BtaINT0073175 @ bosTau6
Intron Retention
Gene
ENSBTAG00000024341 | HOXA6
Description
homeobox A6 [Source:HGNC Symbol;Acc:HGNC:5107]
Coordinates
chr4:69349548-69351620:+
Coord C1 exon
chr4:69349548-69349998
Coord A exon
chr4:69349999-69351372
Coord C2 exon
chr4:69351373-69351620
Length
1374 bp
Sequences
Splice sites
5' ss Seq
CGGGTAAGG
5' ss Score
10.17
3' ss Seq
CCGGCCATTTCTGCCCGCAGGTG
3' ss Score
11.06
Exon sequences
Seq C1 exon
GGCGCGCAAATGAGTTCCTATTTTGTGAATCCCACTTTCCCCGGGAGCCTGCCCAGCGGCCAGGACTCCTTCTTGGGCCAGCTGCCCCTCTATCCGGCCGGCTATGACGCGCTAAGGCCCTTCCCGGCCTCGTACGGGGCGTCGAGCCTCCCGGACAAGACGTACACCTCACCTTGTTTCTACCAACAGTCCAACTCGGTCCTGGCCTGCAACCGGGCATCCTACGAGTACGGGGCCTCATGTTTCTATTCTGATAAGGACCTCAGTGGCGCCTCGCCCTCGGGCAGTGGCAAACAGAGGGGCCCCGGGGACTACCTGCACTTTTCTCCCGAGCAGCAGTACAAACCCGACAGCAGCAGCGTGCCGGGCAAAGCCCTCCATGACGAAGGCACCGACCGGAAGTACACGAGCCCTGTTTACCCCTGGATGCAGCGGATGAACTCCTGCGCGG
Seq A exon
GTAAGGTGTTTCCCTGCAGCCCCTCAAAGAGTGTGGAGGGAGAGGGGGAAGGAGGCAGGGAAAGAAGGAAGGAAGGAGGAGACAGTAGAAAGAGGACATAGAAAGAAGGGAGGAAAGAATAAACAAAGTTTCTTTGGTTTTTAAAAAAAGAGGTTTGTTTTTTTTTTTTTTTTAAATAAAAAACCCAACCCATTCCCAATGGGACAATCAGGCTGTGAAAGAGTGAAGGCAGGGCCCAAGTGCCCATGTAAGGTGACACCTTAGGGGAGCGTGGGGGGGGTCACTCCACGCTGTGTGAAACCCAGTGACAGGGACAATCTGAAGAGAGAGCAAGGCTGGATGGGAGAGTGCGCCTGCCCACCCTGCACCCTGGTAATACCCTGCTCAGTTCCCTAGTCCTGATGGCCTTCTGCACCCGTCCTGAGAACGCCTCTTTCCCTCGCTGTCTCCTCACCTTTCTGCCCTTCAGAAACCCATCTAGAAAGAGGCCCTCATTTGGCCCCTTGCAGTGTCTCCCCAAAGCCTTGGAGGGCCACATCCCCGGCCTCAGGATTTTTCCGCTCTCTCCTCCCTCCCCTCCTCCCCCCTCCACTCAACTGCTCACTCACAGCCAACTTCTGCCTCCTTCTGAGGCCCTGCCTGAGTCTCACACACCCAACTTGGGGGGAGCCCCCAACCCATGGGTCTTTTTGGCATCAGAATAGATAGCCCATCACAGCCCTACATTCTAGAAGCCCCAGATGGCCCATATCTCCATCTCTTTGCCCCTGATTTCCAAAACTCCACAGGGAATTCTTGGAGAAGGAAGGAGCCTAATGCGGATTTTAGAACTTACAGTCTTTTGCTTTAAAAGTCATTTGTGTTTTCAAGAGCTCGGCTTTTCTCAGAAGGGTCATACAATGGGAAGGCATTTGCGAAGATCTAAGAGGGCTGACCATTTAAAATTTTCCAAAAAGTATATTGTGTCCTGAAGTGCTGACCACAGTAATAACTCCACAGAGGTCAGTGTGTGAATTCGGAGTGTGTACCCTACTCACAGGGTTCCATACCCATCATTTCCAGACACACACACTGTACCCTCACAAAACAGGCTCAGGTGCCCGGATTTAAGAATGCTGTTCTATTCTTTTTTCTTGTAATATTTTTACTGAGCAGATTTTGCAAAAACAATCATTTCCCACCCTAAGTCGTTTTAGATGGAAAATATCTCGCTTGGTATGAAATAATCTTCTCCTATCCAGTCCGCTTTCGGCCCCAGACATAGTGGGAGAGGCGGGTGGTTTCCAGCCCCGAGGCCAGAGCGTGGGGCTCAGGGCTGACTGGTCAGGGTGCCTGGATCCTGGCTTACTGGCGTCCGGCCATTTCTGCCCGCAG
Seq C2 exon
GTGCTGTGTATGGGAGTCACGGGCGCCGAGGCCGCCAGACCTACACGCGCTACCAGACGCTGGAGCTGGAGAAGGAGTTCCACTTCAACCGCTACCTGACGCGGCGCCGCCGCATCGAAATAGCCAACGCGCTCTGCCTCACCGAGCGCCAGATCAAGATCTGGTTCCAGAACCGCCGCATGAAGTGGAAAAAGGAAAATAAACTCATCAATTCCACACAACCCAGCGGGGAGGACGCTGAGGCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000024341:ENSBTAT00000033679:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.243 A=NA C2=0.277
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=68.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAACAGTCCAACTCGGTCCTG
R:
GGAACTCCTTCTCCAGCTCCA
Band lengths:
349-1723
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]