BtaINT0072454 @ bosTau6
Intron Retention
Gene
ENSBTAG00000015235 | HMCN1
Description
Bos taurus hemicentin 1 (HMCN1), mRNA. [Source:RefSeq mRNA;Acc:NM_001192537]
Coordinates
chr16:68731200-68733392:+
Coord C1 exon
chr16:68731200-68731326
Coord A exon
chr16:68731327-68732835
Coord C2 exon
chr16:68732836-68733392
Length
1509 bp
Sequences
Splice sites
5' ss Seq
AGGGTATGT
5' ss Score
8.34
3' ss Seq
CATGTGATTATTGTCCTTAGGTT
3' ss Score
8.86
Exon sequences
Seq C1 exon
ATATTGATGAGTGTCTGGAACAGAATGTGCGCTGTGGGCCGAATCGCATGTGCTTCAACATGAGAGGAAGCTACCGTTGCATTGAGACACCCTGTCCACCTGACTACCAACGGGATCCTGTGTCAGG
Seq A exon
GTATGTCTTGCTTTCTCTTCCCAGGCATGCTTTTGAAAATCCTCCTGCCTCTCTCTCCTTGACCAACAAGCCCTGTCTGCAGTCATGTTTCTCACTCACAGGAAGTCAGTAATCCCTCAGGGGCTAGGGGTTTACTGTGTGTTCCTTCTTCAGAGAGTGGGCAAACAAACGAATTCATCCTGCAGCAGCGATTGCCAGCTTTGAGCTGCCAGGGTTTCCTGGAACAAGTCTGCTCAGTGTGTAATGCACCAGGCAACATCTAGAATCCCTCCTCAGCAGGGAGCATTTTATAGGGTGATAGAGCCGACCCATCTTTGAAATTGTCTTTTCTGTTGGTGTTGCCTCAGGGTTTTCAGGGCTCTCTGCTTTTAGAGCACTGGCTCTAAGAGGTACCACGGCTGTTACAGTGATGAGTCATCATGACTCCATGGGAGTGTGGAGGAGACCAAGGATGAGTCAGTAGTCTGTCTGTTCATTCACATCTCATCTTGTTTACATATTCTGCTGTCTGAAACACTGTCTTTTCTGGTTTTGAATAAACTGCTTTGTTCTCTCCCTCCCCTTACAGAAACATTGCACTCCGTTTAGGTACCAAGTTGGGGGGGTGCTTGGAAAATGAGATAATGGCCATCGTGAATAGGCTCCACTAATAAGGAGGTAGTTCTGAAACCGAACTCTGGTTGGATCTCACTTTGTTTTCCTCTCAGTGGTGACTCCCATGTTACTGTAACATGGTCAAGTGTGCGCTGCCCAGGATTCATCCAAAACCTATTTGTAATCTGTCTGAGGGGAATAGGGAAGGGGAAGATAAAAATTACAGACTTATCAGACTTTTAAAAATACTTTGAGAATCTGTATCTTCAGAACATGGTCCTTTGTGCATTTTTTTGTTTTACTCTTTATTACCAGTGATTTGGGGCACACAAGTTCAAAGTCATGACGACTCAAACAACTGCTGTGGGCTCTGGAAAAAGAAAATATACTATTTTTAATCTAAAATGATGTGGAAAGCAAATACCGAAAAGAAAGTTGTTTTTTTTGGAGTTGTAATTGACCTTTTATTTATTTTTAGAAAAATAAACCAATATCAATATATTCTATTTCTGCTTTCAAATAGTCTTAGGGTAGATGTTAACATTTTAAAGTCATTTGTAGTCCTCTCCTTTAAGAAGTCCTTGTTTCCAATATATATGCAGATGTTTCTCTTTCCAAAACTGGCTTTTCACTTTAAAGATGTTCTGTGGTACTTTTTTCTGTGGTTCAAAAGCTTCTGATTTTAATGGAGCTGAGAGAAATATACGACTCTAGACCAGCACACTCTCATCGGCATCTGGCATCTGGTTTCAGTTAATAACACAGACCATGGGGTGAACCTTAGTATTTTGCAGTCAGACTGTCTCCTGCCTTTAATGCCCCCAAATTGTCATGGATCGTGATCACCTGCATCATGCCTTCTCCTGCTTCCAAGCCATGATAACTTTATATATTTCATGTGATTATTGTCCTTAG
Seq C2 exon
GTTCTGTCTCAAGAACTGTCCACCCAATGATTTGGAATGTGCCTTGAGTCCATATGCCTTGGAATACAAACTCGTCTCCCTCCCGTTTGGAATAGCTGCCAATCAAGATTTGATCCGGCTGGTTGCATACACTCAAGATGGAGTGATGCATCCCAGGACAACTTTCCTCATGATAGATGAGGAACAGACTGTTCCCTTTGCCTTAAGGGATGAAAACCTGAAAGGAGTGGTGTACACAATACGACCACTACAGGAACCAGAGACCTACCGCATGCGGGTTCGAGCCTTATCCTACGGTGCCAATGGGACCGTTGAGTATCAGACCACGTTCATAGTTTATATAGCTGTGTCTGCCTATCCGTACTAAGCAGCTCTCCCAAGCGTAAATCCACATAAGTAAGCCACATTTACCATGGGAATTAAGTTCCCTGAACAGTTGCAATCTTTGCAAGTTGAAAACGGTGCTGTGCTCTGTTTTGTGTGCCTTCCTTGGTAGTGTTGAGGTATTTTCATGATCCCACCATGGTCATATCTTTTGGTAAGATCTAGAAAGTCTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000015235:ENSBTAT00000061144:107
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF126622=cEGF=PD(12.5=7.0)
A:
NA
C2:
NO
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:
CGTTGCATTGAGACACCCTGT
R:
GATAAGGCTCGAACCCGCATG
Band lengths:
344-1853
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development