BtaINT0072549 @ bosTau6
Intron Retention
Gene
ENSBTAG00000015235 | HMCN1
Description
Bos taurus hemicentin 1 (HMCN1), mRNA. [Source:RefSeq mRNA;Acc:NM_001192537]
Coordinates
chr16:68696744-68697942:+
Coord C1 exon
chr16:68696744-68696806
Coord A exon
chr16:68696807-68697822
Coord C2 exon
chr16:68697823-68697942
Length
1016 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGT
5' ss Score
10.65
3' ss Seq
GGTCTTGTTTCTTCTTCCAGATG
3' ss Score
10.11
Exon sequences
Seq C1 exon
GAGAACGCAGTAATCAGTGTCCCCCTGGGTTTGCCTTAGACTCGGTTGGACCCTTTTGTGCTG
Seq A exon
GTAAGTACAACAATAAATGATGCATTTTTGTTTTTCATAATCTGTTCATGCTATCATTAACGGACAGTTACTGTCATTTTGATCGATATTTATTAATCACAATAGTCCTCTAACTGTCTCTTTTTACAGGTGAGGAAATTGAGATGTGAAGAAGTTGAGTGCCTAAGTTCACTCAGCTATCAGATGGCAGAGCTAGATTTGAATTTGAGATAGATGCAAAGCCCATGCTGTTTCAGTTAGTTCCACAATCAAGTGTGCCAGGAATCATGATCAAGTCCAGGGATAGACTGAACACAGGAACCAAACACTGGACTGTGTTTGGCCACCTGATTGCACAAATGTGAAACAGCAGTAATTCAAGTCTAAGTCACCTAACCCTAGAATTGCCCAGCTGTAGCAGAGGGCTGGATTGTGGGTGGAGGACTGATGACTAAACCTGCCCTGTGCCATCCATGTGCCAGCGCAGGAGAGTCACAGATAAGTAAACAGCTAAATAAATGGCTAGAGGAGCCCAAACTGGCATACACAGTGCTTTTCTTTTGGCTGGTGTGCAATGAAACATCATACAGTGATAAAAAGGTCGTCTTTAGAAACTGTACTGCCCAGGTTCAAATCCCAGCTCTGCCGATAATGACCTAGGTGACCTTCAGCAATTTAGTTAACCTCTTTGTTCCTCAGTTTTAGCATGCAAATGAGAATAGGAATAAAAATACTTATCTCCTAGAATGTTGAGATGAGTTACCTTAGGTATAATAAAAAGCATTTCCATCACAGTAAATGGTCATTATGTCTCAGCTTTCATCATTGTTGTTTTAAAATTAATGCCACCACTGTCAGAGATAATGTGAGGACCCAAAAGTAATTTCATTTTGTGTTTCTATTCTGTGGCATATGGAGCATTTTCTGTTACACTGGATCCGTTCATTGGCCTCTACAGGCAACTCTTTCCACCCACTTTAATAGCTCCTTGAAAGTAGGGCTTCTCCATACTAATTGGGTCTTGTTTCTTCTTCCAG
Seq C2 exon
ATGAAAATGAATGTGCCGCAGGGAATCCCTGCTCTCATTCCTGTCACAATGCCATGGGAACCTATTATTGCTCCTGCCCTAAAGGCCTCACCATAGCTGCCGATGGAAGAACTTGTCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000015235:ENSBTAT00000061144:99
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=PU(4.9=9.1)
A:
NA
C2:
PF146701=FXa_inhibition=PD(92.7=92.7),PF0764510=EGF_CA=PU(0.1=0.0)
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:
GAGAACGCAGTAATCAGTGTCCC
R:
TTGACAAGTTCTTCCATCGGCA
Band lengths:
182-1198
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development