BtaINT0072537 @ bosTau6
Intron Retention
Gene
ENSBTAG00000015235 | HMCN1
Description
Bos taurus hemicentin 1 (HMCN1), mRNA. [Source:RefSeq mRNA;Acc:NM_001192537]
Coordinates
chr16:68672447-68673461:+
Coord C1 exon
chr16:68672447-68672716
Coord A exon
chr16:68672717-68673290
Coord C2 exon
chr16:68673291-68673461
Length
574 bp
Sequences
Splice sites
5' ss Seq
AGGGTGAGT
5' ss Score
9.25
3' ss Seq
GTACGGTGTTTTATTTGCAGTGC
3' ss Score
7.56
Exon sequences
Seq C1 exon
GTACTCCTATTATCACTCTTGAACCAGTAGAAACTATTATTAATGCTGGCAGCAAAGTCATCTTGAATTGTCAAGCAACTGGAGAGCCTCGTCCAACCATTACATGGTCCCGTCAAGGGCACTCTATCCTCTGGGATGAGAGAATTAATGTGTTGTCCAATAACTCATTACATATTGCTGCTGCTCAGAAAGAAGATACGTCTGAGTATGAATGCGTTGCTCGAAACTTGATGGGTTCTGTCCTTGTGAGAGTGCCTGTCATAGTCCAGG
Seq A exon
GTGAGTGTGATATTCGTTTACCCTGATATATTCTTATTAAACAGTACCTGGGGCAATCTAAACAATAAAAATCATTAAGCATCTTAGACCACAGCTCTTGTACCCTTAAGATACTTCTAGATTATAGGGATAGGACAAAAATCACATTACAAACTGATGAGATTAAAAACAGTACAGATGAGAGCTGCAGAATACCAAGTTAATAATTCAAAATCCCAAATGGAATTTTGTTTTTAAAACTTGGTTAAAATTATTCTCAAAAATCAGTGGATAGTTTTGCTTCAAAGAATGATTTATTTCCAAAAGGTAAACAGCATATAAATGTCTTCATCGCTCACTCTTTCAACAGCCATGCCCAAATGAGTCAGGACTGGAACCAGGAAGAAACTCTAGTTAACCGCTCAGTTCTTCTTGGATGCTTCGGTTTTAATTTTACACGGAAGAAGAGCTTCCATAAACAATGTCTCAGCCTTTCTAGGTTCAGCGCTAGACCCAGTGCATATCTTCCATGAGATCTGACTTACAGTGTTGGTGTTTACAATAACGGAGACCAAGTACGGTGTTTTATTTGCAG
Seq C2 exon
TGCCCGGTGGCTTTTCCCAGTGGTCGGCCTGGAGACCCTGCAGTGCCACCTGTGGAAAGGGGATCCAGAAGAGGAGTCGTCTGTGCAACAACCCCTCTCCAGCCAACGGGGGGAAGCCTTGCCAGGGATCAGATTCAGAAATGCAAAACTGTCACCAGAAGCCATGTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000015235:ENSBTAT00000061144:88
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.044 A=NA C2=0.069
Domain overlap (PFAM):
C1:
PF0767911=I-set=WD(100=95.6)
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
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGCCTCGTCCAACCATTACA
R:
CTGGACATGGCTTCTGGTGAC
Band lengths:
358-932
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development