BtaINT0072568 @ bosTau6
Intron Retention
Gene
ENSBTAG00000002319 | HMCN2
Description
hemicentin 2 [Source:HGNC Symbol;Acc:HGNC:21293]
Coordinates
chr11:100692522-100693827:+
Coord C1 exon
chr11:100692522-100692716
Coord A exon
chr11:100692717-100693648
Coord C2 exon
chr11:100693649-100693827
Length
932 bp
Sequences
Splice sites
5' ss Seq
ACGGTGAGT
5' ss Score
11.45
3' ss Seq
CTGCTTCTCCTTCTCCCAAGTGC
3' ss Score
7
Exon sequences
Seq C1 exon
GGACGCCCAAGCCGCAGGTCACGTGGCGGAAGGGCCCGTCGTCCGAGCCGCTGCGTGACCGGCCCGGCCTGGCGGTGCTGGATGAAGGCTCTCTGTTCCTGGCCTCCGTCTCTCCCTCCGACGGCGGAGACTACGAGTGCCAGGCCACCAACGAGGCGGGCTCCGCGTCCAGGAGAGCCAAGCTGGTGGTCCACG
Seq A exon
GTGAGTAGGGACCCCAGAGCTGGGGGTGATGGCACCTGGGGTGCCAGGCTGGGGCCGCGTGAGCTCCCTGGCCCAGAGCTCACTGCTCGGAGGATACAGGTCCTTGCTCCTCTGTCCCTCGTGCCTGTCAGGGAGGGCTTGAGGGTGCTGTTGGGAGAGTGCATTCTTCATGCAGAGAACCCCCCGCGGAGACAGTGTAAGGAGACCCCGGAATTCCATAAATGACTTTAAAATGGGCTAGGAGTGAATCTTCTTTACAATTCTCACCAGTGGTCAAAGCCCACCTCCCACTAAAGCCGCTGAAACCACCTGAGGCTCATATGCCCACTTCCCAAGGCCCACGTGTCTCCCTGGTACCCGGCCCCCTCATCCAGGGTGCTGTGTGCAGGGGGAGGGGAGCGCTTCCCTCAACTTGGGCTCACAGAGAGGGTGAGAGAAGCCGTTTTAATAATGGGCTCCTAATGGAACCACCTTCCGCCTCCCGTAACCAGCCACACCCACTTGTCCTGTAATGACTTGCCTGGGAAGTTTGTTTCAAAGACATACCCAGGCCCCACCCAGAGAGGCTCTGACTCCATGGGTGGGGGGTGGGGTGGTCCCCTAGGTACCCTCCTTCGTGACCATGACAACCATTTGGGTGGAGAACTAGATGGAACCAATGGCTCCCGCATCTTGGAGAGCTGAATGTCAGAGCAAGTAGAGAGTTCCTGGGCTCGACTAGGGTGAGGTCCCAGGGCGAGGCCGCCATGGCCATTCCCAGGTCCACACGGCTCCTGACGGCCAGGGTCTAGAATGGGCGTCCTGGAAGCCCAGAAGCTGGGGAAGGGGGGAAGTCAGGACCGCCCTCGAGGCCAGGAAGAATGGCCCAAATGGGGTCCCTGGCCGTGGCTGACCTGCGGAGGGGCGGCTCCTCTGCTTCTCCTTCTCCCAAG
Seq C2 exon
TGCCCCCCAGCCTCCGGGAGGATGGGCGCAGGGCTAACGTGTCAGGCATGGCCGGGCAGTCCCTGACGCTGGAGTGTGATGCCAATGGCTTCCCGGCCCCCGAGATCACATGGCTCAAGAACGGGCGGCAGGTGGGTGTCCCCCAGGGGTGGATGGGCTCTGGGTGGGATATGGACAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000002319:ENSBTAT00000007111:26
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.621 A=NA C2=0.317
Domain overlap (PFAM):
C1:
PF0767911=I-set=PD(74.1=95.5)
A:
NA
C2:
PF0767911=I-set=PU(51.5=86.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Mouse
(mm10)
No conservation detected
Rat
(rn6)
No conservation detected
Chicken
(galGal4)
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:
CAGGTCACGTGGCGGAAG
R:
ATATCCCACCCAGAGCCCATC
Band lengths:
353-1285
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development