BtaINT0073189 @ bosTau6
Intron Retention
Gene
ENSBTAG00000003304 | HOXC4
Description
Bos taurus homeobox C4 (HOXC4), mRNA. [Source:RefSeq mRNA;Acc:NM_001102373]
Coordinates
chr5:26136686-26138815:-
Coord C1 exon
chr5:26138335-26138815
Coord A exon
chr5:26137851-26138334
Coord C2 exon
chr5:26136686-26137850
Length
484 bp
Sequences
Splice sites
5' ss Seq
CGGGTAGGC
5' ss Score
7.5
3' ss Seq
GCTTTCCCCCCTCCCCTCAGTGA
3' ss Score
9.94
Exon sequences
Seq C1 exon
AAACGACAAAGCGAGAAAAATTATTTTCCACTCCAGAAATTAATGATCATGAGCTCGTATTTGATGGACTCTAACTACATCGATCCGAAATTTCCTCCATGCGAAGAATATTCGCAAAATAGCTACATCCCTGAACACAGTCCGGAATATTACGGCCGGACCAGGGAATCGGGATTCCAGCATCACCACCAGGAGCTGTACCCACCACCGCCTCCGCGCCCTAGCTACCCTGAGCGCCAGTATAGCTGCACCAGTCTCCAGGGGCCGGGCAATTCGCGAGGCCACGGGCCGGCCCAGGCGGGCCACCACCACCCCGAGAAATCACAGCCGCTCTGCGAGCCGGCGCCTCTCTCAGGCGCCTCCGCCTCCCCGTCCCCAGCCCCGCCAGCCTGCAGCCAGCCAGCCCCTGACCATCCCTCCAGCGCCGCCAGCAAGCAACCCATAGTCTACCCATGGATGAAAAAAATCCACGTTAGCACGG
Seq A exon
GTAGGCAACTTTGCTTTTTGCTCTCCCCCTCCCCTCTTCCCCAGCGCTCCCCACCCTCCTCGGCCCCCGCCGGCCCCGTCCTCCTTTCTCTCCTTCCCCCTCTCTCTCCAGGAGCGACTCTGGGTTAGCACAATTGAACTGGATTTACGAGCGAGAATGGGTAATTACATCCCCCATAAATTTTATGGCTTAGCTACTCTGGGCAGTCCGAGCCATGTGCTACGATCTGTTATGTATGTGTGAAAACTATGCTCGCTTTCTAAGGGCGCATAAATAATTCAGTGTCGTTACAATGAGGATTCCCCTCTTATTACACTACAAAGTCTCCAGCTCCCTTCAACTTCTTTATAACCCATTTAGCTTGATGACTTTATTTCCATCACCCCCTCCTCCTGTTCCAACAGAGCTGAGGATGGGGTGAGGGTGGGGGGCGGGGAGCCTGCTGCCTTTGAACCCCACTATTTGCTTTCCCCCCTCCCCTCAG
Seq C2 exon
TGAACCCCAATTATAACGGAGGGGAACCCAAGCGCTCGAGGACAGCCTACACCCGGCAGCAAGTCCTGGAATTAGAGAAAGAGTTTCATTACAATCGCTACCTGACCCGAAGGAGAAGGATCGAGATCGCCCACTCGCTGTGCCTCTCTGAGAGGCAGATCAAAATCTGGTTCCAAAACCGTCGCATGAAATGGAAGAAGGACCACCGACTTCCCAACACCAAAGTCAGGTCAGCGCCCCCGGCCGGCGCTGCGCCCAGCACCCTCTCCGCAGCCACCCCGGGCACTTCTGAAGACCACTCCCAGAGCGCCACGCCGCCGGAGCAGCAACGGGCAGAGGACATTACCAGGTTATAAAACATAACTCACACCCTGCCCCTATCCCAGGCCCCCCATCCTCCCCTCACACACAAATTGACTCTTATTTATAGAATTTAATATATATATATATTTTGGTTCTTTTCTCTCTTCCTCCCACCTTCCCCCTTGTCAGTTCCAAACAGACAAAACAGATAAACAAGCCCCCTGCCCTTCTCTCCTTTCCACTGTTAAGGACCCTTTTAAGCATGTGATGTTGTCTTAGCATGGTACCTGCTGGTTTTTTGTTTTTTTTTTTTTAAGGCCATTTTGGGGGGTTATTTATTTTTTAAGGGAAAAAAACTGCAAAAATTATATATTGCAAGGTGTGATGGTCTGGTTTGGGTGCATTTCAGGGGAAATGAGGAAAAGAAAGAAGGAAAAAGATTTTTAAGCCAGTACTCCTCCTCCTCCTCCTTCCCCCCTCTTTCCTTAGGCCTTTTGCATTGAAAATGCACCAGGGGAGGTTAGTGAGGGGGAAGTCATTTTAAGGAGAACAAAGCTATGAAGTTCTTTTGTATTATTGTTGGGGGGAGCTGGGAGGAGAAGGGGGAAGACAGCAGACAAAGCTAAATGCATCTGGAGAGCCTCTCAGAGCTGTTCAGTTTGAGGAGCCAAAAGAAAATAAAAATGAACTTTCAGTTCAGAGAGGCAGTCTATAGGTAGAACACCCCACCCCACCCCCATCATGGTTATTGTGTTTTTGGACTGAATTTACTTGATTATTGTAAAACTTGCAATAAAGAATTTTAGTGTCGATGTGAAATGCCCCGTGATCAATAATAAACCAGTGGATGTGAATTAGTTTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000003304:ENSBTAT00000004277:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.796 A=NA C2=0.669
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=47.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Chicken
(galGal4)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCCAGTATAGCTGCACCAGTC
R:
CTTCGGGTCAGGTAGCGATTG
Band lengths:
358-842
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]