BtaINT0072538 @ bosTau6
Intron Retention
Gene
ENSBTAG00000015235 | HMCN1
Description
Bos taurus hemicentin 1 (HMCN1), mRNA. [Source:RefSeq mRNA;Acc:NM_001192537]
Coordinates
chr16:68673291-68673767:+
Coord C1 exon
chr16:68673291-68673461
Coord A exon
chr16:68673462-68673596
Coord C2 exon
chr16:68673597-68673767
Length
135 bp
Sequences
Splice sites
5' ss Seq
CAGGTACAC
5' ss Score
7.29
3' ss Seq
AACGTGTCGCCTTTGGATAGTGG
3' ss Score
3.28
Exon sequences
Seq C1 exon
TGCCCGGTGGCTTTTCCCAGTGGTCGGCCTGGAGACCCTGCAGTGCCACCTGTGGAAAGGGGATCCAGAAGAGGAGTCGTCTGTGCAACAACCCCTCTCCAGCCAACGGGGGGAAGCCTTGCCAGGGATCAGATTCAGAAATGCAAAACTGTCACCAGAAGCCATGTCCAG
Seq A exon
GTACACCTCTTTATTCAACAGACAGGCACGTGGTTCAGTAGGTACCCTCTTCTGTCCCCCAAGTCTGGCTTGTCTCAGTATAAGTTCTTTCTACTGAAATGTCTCTGATCGTGTTAACGTGTCGCCTTTGGATAG
Seq C2 exon
TGGACGGGAACTGGTCAGAATGGAGTCCCTGGGAAGAATGCACGAGGAGCTGTGGACGCGGCAACCGAACCAGGACCAGAACTTGCAATAATCCATCAGCTCAACACGGTGGGCGACCGTGTGAAGGGACTGCCATGGAAATCATCATGTGCAACATTCGGCCTTGCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000015235:ENSBTAT00000061144:89
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.069 A=NA C2=0.034
Domain overlap (PFAM):
C1:
PF0009014=TSP_1=WD(100=87.9)
A:
NA
C2:
PF0009014=TSP_1=WD(100=87.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTCTGTGCAACAACCCCTCTC
R:
AGGCCGAATGTTGCACATGAT
Band lengths:
257-392
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development