BtaINT0072519 @ bosTau6
Intron Retention
Gene
ENSBTAG00000015235 | HMCN1
Description
Bos taurus hemicentin 1 (HMCN1), mRNA. [Source:RefSeq mRNA;Acc:NM_001192537]
Coordinates
chr16:68636463-68638238:+
Coord C1 exon
chr16:68636463-68636544
Coord A exon
chr16:68636545-68638101
Coord C2 exon
chr16:68638102-68638238
Length
1557 bp
Sequences
Splice sites
5' ss Seq
ATGGTAATG
5' ss Score
5.46
3' ss Seq
GTATTTGTTTTCCCATCCAGTAC
3' ss Score
8.17
Exon sequences
Seq C1 exon
GTGGAAGATACAGGAAGATACACATGTCTGGCATCCAGTCCTGCAGGAGATGATGATAAAGAGTATTTAGTGAGAGTGCATG
Seq A exon
GTAATGCTGGAAAATGTCCTGCAGTCCATCATACACTTATACCTAATTAAAAGGCATAATTTATGGAACATAGGGCAGCTATCCAACACATCATAAAACTATGTTTATATATTAGGAAATATGTATTTTGCAAATTTGATTTTTATATTTGACTGATCATGTGCTCATGGGACTAGTTTAATGGATTTTTGAGTTATATGTCTGTTCCTGCACAAGTAATTCATATAAATTTATTTTAAATCATAGAATATAAATTGGAGTAAAAATGAAAATAAAAAGTATTCATAATCTCATCTCACAGAATAAGACCTTTTTACATATAAATATTGTCACAGAAATGTGATCATGTGGCATATAGTATTTAACTCTTTATCTCAGTGGCATGTTGAACATGTTTTCATGTCAAAAAAATATATATTTTTATAACATTACTTTTAAGCGATTGCATGATTTCCAATTTTATGAACATGCCATTACTTAATACATTCCTTATTTTTGGCTGTTTCTATATTTTCACCAACTTAATAAGCAGCACTATTATAGACATTCTTGTATAAGTCTGTTGGCCTATTTTTAATTATTTTGTTTTAATAAATTTCTATAAGTCCACTTTCTTGATTATATGCAAGTATATGCATATGCATGTACATACACACACACACACACACATTCAAGACCAAATTACCTTCTAGAAAAGTTGGGCCAATTAGACTATGGCTGGTCCTACTTTGACATAGAGCTGGAAATTACTGTTCAAAGAGAGGAACATTTAAAGAACTTAACAGAAGATCTTTATCTCTTCGTAGCCTAAATCACTAAGCAATCCAAACTGTATGCCTGGTGTGATGTAGGAGTGTTCTCCTGCCCCCACCAGCCCCACACACAAATTAGACCAACTGACGTGTAAACTGTGTATACAGCAGTCACATAAAAAATATACACTTTTAAAATTGTGGTATAGTTGATTTACAATATTAGTTTCAGGTATACACCATAGTGATTGAAAATTTTTTAAAATTATACTCCACTTAAAATTATTATGAAATATTGACTCTGTTTCCTTCACTTTATATCCTTGTAGCTTATTTATTTTATATATAGTAGTATATACCTCTTAATTCCTTACCCCTCTTTTGCCCCCCTTTCTGCATATATTTCTGTTTGTTATGATGGACAGAACCTAATTTAAAAGTTTTAAAATATGTCCAGAGAAAATTATTACCAAGTGTAGACCTGGACAAAAAAAAAAAAAAAAATCCCTTCTTTGGGCCTTAGTTTCTTTACCTATTAAATGGTGATAAACTGTGGTTATATTACTTATCCTATCATTCATGTGGCTCTTAGAAGAATTTCGTTACTTAAGGTACTTAAGTACTGAGTACGATTTTAAAAGTTCACTATTTGTTACCAGGGTACTATAAATTGAATGAGTAGCATTTTAAATTAATGCTGCTGCTTTCATACAGCACAAAGAACACTGTTGAACACCTAAGATAAGCCAGAGCATTTTATATCTCATTTGTTAAAAGCCTTTTGTGTATTTGTTTTCCCATCCAG
Seq C2 exon
TACCCCCTAATATTGCTGGAACTGGCGAGCCCCAGGATTTCACTGTGTTACGGAACAGACAAGTGACACTGGAATGCAAATCGGATGCAGTGCCTCCACCTGTAATCACTTGGCTTAAAAATGGAGAACGGTTACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000015235:ENSBTAT00000061144:71
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.357 A=NA C2=0.196
Domain overlap (PFAM):
C1:
PF0767911=I-set=PD(28.7=89.3)
A:
NA
C2:
PF0767911=I-set=PU(45.3=84.8)
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:
GTGGAAGATACAGGAAGATACACA
R:
ACCGTTCTCCATTTTTAAGCCA
Band lengths:
214-1771
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development