BtaINT0072573 @ bosTau6
Intron Retention
Gene
ENSBTAG00000002319 | HMCN2
Description
hemicentin 2 [Source:HGNC Symbol;Acc:HGNC:21293]
Coordinates
chr11:100695744-100697123:+
Coord C1 exon
chr11:100695744-100695898
Coord A exon
chr11:100695899-100696844
Coord C2 exon
chr11:100696845-100697123
Length
946 bp
Sequences
Splice sites
5' ss Seq
ACGGTGAGC
5' ss Score
9.44
3' ss Seq
CTCGCCCCCGCTGTTTTCAGCAC
3' ss Score
8.83
Exon sequences
Seq C1 exon
ACCTGTCTTTCTGGGGGAGCCTCGTGTCCAGCTTCAGGAGGATGGCCAGGTTCTCAGAATCACCAACAGTCACCTGGGAGATGAGGGCTGGTACCAGTGTGTGGCCTTCAGCCCGGCTGGCCAGCAGACCAAGGACTTTCAGCTCAGAATCCACG
Seq A exon
GTGAGCCCAGCCCCTTCCCGTCATCACCACGGGCTGCCCACTGTGTGGAGGGGTGGTGAGGGCAGAAATGGGAGTCTCTGAGGAGTCTGCCCCCAGTCCAGTAAAACCAGAGGGGGACAGACAGAGGGAATCCGAAACGTTCCCCAAATCCCATCATCCCCATCGGAGCTTCCCAAGTCCTCCCATCCGTGGTACACTCTGGATGGTCATTTCTTTAAATCAAATCACTTTTCTTTCCACTGAAACCCAGTTACCTAAAAGGATGTTGGCTATTTCAAAGGGAAGTGGGAACCAGGGTTGCTTGGCCTTCGTGGGAGGAAGCTGTGAAAACAAATGCCACCAAAGAGGGATGTTGGAACCCCTGAGGCCTGAGCTGCCCGCCTGCGGTAGAAAGTACAGGATAGAAAGTGCTAGAAAGATTAAGAACCAGACGCACCAAACCACCTTGTCCTCTGTCATAACTGGGCCAGAAGGAGATGTGGGAAGGGCATAACAGTTCTGTTATGAGGTGCATGTCCGTGTGTCCCAAGGTCCTCTTGGGTACCACCCGTGGTGTGTGACCTGCCCTGTGGGACCCCTGATCCAGTTCAGCCCCTCATTTTACAGATGAGGAGGCTGAACCCCAGAGAAAGTGACCTCTCCAGGTCATGCAGCCACTTAGAGGCGGGGGGTGGGGGCATCCAGAGCCTGACTTGCGGCCCCTGCCCCACCTCCTGCACCTCTTGCAATGGCCAGGCTCGCCTACGACGTCAGCATGTCCCGAGCTGGCCTCTCCCATCTGTCCCCAGAGTCCCCCGCCCCTCCCCGCCCCCTGCAGCGGAAGCTTGTGACGGGTGCGGTGCTGTGACCCACGGGCAGGGGCTTGGGCGCTGCAAGGGGCGGTGCACCAGCCGCCTCCACGCTGGGCAGCCTCCCTGAGACCTTCTCTCGCCCCCGCTGTTTTCAG
Seq C2 exon
CACCCCCCACCATCTGGGGCTCCAACGAGACGAGCGAGGTGGCCGTCATGGAGGGCCACCCCGTGTGGTTCCTGTGCGAGGCCCGAGGGGTGCCCACGCCCGACATCACCTGGTTCAAGGATGGTGACCCCCTGGTCCCCAGCACTGAGGTGGTCTACACCAGAGGCGGCCGGCAGCTGCAGCTGGAGCGAGCCCAGGGCTCAGATGCTGGCACCTACAGCTGCAAGGCCAGCAATGCTGTGGGGGTTGTGGAGAAGACCACCCGGCTGGAGGTTTACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000002319:ENSBTAT00000007111:30
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.075 A=NA C2=0.096
Domain overlap (PFAM):
C1:
PF0767911=I-set=PD(58.1=94.3)
A:
NA
C2:
PF0767911=I-set=WD(100=90.4),PF139271=Ig_3=PU(3.6=3.2)
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:
ATCACCAACAGTCACCTGGGA
R:
TCTTCTCCACAACCCCCACAG
Band lengths:
355-1301
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development