BtaINT0072546 @ bosTau6
Intron Retention
Gene
ENSBTAG00000015235 | HMCN1
Description
Bos taurus hemicentin 1 (HMCN1), mRNA. [Source:RefSeq mRNA;Acc:NM_001192537]
Coordinates
chr16:68688708-68690292:+
Coord C1 exon
chr16:68688708-68688845
Coord A exon
chr16:68688846-68690170
Coord C2 exon
chr16:68690171-68690292
Length
1325 bp
Sequences
Splice sites
5' ss Seq
CTGGTTCGT
5' ss Score
5.4
3' ss Seq
GAATAAATTTTAATTCCTAGGAG
3' ss Score
6.34
Exon sequences
Seq C1 exon
GTCCAGCAATGAGAAAGATAGTTTCTATTCTAAATCCCATTTATTGGACAACAGCAAAAGAAATAGGAGAAGCAGTCAATGGCTTTACCCTCACCAATGCAGTTTTCAAGAGAGAAACCCAAGTGGAATTTGCAACTG
Seq A exon
GTTCGTATCAACTGAACTTAATATCCTATTGCTATTTAAAAATATGATCGCTGTAAAAGTTGGAAGTTTAGAAAAATACATTATATGTTCCCACAGAGGATAATTTCAAAGTTTTGTTGCCGTCTTATCATAAATGACATAAAAGCTAGTTTATATTTTCCTATAAACTTTTACTGACATGGCTCTATAAGAGGCCATATGTTTTCAGATACTATAGTGATTTTTATAACCTAAAAGTTTTTTTCCCTTCATCTTTCCTGTATCTGTTCTCTTTAATTCCTTAGAGAGGGTTTTGAAGGCCAAGCAGAGCAGGAAGCTGAGTCATAGCTATTAATTAAAGGTTTTTGTCTTTGAACCAGAGATTCAGTTATGATATCTGATAGGGATTCTTTAATCAAAAAATTGGAAATATAAACAAGCAAATCTAAAGACTTTTCACTTTATCCCTAGCCTTAATGCATATGGATTAGCAATTCATGGTCTTTTCCAAGGGCAGATGACTTTTTAAAGACCTTCATATGAAGTATCTTTGAAGGTGGTCCGCCTTTGCAGCAGTGATCTTTAAGGTAGCGGGGCTGACGAAAACCATAGCTTTAATCAGCCCACAAGACGTGTGGGTCTTTGTATGGCAATCCACTTCCTAAGATGCCCCTTTGCTGTTTCTAAAAGCACCAGAAAGAACAAAGCGCTGGAGCCAGACTTGTGGCTCTTGTGGCTCAGACTCGTGACCAGTCTTCCTGGTCGCGCTGTCTGTCCCCTTCTCACAGGCAATCCGTCCATTTCTGTAGAACTGCCTTGCTATTGCTTGTCAGTTGACAGTGTGGATTCCTTCACCTAATTATAGGTGTAATCAGGTGAAATTTTTGTAAAAAATGTAAAAAAAGGAATTTTAAAATCAATTTAATTAAGTTTAATTTGGGGGCTAAGTGCTATTTTCTCTTATGATTTGTGTTTAATCAAGTTTGAAGTACAATAACATAGCTGAACTGGTATAAAAATAAGTCTGTAATGTGCTTACACAAACCATATTTTATAAACACACACACATATATGCATGTGTGCATGCTCAGTTGTATCCGGCTCTTTGTGACCCCATGGACTGTAGCCCGCCAGGCTCCTCCGTCCATGGAGTTTTCCAGGCAAGAATACTGGAGTGGGTTGTCATTTCCTTCTCCAGGGTATCTTCCTGACCCAGGGATCGAACCTGCACCTCCTGCATTGGCAGGTGGATTTTTTACTACTGGGAAGTGTATCTGTATATATACATACACACACACGTATATGTAATACATCTGCTGTTGAAATGAATAAATTTTAATTCCTAG
Seq C2 exon
GAGAAATCTTGCGGATGACTCACGTTGCCCGGGGCTTGGATTCTGATGGTGCTCTGCTGGTAGATATCATCGTGAGTGGCTATGTCCTGCAGCTACAGTCACCTGCCGAAGTCACCGTAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000015235:ENSBTAT00000061144:96
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:
PF074747=G2F=FE(24.5=100)
A:
NA
C2:
PF074747=G2F=FE(21.3=100)
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:
GTCCAGCAATGAGAAAGATAGTTT
R:
CTTTACGGTGACTTCGGCAGG
Band lengths:
260-1585
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development