BtaINT0072622 @ bosTau6
Intron Retention
Gene
ENSBTAG00000002319 | HMCN2
Description
hemicentin 2 [Source:HGNC Symbol;Acc:HGNC:21293]
Coordinates
chr11:100748712-100749816:+
Coord C1 exon
chr11:100748712-100748868
Coord A exon
chr11:100748869-100749694
Coord C2 exon
chr11:100749695-100749816
Length
826 bp
Sequences
Splice sites
5' ss Seq
CAGGTGCTG
5' ss Score
4.87
3' ss Seq
CTGTCTGTCTGTCCTTCCAGACT
3' ss Score
11.43
Exon sequences
Seq C1 exon
AGCCTCCAGCCATCGCCCCCGGCCCCTCCAACCTGACCCTGACTGCTTACACCCCAGCCTCACTGCCCTGTGAGGCCAGTGGCTCCCCCAAGCCCCTCGTGGCCTGGTGGAAGGACGGACAGAAGCTGGACTTCCGCCTGCAGCAGGGCGCCTACAG
Seq A exon
GTGCTGAGCCGGTCCTTCCAGGGACTTTGTGAGATCCTCAGGGTGGAAGAGGGCTTGCCCATCTCACAGACGGGGAGCTGGGTCAGAACTGAGGTAGGGACTTGCTTGGGTCAGAACCGAGGTAGGGACGTGCTTGGGTCTCACTCACCAAAGCCAGCACCAGAACTTTTGTGTCCGGACCTCAGGGGGCAAGGAGGTCTTTACAGGAGATGCTCGGTAGGAGGTGGGGGCATTGGGGACATACAGCCAAATGGGGAATATATGGCCTTTGAAACCACTTCAGTCACTATTTCAAAACCCACCTAGAAGCTTAAGTTCATGCTGGCTGAGACTGAACCCGTATAGTGCCTGTAGCAGCCTTGGTCTCCCTGTTTCTCAAGTGTGATCCTGAACAGATCCCTGGGAGGATTGAGGGAGCCGGTTCAGCAGTGAATTCACCAGGTGTTTCTTGTATTAGGTGCCGGGTCATGTGGAGCTTTGTGATGAAACAGGCGTTCAGTGGACACAAGCAGTTCTAATCAGGGCTTTGGATGTGGTTGTATTGCAGAAGTTATCCTAGGTGGTGACTTTAGAAAACGTTCTCGAGTTATGGAGAAACCCAGGCGCAGACATTAAAACGCCCACAAACTCAACAGCTAGACCTTAGAAGGTGGAAAATTCTAGGAGAAACTTTTTGAGTCGGCACTGGGGGCCAAAGACGGGAAGGGGGAACAGTCTGGAGACACATGCCCTGCCTCCAAGTTCCCCAGGCGGGGAAGCCATGGCGGCTGGTTTCAGGTCAGCCAAGCCAGTCACTTAGCAGGTGACTGTCTGTCTGTCCTTCCAG
Seq C2 exon
ACTCCTGCCCTCCAATGCCTTGCTCCTTGAAGAGCCCAGCCCCCAGGACTCAGCCCTGTTTGAGTGTGTGGTGAGCAATGGAGTGGGCGAGGCCCGCAAGCTCTACTGGGTGACGGTTCATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000002319:ENSBTAT00000007111:77
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=0.000
Domain overlap (PFAM):
C1:
PF138951=Ig_2=PU(55.3=98.1)
A:
NA
C2:
PF138951=Ig_2=FE(43.6=100)
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
Mouse
(mm9)
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:
CCTCCAACCTGACCCTGACTG
R:
CATGAACCGTCACCCAGTAGA
Band lengths:
255-1081
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development