BtaINT0072483 @ bosTau6
Intron Retention
Gene
ENSBTAG00000015235 | HMCN1
Description
Bos taurus hemicentin 1 (HMCN1), mRNA. [Source:RefSeq mRNA;Acc:NM_001192537]
Coordinates
chr16:68540894-68541751:+
Coord C1 exon
chr16:68540894-68541070
Coord A exon
chr16:68541071-68541599
Coord C2 exon
chr16:68541600-68541751
Length
529 bp
Sequences
Splice sites
5' ss Seq
ATGGTTAGT
5' ss Score
7.07
3' ss Seq
ACTTTTTTGTTCCTTTCCAGTGC
3' ss Score
11.34
Exon sequences
Seq C1 exon
CTATTACATGGTACAAAGATAATCGTCCACTATCAGATTCCAGTAGTGTGACTTTCTTGAACAGAGGACAGATCATCAATATTGAAAGTGCCCAGATCACAGATGCTGGCATATATAAATGTGTGGCCATCAACTCAGCTGGAGCAACCGAGCTGTTTTACAGTCTGCAGGTCCATG
Seq A exon
GTTAGTGCCACTACTTGATTGATCCAGGGTAAAGCAGCATTCAAAACGGTCAAGTGCATCTAGAAAATTCTAGTGTTGATTTTTAACAGAGTGTGTTATTGTCATCTTTATTTAAGGATGCAGTGTTCTAAAACTGATGTGTTTGCATTTTTGATTCCTATTAAATGCTCTGTTTTCACATGCTATTGGACTTGTTTGCTTTAGATGAATTGTTCAGAATAGTCATCAACTGTCTTATCAGCTAATGACAGTAGCCCTGTTTGTCAATATTGTCTATCAGAATCATAGGTTCAGGAAATGTTTTCAAGTTGTTTTCTCTAATAGTGCTTTTAAGAGGAGTTCGTAGTTAACGTACTAGCGTGCATACAGTGGAGGGAAACACGCGTACACACACAAACCTGGAAGGCAAGAAATAAGAAATATAAAACACATTACTATGGACAGAACACATAGTTGTTATTATTCTGAGATGAAATATTCTGCGATGTTAGCATGCCTTACTTCTGTTTACTTTTTTGTTCCTTTCCAG
Seq C2 exon
TGCCCCCATCGATTTTTGGCAGCAATAACATGGTGGCAGTGGTGGTTAATAACCTGGTGAGGTTAGAGTGTGAAGCCAGAGGTATCCCGGCCCCAAGTCTGACCTGGCTGAAAGATGGGAGCCCCGTCACGAGTTTCGTTAATGGGATACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000015235:ENSBTAT00000061144:39
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.033 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0767911=I-set=PD(67.9=95.0)
A:
NA
C2:
PF0767911=I-set=PU(53.9=94.1)
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:
TGGTACAAAGATAATCGTCCACT
R:
GAAACTCGTGACGGGGCTC
Band lengths:
306-835
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development