BtaINT0072582 @ bosTau6
Intron Retention
Gene
ENSBTAG00000002319 | HMCN2
Description
hemicentin 2 [Source:HGNC Symbol;Acc:HGNC:21293]
Coordinates
chr11:100705939-100707243:+
Coord C1 exon
chr11:100705939-100706115
Coord A exon
chr11:100706116-100707085
Coord C2 exon
chr11:100707086-100707243
Length
970 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGC
5' ss Score
8.27
3' ss Seq
GTGTCGCCCTCGCCCTGCAGTGC
3' ss Score
9.23
Exon sequences
Seq C1 exon
ATATCTCCTGGTTTAAGGGCCGCCAGCCTATCTCTGCCTGGGACAGAGCGATGGTGTCAACTGATGGGAGAGTCCTTCTCATTGAGCAAGCCCAGCTTTCTGATGCCGGGAGCTACCGCTGCGTGGCGTCCAATGTGGTGGGCAGCACAGAGCTGCAGTACAGCCTGCGGGTCAATG
Seq A exon
GTGAGCTGCTCAGGACTAAAGGCATCTGTCCCCAGAGTTGTTGTTCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTATCATTTATCCATCCATCCATTCATCTATCCATTCTTCCATCTACCCATGGAAACACCCAACTGTCCATCCATTGATTCAACCAACCATTTCAATTCTCTGCCCATCTAACCCACCCACCCATCTAACCATCCAGCTGTCCATCCCCCAACCGTTCTTCTGTTCAAACATCAATTCCTCCATCTGTCCATTTTCTATCCAACCACATTTATTGGGTATAGACACAACTCAGAGATATTGCAGTTTCGGTTCCAGACCACCACAATAAAGCAATACCAAAATAAAGCAAGTCACATGAGTTTTTTTTGGCTTCCCAGTGCATAGAAAAGTCCTATATACACTGTACTGTAGTCTGTTACATGTGCAATAGCACTGTGTCTAAAACATGGACATATCTTAATTAAAAAGGACTTATTGCTAAAAACTGCTATCATCTGAGCCTTGGGTGAGTCATAGTAACATCAAAGATCACTGATCACCCTAACAGGCATTCTCAACCCCTGTGACCCCTACACCATCAGCAATGATGATGACCTCACGGTAACCAGGAGGCCCAAGTTCAAGGGCTGCTTCTGCCAGCTCCTGGTGGGTCAACCTTGGGCAGGCCACTGGCCCTCTCTAAGCCTCAGTTTCCCATCTGTGGGGCCGGAAGGATGAAACAAGCAGCCTCGAGACCCGGGGCGTGCCCTGCCCGTGTTGGGAGTCGCTGTCCCTGAGCTTTCATCAGTGGCCATGCACTCCTGCGGGGGTGCCCGGCCAGGGGCCCTGCCCGCTTCACCCTCAGCGGGGTCAACCCGTGCCCTGTGTCGCCCTCGCCCTGCAG
Seq C2 exon
TGCCCCCGCGCATCACGCTGCCACCGAGCCTCCCGGGCCCCGTGCTGCTCCACAGCCCGGTGCGGCTGACCTGTGACGCCGCTGGGGCGCCCAGCCCCATGCTGATGTGGCTGAAGGATGGAAACCCCGTGTCCACTGCAGGGACCGCCGGTCTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000002319:ENSBTAT00000007111:40
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.019
Domain overlap (PFAM):
C1:
PF0767911=I-set=PD(64.8=95.0)
A:
NA
C2:
PF0767911=I-set=PU(52.3=84.9)
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:
ATCTCCTGGTTTAAGGGCCGC
R:
TCCCTGCAGTGGACACGG
Band lengths:
319-1289
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development