BtaINT0073174 @ bosTau6
Intron Retention
Gene
ENSBTAG00000008139 | HOXA3
Description
Bos taurus homeobox A3 (HOXA3), mRNA. [Source:RefSeq mRNA;Acc:NM_001076825]
Coordinates
chr4:69386129-69389905:+
Coord C1 exon
chr4:69386129-69386774
Coord A exon
chr4:69386775-69388198
Coord C2 exon
chr4:69388199-69389905
Length
1424 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAG
5' ss Score
9.65
3' ss Seq
TCTCTTCTCTGATCTCGCAGGGG
3' ss Score
10.61
Exon sequences
Seq C1 exon
GTCTGCGCGGGGCGGCCATTGGCTGCGGAGCGTCACGTGACCGCGGGGGCGTGCCAATGTGCGCCCTCACGGGTGTCAAGCCTCTGTCAGAGCGTGCGATCAAGATCGTGAAACAACGCGATGCAAAAAGCGACCTACTACGACAGTTCGGCGATCTACGGTGGCTACCCTTACCAGGCAGCCAACGGGTTCGGTTATAATGCCAATCAGCAGCCGTACCCGGCATCCACAGCGTTGGGCGCCGATGGCGAGTACCACCGACCCGCCTGTTCACTCCAGTCGCCTGCAAATGCCGGGAGCCACCCCAAGGCGCACGAGCTGAGCGAGGCCTGTCTGCGCACCCTGAGCGGTCCGCCCAGCCAGCCTCCGGTTCTTGGCGAGCCGCCCCTGGCCCCACCGCCACCTCAGGCTGCGCCCCCTGCCCCACCGCAGCCTCCAGCCCCGCCGCAGCCCCCTGCACCCACCCCCGCCGCGCCCCCGCCCCCCTCTTCAGTCTCCCCACCTCAGAATGGCAGCAGCAACCCCACCCCCGCCAGTGCAGCCAAGAGCCCCCTCCTCAACTCGCCCACCGTGGCCAAACAAATCTTCCCCTGGATGAAAGAGTCTCGGCAAAACACAAAGCAGAAAACCAGCGGCTCCAGCTCAG
Seq A exon
GTAAAGAGGTGCCTTGCGCAAGAGGGCCCTCCATCCTGGCTTCCAGCCCCCCAAACCACCTCCAGCCACAGCCAGCAGGGTCTGGGAGCACTGGAATATTTCCAGAATTCACTGCTCCTCCTTCCCCCAACCCTCAAAGGTTTCCAGAGTCTTTGCAACTAGGGAAATGATTGGACTCTGTGTGCCTGGGAAACCCTAGAGGGAGACTTGATGAGTCTTTCTGGATCTAAGAACAAGTGGGCCCTAGTGACTTTGGAATACCTGCTTGTAGAGTTAGGACCTTTGGGCAGAACAGACATGGGCACCACTGTTTCTCTTTTTAGCACAGCTCCTTATTTCTAATGAAACGGTGGTACCTACCCCACAAGGAAATGTGGCAGAATAAAAGCAGGCCTCCAAGTCAGAATCAATGGTCTGCCTATAATCAGAACCTATTTTTAATTTTTGCTCCAGCAGATGGAGTGGCTGCCTTACCTCTGGGAAGGCCCTGCTCAGACTTAGTACAATGAAGGTCGCCAGGGATTTCCTGGGGGAGGGGATTCAGCCTTGTCATCTTAATGGGAACCACATGGTCCTCCTGGAACCAGATTCCAGGACAGGCTCTGGGTCTTGTGCTTCCCAGCATCTTGGTTTCCTATGCCACTGCCTTCTCCAGTTGCTAGAGCTCTGTTCTGAACCTGAGCATCTGGAGCCATCCGGAGCCAGGAATGGGGCAGGGCAGGGGGAGGGGGGGTGGGTGGGGAGCAGGGAGAAAAGGAGGGTCAGGATTAGTGGGCATAGCTGGGGCATGCTGCTTGGTGACATGAAGAACCCTAATTAATGGCATCCAGCACCAGATGCCTGGGCCTCCCCACCAGAAACGGGATTTCTTTTCAATGGGATCTCCTTCTTTGGCCAGAGAAAGCCTTCCAGATTGGAGCTTCCACTCCAGTCCTCTTTACTGGACAGAGTAAATAAGAGGCCAGTGGAGGCAACTGTCCAATCCTTCAGTGAGATAGTGATGGAGGGAAGGTTTATTGAGTGTATATTAGGTGCCCCACATTCCAGTTACTGTAAAGGGAATAAACAGAATGAGACCTGCCCACGCAGAGCTTGTAGTCTGATAGGGCAAAGGATCAGGAGATGAACCAGAAACTGAATAGCTCCAGAAGGGAAACACAGTGTAGGAATGCAAACAGGGCGTTCTGCTTTTCTGTTCCTTGCCCCCTTGGAGAGGCTTATGACTTGCAGCTTTAGTCAGTGAGAAACTGCTGACACTGTTTCCCTACCAGGACAGAAAATAGTACCTACGTCCTTCTTCCTCTTTCTGGGCCCTGATAGATGGAGGGATCTTTGGGGCCTGGAGGAAGGAGGGGCCTGGCTAGGTCAGGGGCTGGGCGGGGCAGCCCCTGATGCCACTCTTCCTCTCTTCTCTGATCTCGCAG
