BtaINT0072449 @ bosTau6
Intron Retention
Gene
ENSBTAG00000015235 | HMCN1
Description
Bos taurus hemicentin 1 (HMCN1), mRNA. [Source:RefSeq mRNA;Acc:NM_001192537]
Coordinates
chr16:68708287-68709225:+
Coord C1 exon
chr16:68708287-68708400
Coord A exon
chr16:68708401-68709099
Coord C2 exon
chr16:68709100-68709225
Length
699 bp
Sequences
Splice sites
5' ss Seq
TGGGTAAGG
5' ss Score
9.08
3' ss Seq
ATCTTTGTTCTTTTATCGAGATA
3' ss Score
-2.9
Exon sequences
Seq C1 exon
ATATTAATGAATGTCAAGAATCCAGCCCCTGTCACCACCGCTGTTTCAATGCCATAGGAAGTTTTCACTGTGGATGTGAACCTGGGTATCAGCTCAAAGGCAGAAAATGTGTGG
Seq A exon
GTAAGGCAAGGGCTATGAATTCAAAGCATTGACACCTTTGTAATGTCTTAATGCTGTCTGATCTAATCTATGGGTTGTGTCTGATATAGGGCACCATTTATGTGATCTATGCAAAAACAAAAGGAAACAAATGTACAAGTTTCACTTTCCAATTTTAAAACCATTTTTAACATGTTCTCTATTATATTACCATTTTTTCACAAAACCATGATATATGTGTGTATATAGTTATATATGGGCTTCCCTGGTGGCTCAGACAATAAAGAATCTGCCTGCAATGTAGGAAACCCAGGTTCGATCCCTAGGTCTGGAAGATCTCTTGGAGAAGGGAATAGCTACCCACTCCAGTATTCTGCCTGGAGAATTCCATGGACAGAGAAGCCTGGTGGGCTATAGTTCACGAGGTCACGAAGAGCTGGACACAACTCAGCAATTAAATATACATATAATTTTTATTTTTCTAGGAGGGGGAAATGTTTTGGCATGGCTTCCATCTATGTGATGTAATATTTTTTATTTTTATCATTATGTTCTAAAATAAAGTGTGTTACATACCTTGATGGATTTAAACACTTCAACCTTATACCATGATTATATAATCATCTATATTATTTATCCTTAAAATCCAAAGGCATATTTTTATGAAAAAGTGGAAGAAATCACTTTCTCAATCTGCATTATCTTTGTTCTTTTATCGAG
Seq C2 exon
ATATAAATGAGTGTAGACAGAATGTATGCAGACCAGATCAGCATTGCAAGAACACTCGTGGTGGCTATAAATGCATTGATCTCTGTCCAAACGGAATGACCAAGGCAGAAAATGGAACCTGCATTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000015235:ENSBTAT00000061144:102
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:
PF126622=cEGF=PU(81.8=46.2)
A:
NA
C2:
PF126622=cEGF=PD(13.6=7.0),PF0764510=EGF_CA=PU(0.1=0.0)
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:
ATGAATGTCAAGAATCCAGCCCC
R:
GCAGGTTCCATTTTCTGCCTTG
Band lengths:
230-929
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development