BtaINT0072646 @ bosTau6
Intron Retention
Gene
ENSBTAG00000002319 | HMCN2
Description
hemicentin 2 [Source:HGNC Symbol;Acc:HGNC:21293]
Coordinates
chr11:100776163-100777880:+
Coord C1 exon
chr11:100776163-100776289
Coord A exon
chr11:100776290-100777496
Coord C2 exon
chr11:100777497-100777880
Length
1207 bp
Sequences
Splice sites
5' ss Seq
CGGGTAAGG
5' ss Score
10.17
3' ss Seq
TCGGTCTGTCTGTCCCGCAGGAC
3' ss Score
11.31
Exon sequences
Seq C1 exon
ACATCAACGAGTGTGAGGAGGACGGCATCGAGTGTGGGCCCAGCCAGATGTGCTTCAACACCCGTGGCAGCTACCAGTGTGTGGACACGCCGTGTCCCGCCACCTACCGGCAGGGCTCCAGCCCCGG
Seq A exon
GTAAGGGCTGAGCTGGTTGGGGGTTGGGGGGTGGGGGCAGATGGTCTGCCAAGAGCTGGGCAGCGGGACACTCTGGCTCCTGGAGAGCCCGACTCCTCCTTCTCCAGGAAGGCCCTGTCTCGGGCCAGAGGCCCTCGAAGGGCCAGAGGGTCAACCCTGCCAGAACTCCTGGGCGGGGCTCCTGAGCTCAAGGGCAACATGCCATCAAGGAAAGCACTTTTCCTGCAGCTATTTGGGATGTGAACTCACTTGAACGGTTATCGTTTCCTGCACAGCGCTGCAACCGCTAAGCGCGGAGCGCAGGGAGAGGCCAGAGCCGGGAGACAACTGGGAGGCAGGGGTGCTGGGGGATGGACACACAGGGACACATGGGAACACGTGAGTCCATTCAGGAAAGCGGACACAGGAACACACGCGCAGGCGCATAAACTCCACCCAGAACCACAGGCAAAACCTGAGGACTCACACACAGCCACACAAACACAAAACACATTTCCTCCAGGTCTCTCACTGTGGCTACAGATACTCATAAAGATGCACAGACGAAGGGACCTTGGCTGGCAAGAGATGCAGCTGTCAGGGCAAGGATTTTGGGTGGCGACCTGCCGGGGGCTCTATTAATCACGAAGCCTAGGCTGAGGCTTGGAGCCGGTGGTGGGGGGAGGGGGGCACCCTTGGCAAGGTTGAACCCCCTTGGTGGTGGTGATGGTTTAGTTGCTAAGTCGTGTCCAACTCCTTGCGAGCCCATGGACCGTAGCCCACCAGGCTCCTCTGTCCATGGGTTTCTCTAGACAAGAATACTGGAGTGGGTTGCCATTTTCTTCTCCAGGGGATATTCCCCAGCCAGGGATCAAACCCTGGTCTCCCGCATTGCGGGCAGGTTCTTTACCAACTGAGCTACAAGAGAAGCCCCCCTTACCCTGCTGCAAATCCAAAGCCAGTTCTGGGGTTCCGGAGTGCCTAGAGGGCTTATCACTGATGGGGGACCTGTTCGGGTGGGAAAGGGCAGGTCTCTGGCTTCCTGAGGCCTCAGTTTGCTGCTCTGTAAAATGGGCTGACAGTGACGCTTGTAGAGGCATGGGGCGCGCGAGGTGGTGGTCGGGCAGCTCACAGCTGAACTGCGGGAGTTGGGGGTGGAGTCTGCTTTATGCAGGCGGCCGGGCACGCGGATGGCAAACCGGAGTCGGTCGGTCTGTCTGTCCCGCAG
Seq C2 exon
GACGTGCTTCCGGCGCTGCTCACAGGACTGCAGTTCAGGCGGCCCCTCCACGCTGCAGTACAAGCTGCTGCCGCTGCCCCTGGGCGTGCGCGCCCTCCACGACGTGGCCCGCCTGGCCGCCTTCTCCGAGGCCGGCATCCCCGCCAACCGCACGGAGCTCAGCGTGCTCGAGCCCGACCCGCGCAGCCCCTTCGCGCTGCGCCCGCTGCGCGCCGGACATGGCGCCATCTACACCCGCCGCGCGCTCACCCGCGCCGGCCTCTACCGGCTCACCGTGCGCGCCGCAGCGCCGCGCCACCAGAGCGTCTTCGTCCTGCTCATCGCCGTGTCCCCCTACCCCTACTGAGGGCCGCGGGCAGGGGCAGCGACCTCCGGGGATGGGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000002319:ENSBTAT00000007111:99
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.017
Domain overlap (PFAM):
C1:
PF126622=cEGF=PD(12.5=7.0)
A:
NA
C2:
NO
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:
TCAACGAGTGTGAGGAGGACG
R:
GTGTAGATGGCGCCATGTCC
Band lengths:
358-1565
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development