Seq C2 exon
GGGAGAGCTGCGCAGGTGACAAGAGCCCACCTGGGCAGGCATCATCCAAGAGGGCGCGCACGGCCTACACAAGCGCGCAGCTGGTGGAACTAGAGAAGGAATTTCACTTCAACCGCTACCTGTGCCGGCCGCGCAGGGTGGAGATGGCCAACCTGCTGAACCTCACTGAACGCCAGATCAAGATCTGGTTCCAGAATCGACGCATGAAATACAAGAAGGATCAGAAGGGCAAGGGCATGCTGACGTCATCAGGGGGTCAGTCCCCAAGTCGCAGTCCCGTGCCCCCCGGCCCTGGCAGTTATCTGAACTCTATGCATTCGCTGGTTAACAGCGTCCCATACGAGCCCCAGTCGCCCCCGCCTTTCTCCAAGCCCCCTCAGGGCGCCTATGGGTTACCCCCCGCCTCCTACCCTGCGCCCCTGCCCAGCTGCGCACCGCCGCCTCCACAGAAACGCTACACGGCGGCAGGCGCGGGCGCGGGGGGCACACCTGACTATGATCCACACGCGCATGGCCTGCAGGGCAACGGCAGCTATGGGACTCCACACTTACAGGGAAGCCCCGTCTTTGTAGGGGGCAGCTACGTGGAGCCCATGAGCAACTCTGGCCCGCCCCTCTTTGGCCTAACTCACCTGCCCCACACAGCCTCGGCTGCCATGGACTACGGGGGTGCTGGGCCACTGGGTAGCGGTCACCATCATGGGCCCGGGCCAGGGGAACCGCATCCAACCTACACGGACCTTACCGCCCACCATCCTTCTCAGGGAAGAATTCAGGAAGCCCCCAAGCTCACCCATCTGTGATGGTGGGCTTGGGGCTGCGCGCCAGGAGAGTCCCGTCCCCCCGCCCCCCCCCCCCCGCCCATCTTTCTTCATTTGCTTTTTTTGTTTTAAGGTTCTTTCTGCACCTCCCTTTCCTCTCTTCTCCACCCGCCCTGCTCTCCCCCGACCCGTTTTGTTTTCTTTGGTAACACGTTTTTATGGTTTATGTGACGTAGCAATCTTGGTTGCTGGAATGGCTGTTGGTATCAGTAGCGATATGTATCTGCTCCCGCCCCTCGCTGGGCCGTTGGCCTCGCACCCTTTACCTTCTCTACTCTTTGATCAGAAACAGGGTATATGAACAAATTTTCTAGCCGAGTTGTTCAATGTGAATTTGTTCGTACATTATGGCTCCCGAGGGGAAGCAATTAATTTTTAGTTTTTTTTTTTTTTATTGCACTTCTTGTAAAGAGCGAGAAAAAATCAAAGGCGCTTTGAGACAGGGGCTCCCTGTACAAGGATGACTAAGTGTACGTCTTTCCGTGTGTGTATGCTGGTGAAGTCAGATTTATTTATATTTTTTTTGCAAGCATTGAATAAGTTTTAAATATTATTTATCCCCATCCGTCTGTATTTATATTAAAGAAATTCTGTACCCTGATTGTTCAGAAGGTTTCTTGGGCCTTTTGTTCAATGGTGTATTGGCATACATAGAAAAAAATTTTATTCGAAAGGGAAATATAATTCCTTTATAAAGATGGTAATGATGCAATAATACCAGAGAGGATCCAGCTTTTGAAAACAGTGATTTAGGTTTGTAACATCCGGCGAAACTGAAAAAAAAAAAATCTGTAAACGCGAAAAATGCTAGATTTGTTTTGAAAGTTCTACATTCCTTGCTGCTCACATTCTGAGAAACAAAACAAAAAAAATAAAGTTTATTCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000008139:ENSBTAT00000010700:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.869 A=NA C2=0.858
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=21.3),PF132931=DUF4074=WD(100=24.6)
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:
CCTCTTCAGTCTCCCCACCTC
R:
TGATCTGGCGTTCAGTGAGGT
Band lengths:
342-1766
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]