BtaINT0072492 @ bosTau6
Intron Retention
Gene
ENSBTAG00000015235 | HMCN1
Description
Bos taurus hemicentin 1 (HMCN1), mRNA. [Source:RefSeq mRNA;Acc:NM_001192537]
Coordinates
chr16:68562436-68567155:+
Coord C1 exon
chr16:68562436-68562603
Coord A exon
chr16:68562604-68567041
Coord C2 exon
chr16:68567042-68567155
Length
4438 bp
Sequences
Splice sites
5' ss Seq
CAGGTATTA
5' ss Score
7.26
3' ss Seq
CCGGTGGTTTGCTTCTCCAGGAG
3' ss Score
8.49
Exon sequences
Seq C1 exon
CCCCTCCAAGCATCATTGGAAACCACAGGACACCTGAAAATATAAGTGTGGTGGAAAAAAGCTCAGTGTCGCTAAATTGTGAAGCTTCAGGAATTCCCCTGCCTTCAATTACGTGGCTTAAAGATGGGTGGCCCGTCAACCTTAGCAGCTCCCTGCGAATCCTCTCAG
Seq A exon
GTATTAAAAATTCTTGTAGCTTGGTAATCTGGTTTAGCTTTCCTGTGGCCACAGCTTATCTTTAATTTCTCATATCTCCATGTTTTATTTTTTTCCTTTTTTGAGCTAACTGCTTACTATAATACCTACTGATCATATTAAGAAAAAACTTTGGAACATCAGAAGCTATAGGACAATGGGGAAAATCTCTAAATATTTCTGGATCCTTGTGAAAGAGTAGTCTTGGCACTCGATTATTACTTAATTCATGGGGATGTCAGAGCATTCATGCTAGAATGAGTACAAACTAATTTGAAAAGTGAAGAATGAAAAGAAGTACTGGAATTGAAACCAGAGCCTAGAGGGTATAATGTTATATAACATATCTCCATATTCAAACAAAGTGTTTGAATTTATTCATGGCTATTCTAAGTGAGATTTGTATTTCCAAGATGGGATAGTTTCTTTTGAGCTAAGACTTTATTATAGAAGATACTCTGCTGATTCCTCATCTAATTATGTAGGAAAATCTATTATCTTATTCTTCATAGATCAGTATAAGTGTAGAGAGAGATGTCTTGGGGCATGCCCCTGGAATCTACCCTTGGCTCCTTTCACTAATGACTTGGATACAGACTAAGAAAATAATCTCTCCAAGTCTGTGGGTAATAAAAAGCAGGGGTACTTAGAAGAATACCTAATGTGTTTAATGAAGACATCTGAATTCAAACACATCTTACTCTGGAACTTCTGAATTAAACCTAACAAAATGAAAGTTAAGTAGACTCCTGTACTCGCTTTCAAAAACCAGTGATGAAAATTAGGGTGAGATATTGCTTCAGAATTCTTCATATGAAAAGATCTCTGAACTGTGTTAGTGATTGAGTATGCATTAGCATTGTAAGGTGTTTTATTGGGAAAAGCAAATACAGTGTTTTGCCACCTGAATATATTTTTACCAGTAAGACAAGACCGGTTGTACTCTGGACTTATCTTACTCATTAGGAAGATGTAAGAAGTATTTATTGACAATATTTTCATGGAGCATAACCATGATGGCCAATAATTGGAAAATAGGCTATATGCCTGATTCCATTTAATCTGAAAAAATAAACTTTGTGTAACCTTATTATCTCATAGTGAAAATTACATTTAAATACTTGAAGAGCCATGGGGTAGAACAGGTTATGTTGGTTGTATGTAGTTCCAGAGGTTAAAAGTAATGCTAATGTATGGAAAATTCTAGGGACAGATTTGGGTCTGAATGCAAACAACTTTAAAACAATATTTGTGTTGTTGAAAGTCAAGATGAACTATTTTAAGAGGTAATGAGCTCCCTGCCCCTAAGGGTATTCAAAGTTTAAATTCCCACTTTTGAAAGATTTTTCAGAAAAGATATTTTCCTAGTATTTGAGTTAGATCTAAATATCCTATTATCTATTTCTTCAAGATCTTGGTCTATAAATGATAGGGACTAAATGAGAAATTTCCATTGCTGTAGTTGTTATATTCATTGCCTATAATTAAATATATAAATGAAAAAATTATTAGCAATGTTTATTGCCTATAATGGACTTCCCAGTGGTAAAGAATCTGCCTACTGATACAGGAGACACAGGTTCAATTCCTGGCTCAGGAACATCCCCTGGAGAGCAGAATGGCAGTCCACTCCAGTATTCTTGCCAGGATAATCCCATAGACAGAGGAGCCTGGCAGGCCCCAGTCCTTGGAGTCACAGAGTTAGACACAACTGAGCATGCACACATTACCTACAACACTAGATCTATGCGCTCCGGCAAGTTACTTCACTTTGCTAACCTCCGTTCTTCACTTGTAAGTGAAGATAGTAGTAGTATTTAGGGGTTTTTATAAAGATGAGTTAATATGTGTAAAGCAGCTAACACAGTGCCTGCTTATATCCTAAGCATCCAATAACGTGTTTGCCTTTATTGTCATAGACAACCTGCTAAAAAGTTTGGGTCTCCCTATCCTGGGAAACCTTCCCATGTCCTACAGTGCATTCATTTTCTTGAGACTTCCATCCTCTGTTGATCTTAGAGAATGCACACTGATGGCAAAGATTTTATTATAATTTGGTTACCAAAAACCTGGACACTTTATCTTCTTCTCTTAAAAATATCCTTGTTTTTGCATTCTCAATTGCTGAAAAAGTAGGAAACTTTTTAAATATAACTACATTAGAGCTCCTGGAAATGAAAAAGTCAAGACAGAGTGATGTACTCTGGCTTATAATAGATTCACAGGAGTAGTGTTTTGGTTTTATCGTATAGTTTTGTTTTGCTTGACTAGCAAATGGAGATCCCTGAGCGAACACAGTAGAAGTATTTCACCTTGTGACGCTGCCAGAGGAGTCATTCAGTTTTACAGTCTGAACATGTGTGCTGTGCAGTTGATGACTGAGAATCAGATGAATGGTGTATGACTCGTTCCTTGATCAGCTGCACGTTCCTGTTTCATTAAGATTAGTTCTCCTGAGACGTTAAGTCAAGTTTTTCATTGTTGAAGCCTCTGTTATTGTTATGAAGTTACCTGCCAAGAACAGATAGCTGACTATAAAATTTAATAGGTACAAGAAATGTCTCCATCTAAGTCTAATTTACTGTCATCTTTTTTTATGAGGGAGAGACCAGGAAACAAAGAGAAAAGAAAGATCATGAGATTTATGAGGTTGAGGTTTGCTGAGCCAGCAATTACTCATAAAAATTGTATTGTTTTAATAATATCTTTCAACCGGCATCATATTATGGTCTCACAGTCTCACTAATTTGAAGTAGCAGTGAGTGCTTGAATCTTTTCCTAATTGATATGTTTTTTGACATGTTTAGAGAATTTTTGTATTCAACTTTGCTTACTTAAATTCAACTGAGAGAAAAGACTAAATTTGGTAGTAGATACTAAACAAAGTTCATCTTTCAATGGGTTGAGGATAAGTAGGTTGCTTAAAGGGAAAAAAAAAAAAAGCTCAATGAGGACTTGCTTTGTTTATAAAAACAGAAAGCAGATGGAAATTCCTGATGAATTCAGATCCAGGTGAATATTTACAAGAAAATTTTATGTTTAACCATTTCAATTGTTTTAGTTCAAATTCAGGGTACTAAGCAAAAATATACCAAATGAAAAATTATTACTAAATCTAAGAAATGATATACATTTTGTTCTTAGAAATTACTTCTCAAATGATTTCAAGGACTCTGCTCTTTCAGCATATGTCTTTGTTCTCTGCTGGCTTTGTTTCAGTCTCATTTGCTGACTCCTCTTTCCTTGATCCTTAAGAGGAATTTTCCTCCAGATCACACCCTTCAGCATATCAGTTTCATTCCTAGTCTACCAGTCTTTCTTCATTATGTAGAATTCAGAATATAAGGAGGAAAAAAAATTAGAGTCATGCTAATATGGGAGGTGGCCCTCATAAACTTTGATATAAATAGCTCTAGAATTCCATGAAACTCAAATTGAAAACTGGTTGTCAGTCTTCATGGTTTCATCCATCTCTTGTATAATTGATGTCATTCCAATCTGGGTTGTTGGTGTAGTATTCTTTCTAATGTTTCCATTTCATATGTTCCATGGAAAACTGGGAATCTTTTCCTAAACATTCTGTCACAGTTGTTTTTCTGAAGTATGAATCATACCATGACTTTGTTTGTTTACATACTTCCATAGCCTTAGTGCAGAGAAGGCGATGGCACCCCACTCTAGTACTCTTGCCTGGAAAATCCCATGGACGGAGGAGCCTGGTAGTCTACAGTCCATGGGGTCACGAGGAGTCGGACACGACTGAGCGACTTCACTTTAACTTTTCACTTTCATGCATTGGAGAAGGAAATGGCAACCCACTCCAGTGTTCTTGCTTGGAGAATCCCAGGGACGGGGGAGCCTGGTGGGCTGCCGTCCATGGGGTCACACAGAGTCGGACACGACTGAAGCGACTTAGTGATAGCGATAGCCTTTAGTGAACATAATAAATCCTACATTCCTTAACTTAGCGTTTGAAGACCCACAGAATCCTCAGAATTGGCCACACTGCAGCTAGTTTCATCTCTCACTGTCTTCTCCCCTGTTCTAAGTGCCACACCTACTTTCTACCTCTGTATCCTCATGCTCCAGCTACAGTGGTATCTTTTGACTCCTTTCTGTGTTAAAGTATACTTACCTTGCAAGACTATGTTCAAACATCACCTCTGTGAAACTCCATTTCTTGCTTGATGTCACCTGGGTTATATTAACTTTCTTTGTCCACTAAACTGGAAAATTGTTCTGAATTATCCATTCTGTTATATACAGCCTCAAAATGTGATATTTATTAAAAACTCGACATAAATACATTTTAAAAGACTTTGAAGTGAATTGATTAAATTTTACTAAAATTCAGCATTGCATGGCAAACTTGTAAAGTTGCAGATTTCTTTTTGAGTCATCCGGTGGTTTGCTTCTCCAG
Seq C2 exon
GAGGTAGGATTCTGCGATTGATGCAGACCAGAACAGAAGATGCTGGCCAGTATACATGTGTTGTAAGAAACGCAGCTGGTGAAGAAAGAAAAATCTTCCGGCTTTCAGTATTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000015235:ENSBTAT00000061144:47
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.158 A=NA C2=0.026
Domain overlap (PFAM):
C1:
PF0767911=I-set=PU(57.0=86.0)
A:
NA
C2:
PF0767911=I-set=PD(41.9=92.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development