BtaINT0072447 @ bosTau6
Intron Retention
Gene
ENSBTAG00000015235 | HMCN1
Description
Bos taurus hemicentin 1 (HMCN1), mRNA. [Source:RefSeq mRNA;Acc:NM_001192537]
Coordinates
chr16:68697823-68698979:+
Coord C1 exon
chr16:68697823-68697942
Coord A exon
chr16:68697943-68698844
Coord C2 exon
chr16:68698845-68698979
Length
902 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGTT
5' ss Score
6.44
3' ss Seq
AATGAATCACTTTGTTGCAGATA
3' ss Score
6.33
Exon sequences
Seq C1 exon
ATGAAAATGAATGTGCCGCAGGGAATCCCTGCTCTCATTCCTGTCACAATGCCATGGGAACCTATTATTGCTCCTGCCCTAAAGGCCTCACCATAGCTGCCGATGGAAGAACTTGTCAAG
Seq A exon
GTAGTTACATGGCTAAATCTAATCAACACATTTAAGCAATGGGCATGGCAATCTCCGACCTAGGGAAAGCATGGAAGACCAAGGCTCTTCTTTACTACTCTTTCTGAGTCTGCCTTCATTAAGTTGAAAAAGTAAGGCAGAGAGAAGACTGCTCACACACTGCCTTCATATGGGGCACTCTGTGGGTAGGGATGCCTCTAATGATTCACTCAATCCCCACAACACAATGATGAGAGGCAGGCAGGCCTATTACCATGTACATTTTACAGGGATAACACCAAGGAAAAATAAGGTTATAAAGAATTTAAGTGAACTGCACAATCCCAGTAGGACTTTAGGAACATTAAAAAAAAAATCACACATTTCTATCAGATTCTAGGTATGCTTCTAAGTTAGAAATTGTATAGGAGCCTAATTTGTAAATAAAAAATGAAAAGAAGAAAGGATTTCTCCCTCTATGCCCAAGGAGGCCTCCGTCTAAATACAAAAGAGAGAGGGAATAAGGACATAAGAGGGCATAGGAATAACTTCTATGGGAATGTCCAGTATGGATTGAGCACTTTGTATACATTATTCCCTTTAAGTTTTAAAGCAGTACTGAGAGACAGATATTATCCTCATTTTACAAATGAGAACTCAGATGTTAGAAAGAAGTACCTTTTTTCAGTCACCTAATTTATAAGTGGTCTGATGGATGGCTTGGTCTTTGAAGATACACACTGTCCTGCTATGAGCTTGTCAGCTCTTTAACCCATCTGAAGGGGCCTACCCCCAAATTCAACATTCTTGCTCTTGTGTATTTCAAGTGTCACTCATTGCTTTCCTTATTCTTATTTCACAGCAGGTTCTTAAGTTGGGTTTTTTCCCCACTCTCCTTAGTTAAATGAATCACTTTGTTGCAG
Seq C2 exon
ATATTGATGAGTGTGCTTTGGGTGGCTACACCTGCCATGCTGGTCAGGACTGTGATAATACCATCGGATCCTATCGCTGTGTAGTCCACTGTGGAATTGGCTTTCGAAGAACCAGTGATGGCCTGAGTTGTCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000015235:ENSBTAT00000061144:100
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:
PF146701=FXa_inhibition=PD(92.7=92.7),PF0764510=EGF_CA=PU(0.1=0.0)
A:
NA
C2:
PF0764510=EGF_CA=WD(100=95.7)
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:
ATGAAAATGAATGTGCCGCAG
R:
TTGACAACTCAGGCCATCACTG
Band lengths:
254-1156
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development