGGGGAGCCCCTCTCAGGCCCAGGAACCATCCTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000015840:ENSBTAT00000021043:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.151 A=NA C2=0.450
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=50.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Rat
(rn6)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGTCTCAAAGAGCCGACCG
R:
TGTTTCATCCTGCGGTTCTGG
Band lengths:
357-695
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]