BtaINT0072644 @ bosTau6
Intron Retention
Gene
ENSBTAG00000002319 | HMCN2
Description
hemicentin 2 [Source:HGNC Symbol;Acc:HGNC:21293]
Coordinates
chr11:100773787-100775360:+
Coord C1 exon
chr11:100773787-100774113
Coord A exon
chr11:100774114-100775240
Coord C2 exon
chr11:100775241-100775360
Length
1127 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGA
5' ss Score
10.77
3' ss Seq
CTACCCTGCCCCGGGGCCAGACC
3' ss Score
3.74
Exon sequences
Seq C1 exon
ATATCAACGAGTGCCTGCAGCTGCCCGGGCCCTGTGCCTACCAGTGCCACAACCTCCAGGGCGGCTACCGCTGCCTGTGCCCGCCGGGCCAGACTCTCCTCCGCGATGGCAAGACTTGCACCCCACTGGAGCGCAGTGGACCAAACGTGACCACCGTCAGCCACGTCAGCCACCGGGACCCCCTGGTGGCCTGGCTGCAGGCCCGTGGCCCCAAGCCCAGAGGGTCCTACCACGCCTGGGTCTCCCTCCGACCGGGCCCCAGAGCCCTGAGCATGGGCCGGGCCTGGTGCCCGCCCGGCTTCATCCGGCAGAACGGCGTCTGCACAG
Seq A exon
GTAAGAATGAACCCGGCGGGACACACCCCGCTGTGCTGACTCAGGCCCCCGGGCTGGGCGTGTGGGCACCACGCCCGTGTTCAGAAACCCAGGGTGCAGGCAAGTAGGATGGCGATGCAGGCAGACGGCTGCCTCCTCACTACATGGTTTCTCGGAACCCCGGCTGTGCCAGTGGGCAGGGGGCTTCCAAAGTGGGTGGAGTGTTTTCCAAACCGTTGACTGCAGGACTTCTTTACCGCTTGTGGCTCAGCCGGTAAAGAATCTGCCTGCAATATAGGAGACCTGGGTTCGACCCCTGGGTTGGGAAGATCCCCTGGAGAAGGGAAAGGCTACCCACTCCAGTATTCCAGCCTGGAGAATTTCTATACAGTCCATGGGGTCGCAAAGAGTCAGACACGACTGAGTGACTTTCACGTTCGCATTACCCAGAGGGAAGGCAAGTGTTCCCAGGAACCCACTTGGAGGAACTCTCCTCCGGTGCGCAGAGGTGAAGCGGTCAGGGAGGGAAGGAGAATGGTCCAGGTTGACCTGAGAAGGTCAACAGGGACTGGGGAGTGCTACAGAGTCATGCGGGTCGAGGGCCCTTGTGTGGAGGCAGGTTGGCGCTGGGCTGCAGACAGGGGAAGGCATAGAAGGCAGGTGTATTTCAGCATCACTGCCTGGACAGAACCGTCTGTCCTGGGAGCGCTATCTGCCCCCGACACCCACCCCATGGCTTGGTGCACATGGAGCCCAGGGACTCTCCCAACCTCCCCATCCAGGGTTGGGTGGGGCATGAAAGTGAAGTCGCTTAGTCATGTCCGACTCTTTGGAATCCCATGGACTGTAGTCTACCAGGCTCCTCCATCCATGGGACTTTCCAGGCAAGAATACTGGAGTAGGTTGCCATTTCCTTCTCCAGGAGATCTTCTGGACCCAGGGACTGAACCTGGGTCTCCCGCACTGTAAGCGGACGCTTTACTGTCTGGGCCACCAGGAAAGGGGCATGGCAGGGAGAAATCCCTGGTGCCTAAGCAGGGGATCTCCCTGACTTGTCCCGAGCCTGGCGATGGGCAGGCGTGCGGCCACCTGGGCATTTGTGACTCAGTGTTTCTCTGCTCGCAACCCCTACCCTGCCCCGGGGCCAG
Seq C2 exon
ACCTGGACGAGTGCCGCGTGAGAAACCTGTGCCAACATGCCTGCCGAAACACAGAGGGCAGCTACCAGTGCCTCTGCCCTGCAGGCTACCGCCTCCTCCCCAGCGGGAAGAACTGCCAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000002319:ENSBTAT00000007111:97
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.055 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0764510=EGF_CA=WD(100=36.4)
A:
NA
C2:
PF126622=cEGF=PU(83.3=48.8)
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:
TACCAGTGCCACAACCTCCAG
R:
GGTAGCTGCCCTCTGTGTTTC
Band lengths:
355-1482
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development