BtaINT0029713 @ bosTau6
Intron Retention
Gene
ENSBTAG00000012735 | C9orf117
Description
chromosome 9 open reading frame 117 [Source:HGNC Symbol;Acc:HGNC:27843]
Coordinates
chr11:98400784-98403216:+
Coord C1 exon
chr11:98400784-98400947
Coord A exon
chr11:98400948-98402944
Coord C2 exon
chr11:98402945-98403216
Length
1997 bp
Sequences
Splice sites
5' ss Seq
CCGGTGGGT
5' ss Score
7.85
3' ss Seq
CCGCCCCACATTTACCCCAGGTA
3' ss Score
7.73
Exon sequences
Seq C1 exon
ATGGCTCCTAAAAAGAAGGGGGCCAAAGAGCCCGAGCTCAAGAAGAAGAAAGGTGGCAAGAAGGATCCCAACCTGGCCAACAAGCCCATGGAAATGCCTATAAGCGAGGAGATCAGAGAGTTCTACCACATCCAGATCCGCGACCTGGAGGACAGGCTGGCCCG
Seq A exon
GTGGGTGGGCGGGCAGGGTGGTCCTGACAGGTCAGGGAGTGACTCACAGCTGGCCACTGTGCAGGTTCAGTCGGTGGGGCCCCTGTGTTCTGGCCTCCCAGGGGATGTCCAGACCCACCCCCATCCCTGCCTCAGTTTCCTGGAAGATAACATTGGGAGGCTTCATGATTTTGAAGAAAAATGGATTTCTTGGCCCCATCTTGGCTCCCAGAGTTTCCAGGGGCCCAGTGCCTAGTTAAGAGCCTAGCCCATCCCGAGGCAAGGACTACGTCCCTCCTGCCTCACAGTTGCCCCCCGGGACCACACATTTTACGTAAGAGGGCAGAGTTCAATCGGAGGGACAAATTGGAGATGGCAGCCCCCTGGCAGGTGGGTGACCATATGCCCCTCCTCCCACCTGCCCCCCACCACCCCCCAGTGCCTGTGCCGTGATCCCCTGAGCTATAGGCCCCAATGGCTCTTCCAGCTGCCAAGCCCACTTGTCCACCAGGGCTGTTTTTCCAAATGTAAACGAGGAGGGCTGTGCGAGGTGGGTGGTGGTGTGTGGAGCGGGGGATTCTCTAACTCTCCTGAGACATGCACTTGCCCACTTTTCTTATTCTTCCACTAGTTCCTGGCCCAGTCTCAGGATGACCCTCAAAAGACACACCCCTTTGGTGGTGGCTCAGATGGTAAAGAATCCGCCTGCAGTGCAGGAGGAGACCCAGGTTCGATCCTTGGGTCAGGAAGATCCCCTGGAGAAGGGAATGGAAACCCACTCCAGTATTCTTGCCTGGAGAATCCCATGGACAGAGAAGCCTGGCAGGCTACAGTCCATGGGGTCGCAAAGAGTCGGGCACGACTAAGTGGCTAACGTGAGGAGTCACATGTTGCTACAAATACTCACAGCTGATGTTGAGACCTTCCTGAACTGGTGCTCATTGTGTCCCTAAAACCGTCCCATGAGAGACGCCCTCTAGTCACCCCCATGATAAGTGGTGGAGAGACTGAGGCTCAGGGAGATAGGAAGGCACCCCAAGGAAGAGGCTCTGGGCCGGCCCTGGGCCCTGACTTCCCTAAACCTTGCTCCACAGATCAGGTCATCCAGCTTTGCACCCTGCACCATGCTTCCGTTCAGAAGATGTTGGTTGAGTTAGTTGTGAAGTTAAACATCTTTCCAAATAGTTTCTACCCATTATTCCATTGGAAACTAGAAAATTGCTTACACAACAACTCTTAAAAATTCACACGCTTCCCTCAAGTTGGAAACACCAGATGGAATGTATTTGGGAAAAATGCATTTGAGAGATGGTTATTGGGCACTTATTATGTGCCAACTTCCTCTGCCAGGCCCCCCAAAATACAGAAATGCGAGGAGTCAGGTCTTGACTTCCCAGTGGGACAAGGGTCAATCTACAGGATAGCCCCAATGAGAGGACCTCAAATGCTGCCTCAGGGCCAGGAAGGCTCCACGGAGGCGGCAACACAGGGGTTCACTCAGTGAAGGAGGGTAGGGAAGATCACAGGTGCAGAAGCTTGGGCTTTGAAGTGTGATATATTAAGCAGGGCACAGAGCTGGCAGCAACCATTATGCTTAAGACCCTTAATTTTGGGGTATCAGACTGACTTGGGTTCAAGTTCTGATTTTGCCATTTACTAACTCAGGGATGCTTCATCCCTCTGTGCCTCAGTTTCTTCACCTGCAAAATGGGTATAATCATCATAGCCCCTACTTGCTTGGTTGTTGTGGATTCAACAAACACACTGAGTACCTACTACATACCAGGCGCTAGGTGTTGGGGACACAACTGTGAACGTTAACAGAGGCTCCACCCTCCCAGAGCTTACACCCTAGTGATGTTATGCACATAAAGCGCTGACCACAGGCATCAGCTGCGGTCACAAGCACTGACCAGGGGAGATGAGGCTGGAACCTCCAGTGCCCCACTATGGGAGGGTCCCGGGAGCAGCCTGACTGCCTGGAGGCCCCCTGGACCCCCGCCCCACATTTACCCCAG
Seq C2 exon
GTACCAGCGGAAGTGGGATGAGCTGGCCATGCAGGAGAAGCTGTTTCGCCAGGAGTTTGAGCAGCTGGCCAACAACAAGAAGGAGATCGTGGCCTTCCTCAAGCGCACGCTCAACCAGCGGGTGGATGAGATCGCCGACCTCAATGAGCAGCTCCAGAGCCTGCAACTGGCCAAGGAGATAGAGAAGGATGCCTTCGAGGCACAGCTAGCCCAGGTGCGCCACGAATTCCAGGAGACCAAGGACCAGCTCACCACCGAGAACATCATCCTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000012735:ENSBTAT00000016929:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.600 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAAGAAGGATCCCAACCTGGC
R:
CTGGTCCTTGGTCTCCTGGAA
Band lengths:
355-2352
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development