BtaINT0027663 @ bosTau6
Intron Retention
Gene
ENSBTAG00000005189 | C11H9ORF9
Description
Bos taurus chromosome 11 open reading frame, human C9orf9 (C11H9orf9), mRNA. [Source:RefSeq mRNA;Acc:NM_001101193]
Coordinates
chr11:102959219-102961170:+
Coord C1 exon
chr11:102959219-102959421
Coord A exon
chr11:102959422-102960152
Coord C2 exon
chr11:102960153-102961170
Length
731 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGA
5' ss Score
7.61
3' ss Seq
CCCTTCCCACCGCCCTGCAGATA
3' ss Score
10.48
Exon sequences
Seq C1 exon
GTGCAGAGCTACATGGAGCACCACTGCAGCAACTCCACAGACAGGCGCATCCTGCTCATGTTCCTGGACATCTGCTCGGAGCTCAGCAAGCTCTGCCAGCACTTCGAGGCCCTGCACGCTGGCACCCCCGTCACCAACAACCTCCTCGAGAAATGCAAGACCCTCGTGAGCCAAAGCAATGACCTGAGCAGCCTGCGAGCCAA
Seq A exon
GTAAGACCCTCCTGGTCCCATCAGGGGTCTCCGCACGTGCATGTGGGAGGGGCCAGGGCGGGGACGGGAGAGGACCGGGCCTGGAGGAAGTGAGTCCCGGGGCTACTGTCCAGGGGTCCCCAGCTGGGAAATCCTAGGCCCCTTGGTTCACCGGAGCAACTCTGACCTGACAAATCATTTACTGAAAATGAAGGACTCTGAGGCCCAGACCTAGCAGAATGCAAACCCTCTGGCTGGAGGCAGCACCGGGCCAGAAGCAGGGCTCACAGAGCAGTTGTTCTCAGGAGCCCACAAAGTGGGACATCAGGAGCCCGATCCCATGGGCGTTAGCTACTGGGTTCCCTCATTCTGAGCCCTGGGGGATCGATCCACAGCACAGAGTACCAGATTCCAGAGCAAGCCATTTAGGTCTAAGAGTGAGCAGAGTCAAAGGGTACGCCGTGGGCCTGGGGCGATGACAGCAGGTTTCCTCGGCCCCTGCCCAGCTCTCTGCCAACCACAGGCCAGGGGTTCTCCGCTCCCACCCTTCACACGGGAACCCTGGGGGGTCTGGGGCCCCAAACCTGCTGAGCCACCACCATGCCTGGCATGGAGAGCCTGGGCTGGCAGGTGCACAGCTCTAAAACCTCCCCAAGGGGTTTTGTGCAGCAGGGGCAACCTTAAGAAAAAACCCTGCCCGGCACACCAGTCCCCGGAGCAGGGCTTACCCAGCCCTTCCCACCGCCCTGCAG
Seq C2 exon
ATACCCCCACGACGTGGTGAACCACCTCAGCTGTGACGAGGCCCGGAACCACTACGGAGGTGTGGTCAGCCTCATCCCCATCATCCTAGACCTGATGAAAGAGTGGGTCGCCCACTCGGAGAAGCTGCCCCGCAAAGCGCTGCAGCAAGTGAGTGAGCCCCAGGCAGCCACGCGGGCCACCGCGCACGCTCCCCAGGCCTCCGGCACCCAGCCCCAGCTTCGGAAACAAAATTGTGGGCAACTGATACAGAACATCCCCAAACCTGGGGGGAAAGACCAAGGAAGTTCAAAACCACCCTGGAGACCACCTGGTGGGAAACTGTAGTTGGGAGCTGGGGGACCCGCCCGACCCCAGCCCTGCCCGACCCCACCGTGTTCCCTCCCATCCCATCCCGCGGGGCAGCCTGTAACTAAGCCTGGTTTCCACCAGTCGATCCATCTCTACTGGTGCTCACCATCTTCGCCACTTACTAATCCCCAGGGAGCCACCCCATGGACGGCCTAAACTCTTTCCCTCTAGCGCTTTAATCTCTAACTTTCCTTTGCCTCCGAGTGTCAGGCCCTGTGCCCAGGAGGAGCACCCCCACTTACGTTGCTGCTGGTGGGTTCAGGGGAGGAGGGTGGGCCCCCAGAAGGGCTGGGGCCCTGACCCTCCCACCCAGGCCCAGCCAGAGGAGAATGCGCAGCTCCCTTCTGGCCACGGGACAGAGCTGCTCCAGCCTGAGGATGCTCAGTGGGGTCAGGTCTCTGAACCAAAGGGGAACAGGCCGCCCAGCCTCTCCTTCCCTCGAGAGAGAGACGGAGAGAAGCCGGAAGAACTGCCAGTGTGGCTCCTGCAGGAGGACGGTCACCTGGTCCTCACGACCTAACGGCAGCCCAGACGCTGGGACTGTGGCGTCGGCGCTGAGCCTGCCAGAGGTGCTGTCTCACTGTTGGTTTTCCCTTCACAGGGGGCGACTTAGCTTCTGTACTCTTGCTTCCTTGGGGGCGACAGTCAAGAATAAAAATGTGTTCTGGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000005189:ENSBTAT00000006841:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.593
Domain overlap (PFAM):
C1:
PF151201=DUF4561=FE(39.2=100)
A:
NA
C2:
PF151201=DUF4561=PD(32.2=50.5)
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:
CAAGACCCTCGTGAGCCAAAG
R:
GTGGTCTCCAGGGTGGTTTTG
Band lengths:
356-1087
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development