BtaINT0072451 @ bosTau6
Intron Retention
Gene
ENSBTAG00000015235 | HMCN1
Description
Bos taurus hemicentin 1 (HMCN1), mRNA. [Source:RefSeq mRNA;Acc:NM_001192537]
Coordinates
chr16:68711749-68714127:+
Coord C1 exon
chr16:68711749-68711877
Coord A exon
chr16:68711878-68713776
Coord C2 exon
chr16:68713777-68714127
Length
1899 bp
Sequences
Splice sites
5' ss Seq
TGGGTAAGT
5' ss Score
10.24
3' ss Seq
GTATCATGGCACACGAGCAGATA
3' ss Score
-0.87
Exon sequences
Seq C1 exon
ATGTTGATGAGTGTAAAGATGGGACCCATCAGTGCAGATATAACCAGATATGTGAGAATACAAGAGGCAGCTATCGTTGTGTGTGTCCAAGAGGGTACCGGTCTCAAGGACTTGGAAGACCCTGTTTGG
Seq A exon
GTAAGTTAAAAGAAACTCTTATCAAGTTAATAAAACTGTTAATACAATTAACCACCCCTACCTACCAACTTGATTAGGACCACTGTGTTTTCAAATGCTTTCTTGCTACATTTAGAAGAGTAAGTTGGTTTAAGTAATCCATTACACAGTTTGAATTACTTCTTAGAGACTTCATATTGAGTTCAACTTACACTGACTTTCAAATGGTAATAATAACTACTTACAGAAAGCTTACTATAAACTACACATACCAAAGTGAGGTGTGGTATAATTACCATGACAACTTAATTATGAAGATTATCCCATTGATTGTCTCGCTATGCACATGATATGTTTGTATAGATACATTTTATTTGAATGTGAAGTATAATTGTATGTACTATGAACGTTTAGTTATGAGGGATTAAAATGTGAACACATTTTAAGTGAATTGGTAATTAGCACTTTATCTACCATATATTTAGCACATGCTATATACCATTCCCAGTGCTAAGAGTCTCACTTAATTCTTCCAATTGCCTATTTGTTTCCATCTTAGTTATAATTGAGTGTAAAGTAAGGCAAGTAGATAGAAAATATCTTCAAGAAGGTAACCATATGCTTTTTTAAAATTAACACATTTATAATCAAGAAACTGACCTATAAAATATTCTACCTCAGAATATTTACATTTACATGCAGCAAAAAACTTGTGTTGAGCTTTTAATTACTGGCTTCTGGTTTGCATGCTATTATACTTTTTAAATTAGATGCCTTGTTTATCTATTTAAGAAACAACCTGTCCTTATAGCCTGTCCTGTCTTTATAGTGAATTCTTCCATAAAAATTTAGTACTGTCGTGATGTAGTTCCTAGCACAGTACTTTGTGCATAGCAAATGTTTATAGTAGTATCATTATTATGAACTCTTTTAAAATAAATACTGTTTAATAGAAATGTATGTAATTTTAGTCTTCTATTTAGGTATTGTAATTTATATATAATTTAACATTTTGATAAGTTATTATTACAGTGACCTAGCAGAATAAAATATGTTCAGCTGTTCACTTGTTTGACTTGAAGCTGAATGTCAGCAATTGGGCTGGGGGATAAATTTGTAAAGAAGGTAGGGCCATTGCCTTAAAGAGATTAAAAATGCTAATTTTAACTTTTGCCTACTGAAATAATTATTAAAGCAAAATTTACTACTTTATTCTAGTTGTTTTCTTTCATGGCACTTTGGTAATGAATTAAAGAATTTGGTTTTGATCTCTGGTATTTATTCACTTTATAAGAAGTGTTGTGAGTACATACTCTGTTGATCTAGAAAAGAAGGATAGCTTTCATTTTTGAACTTTGTGAGTTTCTTAGGAAGAATGATTTTGTGTCATTTCCTTCTTTTTAATTTTTGTTAAGAAAATGTGCTTAGCATGATTATTCATGAGTAATTATTGATTCAAAAGAAAAAAGGAAAATAAAGCTGACTGTAGTTGTACCAATATTCCTGCATCTGAAACTTATATGAAAGATTAGAAGCACTAAGTGATCAAAAGTATAATTAAACTCTAACTAGAGATATGATTGCATTCTTCACCAACGAAAGTAAGATCTATATTAGCTTTGAACTCTAGTTTTTCTGGGTTCAAGACCACATTTTCCATTGTAATCCTATTTGTTTCTACTGTAAAGCAGTGTTTAGGGAGAATCATAGAATCTCTCTATATAGTTATATCTTAATGATGAAAGCTTTTTCAAAAGTTTACAGCAGTTGAAAAATTACTGTATTCCCAGCTTTGGAAGGTAACATAATGTTTTCAGTTTGTTTCACAGACTGATTCTTTATTCCTGTGTTTTCTGTGTGTATATGTGTGTATGTTGTGTTTTTTTTTTCTCTTTTTTATGTATCATGGCACACGAGCAG
Seq C2 exon
ATATTAATGAATGTGAACAAGTGCCTAAGCCTTGTGCATATCAGTGCTTCAACACCCCTGGCAGCTTCAAGTGTATCTGTCCACCAGGACAACATTTGTTAGGGGACGGGAAATCTTGCGCTGGACTGGAGAGGCTGCCAAATTATGGCAATCAATACAGTAGCTATAACCTTGCACGCTTCTCCCCCATGAGAAACAACTATCAACCTCAACAGCATTACAGACAGTACTCACATCTCTACAGCTCCTACTCAGAGTATAGGAACAGCAGAACATCTCTCTCCAGGACTAGAAGGACTATTAGGAAAACTTGCCCCGAAGGCTCTGAGGCGAGCCTTGACACATGTGTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000015235:ENSBTAT00000061144:104
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=0.008
Domain overlap (PFAM):
C1:
PF0764510=EGF_CA=WD(100=95.5),PF0764510=EGF_CA=PU(0.1=0.0)
A:
NA
C2:
PF0764510=EGF_CA=WD(100=33.9)
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:
ACCGGTCTCAAGGACTTGGAA
R:
CCTTCGGGGCAAGTTTTCCTA
Band lengths:
355-2254
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development