BtaINT0072460 @ bosTau6
Intron Retention
Gene
ENSBTAG00000015235 | HMCN1
Description
Bos taurus hemicentin 1 (HMCN1), mRNA. [Source:RefSeq mRNA;Acc:NM_001192537]
Coordinates
chr16:68470566-68471884:+
Coord C1 exon
chr16:68470566-68470661
Coord A exon
chr16:68470662-68471756
Coord C2 exon
chr16:68471757-68471884
Length
1095 bp
Sequences
Splice sites
5' ss Seq
TTGGTAAGA
5' ss Score
8.85
3' ss Seq
GTGTGTTCTCTCTGATTTAGTCG
3' ss Score
8.66
Exon sequences
Seq C1 exon
ACTTATGGGCAAGTGATAAAGGAACATACATTTGTGAAGCAGAAAACCAGTTTGGAAAGATCCAGTCCCAGACAACAGTAACAGTGACAGGACTTG
Seq A exon
GTAAGATCAATGAAGTACTTAGCACACTTTTTGCAAACATCAGGCTTCTCTTACTACCTCATCTCTTCCTTGTACCATTTGAAAAAAAAAAAAAGGTAAGTATCTGATTGCAACATTAGCTGTCCTTCCCTTCTACCCTATTTTGTATTTCCTTGATGTTAAAAGTGGAAATAACCTTAGAGATATCCGCTTTAAGCTCCTTACCTTGCACCTGAAGAAATGAAGCTCAGTTGAATAAATTAAGTCTGAGTGTACACACACACACACACACACACACACACAGGTGGTATTCTTTTCTAGTTCTTTTCTTTACACTTATCATTTTAGTCCACATGGAATGATTTCTGTGTGTGATATGAAGTAGGAATACCAAATCCTTTCTTTTCAAGTGGTAAGACTTTGGTACAGTATCTTTTATTGAATATTCTCTTCCCACTGATTAAAGTTCCCATTATCGAAGTCCCCATTTGGTCACACGCTTAAATTTATATTCGATGTCTGTTCATTGGAACAGCATGTACACATGCTTAAATTTTCCAAGAAGAATCTCTTAGGGCTTTTACTTTGGTTTTTACTTTACTAGGGCTTTTACTTTGACTCATGTTGAGTTTATTCATCAATTTCTAGAAAGGGATACGTTTACAAAGCCTCTGTGCCTTCTATCATTCTGTTTGCCTGAGCTGTTAGGACAGCCTCCTCCTAATCTCATCCCTTCTAATTGTCCCTTGTCCAATAAGTTCCCAGATGAATATTTGCTGATGATTCTACTTTTCTATTTATCGGTGCTTTCACTCACTCTCCATCTGTCTGTTGAATATTTTGCAAATTTCTTGGCTTGACTTTTCTGGCCTTTAAGCTGTAGACCTATTCTATGTAGCTTTCTTTACTTCTATACTATTACTTGTCCTCTTGCCAGTCTCTTTTGCTTAGAAGGGTCCTGTATCTCTATCTTCTAATTTGTGCATTTAAATATCTTGTTCTTGAAAACTCGGTTTTCTAATGGCTTCATTAGTAGTCATCTCGGTCTATAAAAGAATGGGCCTTTCTTTTGAGTGAAATAGGGCTGATGGCGGCTGTGTGTTCTCTCTGATTTAG
Seq C2 exon
TCGCTCCACTCATTGGAATCAGCCCCCCAGTGACCAGTGTAATTGAAGGACAGCAGCTTACTTTGCCTTGTGCTCTACTGGCTGGAAATCCTATTCCAGAACGTCGGTGGATTAAGAATTCAGCCATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000015235:ENSBTAT00000061144:18
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=0.000
Domain overlap (PFAM):
C1:
PF0767911=I-set=PD(30.4=84.8)
A:
NA
C2:
PF0767911=I-set=PU(45.5=93.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACTTATGGGCAAGTGATAAAGGAACA
R:
TGGCTGAATTCTTAATCCACCGA
Band lengths:
222-1317
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development