BtaINT0073180 @ bosTau6
Intron Retention
Gene
ENSBTAG00000021427 | HOXB3
Description
Bos taurus homeobox B3 (HOXB3), mRNA. [Source:RefSeq mRNA;Acc:NM_001099174]
Coordinates
chr19:38573225-38576915:-
Coord C1 exon
chr19:38576404-38576915
Coord A exon
chr19:38575555-38576403
Coord C2 exon
chr19:38573225-38575554
Length
849 bp
Sequences
Splice sites
5' ss Seq
CAGGTACCG
5' ss Score
10.05
3' ss Seq
CCCCTCCCCCTCGGGTCCAGCGG
3' ss Score
7.08
Exon sequences
Seq C1 exon
TGTCCGGTCGTGAGGGTATCTGGCCCTTGCAAGTTGCCACCCACCACCAGGGCCTCACCCAGCGATGCAGAAAGCCACCTACTACGACAACACCGCCGCAGCACTCTTCGGAGGCTACCCCTCATACCCTGGCAGCAATGGCTTCGGCTACGACGGTCCCCCTCAGCCCCCCTTCCAGGCCGCCACGCACCTGGAAAGTGACTACCAGCGCTCAGCGTGCTCGCTGCAGTCCCTGGGCAACGCCGCCCCACACGCCAAGGGCAAGGAACTCAACGGCAGCTGCATGAGGCCGGGCCTGGCCTCGGAGCCCCTGCCGGCCCCGCCCGGCTCGCCCCCGCCCAGCGCCGCACCTACCAGTACCACTAGCAACAGCAGTAACGGGGGCGGTCCCAGCAAAAGCGGCCCCCCCAAGTGCGGTGCCGGCTCCAACTCCACCCTCACCAAACAGATATTCCCCTGGATGAAAGAGTCGAGGCAAACGTCCAAGCTGAAAAACAGCTCCCCTGGCACAG
Seq A exon
GTACCGGCTCTCTGGCTTCGTCGTCGTCAGCTTTTGTCCCGGCCAGGAATGTCACTGTTATTCTAGCACCCAGCCCCTAGGCGCCCAGGCGGCGGCGGCAGCTACGGCGCATTTCCCATACCCTCCCCCCTCACCTGGCGACCCCTGACCCCGCCAGCACCCTCTCCCTCCTGCCCTCCTCCACCTGAACTTCTGAGAGGCCCAGAAGGCCAGGTGCTCGGCCTCAGCCCTTTGCAAGGCCGCAGAGTCACGAGACGCTGCCAGTAGACGCAGAGTCGTCAACGATTGATTGTTATTAAGTATTACTACTGTGGGTATTAATCACAATCGCTCGGGCGGCCCGCGGTCTTGGCCTCCAGGCATGGCAACCTCTTTGCCACCCCCCCCCCCCCCATTTCCGTGCCCTGCCCAGAATGTCCAGACTCGCCCAGGAGCTCTCCTCAAGCACCTGTCTGGGCCACAGGACGGGGCGCAGTGGAGGGCGGAGGAGTGTCTTCTACACCTGGAACTAGGGATAAAAGGGGGGAGAAAGCGTGTGCGAGAAAATCCAGCCCTAAATAAATGGCCATGCGGCTCTGTCTGCGTGACATGATCAAATTTTCATAAGCTGGGGCAGTGAGAGGAGAACAGGTCTCTTAATAAATGCCACTATTATAGAGTGTCCGCTAATGCGGCGGGTGGGGGCGGGGGGCGGTGGAGAGGAGGAGGCGGGGACGCGAAGGGGAGGGCGGCGGGGCCTCCGAGTCCAGGCCTGGATTTATTAAGAAACGATGCATTCAATTTCGGCGTGTTCAGTAATTATCTTTTATTTCATTTTCTCCCCTTCCCACCCCTCCCCCTCGGGTCCAG
Seq C2 exon
CGGAGGGCTGCGGCAGCGGCGGCGGAGGAGGCGGCGGCAGTGGCAGCAGTGGGGGCGGCGGCGGGGGAGGGGACAAGAGCCCCCCGGGGTCTGCGGCCTCCAAGCGGGCGCGGACGGCGTACACGAGCGCGCAGCTGGTGGAGCTGGAGAAGGAGTTCCACTTCAACCGCTACCTATGCCGGCCGCGCCGCGTGGAGATGGCCAACCTGCTGAACCTCAGCGAGCGGCAGATCAAGATCTGGTTCCAGAACCGGCGCATGAAATACAAGAAGGACCAGAAGGCCAAGGGCCTGGCCTCGTCTTCGGGGGGCCCCTCTCCCGCCGGCAGCCCCTCGCAGCCCATGCAGTCCACGGCTGGCTTCATGAACGCCTTGCATTCCATGACCCCCAGCTATGAGAGCCCGTCCCCGCCCGCCTTCGGCAAAGCCCACCAGAATGCCTATGCGCTGCCCTCCAACTACCAGCCCCCCCTCAAAGGCTGCGGCGCCCCGCAGAAGTATCCCCAGACCCCGGCGCCCGATTACGAGCCTCACGTCCTTCAAACCAACGGGGGCGCCTACGGGACGCCCACCATGCAGGGCAGCCCCGTGTACGTGGGCGGGGGCGGCTACGCGGATCCGTTGCCGCCCCCTGCCGGCCCCTCCCTCTACGGCCTCAACCACCTTTCCCACCACCCCTCGGGGAACCTGGACTACAACGGGGCGCCCCCTATGGCCCCCAGCCAGCACCACGGACCCTGCGACCCCCACCCCACCTACACAGACCTCTCCTCTCACCATGCGCCTCCTCCTCAGGGTAGAATCCAAGAAGCGCCCAAGTTAACACACCTGTGATGGGAGAGGGAGGGCTGAGGAGCAGGTCTTGGGGTGGAGAAGACCCAGGAGGGACGGGGGCTGTGGAGTTGGGTGCAGTCGGGAGGTCTGAAAGAGGAGGCAGGGAGATGGCAGCCAGGCTTCCTGGGAAGAAAGGGCCTGGAGGTCCTTCCCCTCCCCCTGGCCTGAGAGGTTGCTTTTTAAGTCCTGCAGCTCTTGTTTAGTCTGCCTGCCAACCCATTGGAAAGGAATCTACAGCAGATTGGAGATGACCCCATCAACCCTAGGCCTCCAGCAATATCCAGTTGGAATTCCACCTTAGGGAGTCCGGTAGAGGAAGAGGAGATAGGGAAACAGGCAAAGAAGCACATTTTAAAAAACAGACAAGATGGCTAGGCCATCACCAGCCAACCAACCAACTTACCTTTCATGTGGTTAATTCCCCCAAATCTTGATTTTTCTTTCCTGGCAATTCTCCTTTAAAAAAAAATTCAAATACATTTCAAAACCAAGGGCACAAAGCATGTCCCCCTCCCACTTTCCTGAATCCTCAGATTTCTTCCCATGATAGGAGAAGGTTGATTGGGCACTCCATTTCTAGTCCCATATTTTTCTGCTCTAGGACATTAATATCTATACCCCACCCCTATCAATTACACTCTTCAGAGGGCTCAGGGATGGTGAGAGATCCTGAAAGAGCTGTCTATATTATAAATATATATATATATATTTTCTTTTATGGCAAAGCTGGGAGGTGAGGGCAGGCAAGTTGTCAGGACTAAAGGTCTGCCCATTCCGCTGTCTCCCATCTCAGCTCCAGGTCCATCCCCCTCTCTTCACAGAAAGCAGTCGGTGACAGCGAGGTTCTACACTTTTCTTTTCTTCTGTTGCTCTCTTGACTTAACGTGAAAACAGGGTATATTTTGACAAACTGTCCCAGGCGGGGGCTGCAGCTGGGCCTGTGTGCCTTGCTCAACCCTGGACAGGACACTTTTGTTGCACTTAGAGTTTACATTTTAATGGATATAAAAACAACTGTGAGAGATGCCTGGGCCTGCAGGAGTCCAGCATTGCTCAAAAAACGTGTGTTCTAGTGAACATTTTCATATATATTTATTGGTTATAGCTTGTTAAGATATTTTCTTTTTTTTTTTGTATTATTTATCCCCCTACTTTATGTATTTATATGAGGGAAAAAGGAAAAAATTGTACTTTTTTTTTAGTATTTACTTGTTATAAAGGACGTTGTGTTCCCTGTCATGTAAAACCAGCTATTTTAGTTATTGTACTCTAGAAAAAAGCTATAGATTTATGTTAAACTTGTACTTATGAACAATTGTAATTAGTTCTAAAAGGCATGAACTCAGCTCCTAATTGTCACTGTATAGTCCTGAATTTGTAGAATTAGAGTTAATTCCCTCTTGGAACTTTCTTTGTTCTTCTGTAGTTACTTTTTTTCCTTACTTAAAAGGGTTGTCTGTCATATAATTCTTGAATAAACTTTCTGTTATCAATTTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000021427:ENSBTAT00000028563:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.840 A=NA C2=0.834
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=20.5),PF132931=DUF4074=WD(100=23.7)
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:
CCGCACCTACCAGTACCACTA
R:
CGGCATAGGTAGCGGTTGAAG
Band lengths:
349-1198
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]