RnoINT0157913 @ rn6
Intron Retention
Gene
ENSRNOG00000039777 | Ttf1
Description
transcription termination factor 1 [Source:RGD Symbol;Acc:1565673]
Coordinates
chr3:7646355-7648129:+
Coord C1 exon
chr3:7646355-7646433
Coord A exon
chr3:7646434-7647998
Coord C2 exon
chr3:7647999-7648129
Length
1565 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGA
5' ss Score
10.77
3' ss Seq
ATCTTTTTCCTTCTCTTCAGGTA
3' ss Score
12.6
Exon sequences
Seq C1 exon
GGAAGGGCATTGCTCGGCCCTGGAAGCTTGTGTACTATCGTGCAAAGAAGATATTTGATGTGAATAATTACAAAGGCAG
Seq A exon
GTAAGAAACTCTCAGTGCGGGACCAAAATTTGTCCTGATGTCAAGAAACAAAATAGCCACAGCCCCGAGTGACAGGTGAGGGTCACAGAGGTTTCTGCATTAAAACCTGACTGGAGATTGTTAGGCTTACACCTTTAAGATTCATTTCCACTCCCAATTCTTTAATAAGCCTTCTGGAATTTTCTGTTTTCTGTGTCCTCTGTCCCTTTGTACCTGGGCTTCAGCACTGGACATCTCCTGCCTTTCTTCTGTGGCTCTTGTATGCTCTGCTCTCTGATGCAGTAAGCACCATAGTGTTCCCTTCTGCCCTGTGGTTCATCCTCTCCCTTCTTCTTCCCCAAAAAGTCCCCAGTTCTCATCTATGTCCAACACTCTGAATTGAGTTGGGAGTCTGAACTGAGGCACTCATGCTGACTTGCAAACACCATACCTACTGCGTCATCTCCTGGACCCATTCCCTCCCTCTCTCCCACCACCACTGCCCACTGTAGCCTTATGCTCCCACCCACAATTCAATCCTTTTTAATCTAGAAAACCTATTTTGTTTGTGTGTGTCTGAGTATGTGCGTGCGCACATACACCATGCATACTCAGGAGCCTGCAGAGGTCAGAAGAAGCATAAAATTGCTTGAAACAGGGGTTGCAGGCTGTGAGCCACCATGTGGGTGCTGAGATCTGACCTGGGGCCTCTCAAGAGCAGTCAGTGTAGCTAGGTATGATGGTGCATACCTTTAATCCCAGCATGGGGAGACAGAGACAGGAGGAGCTCTGTGAGTTTGAGGCCAGCCTAGTCCACACAGCAAGTTTTAGGACAGCCAGGGCTATCCCAAAAAACAAAAACAACCAAAAAAGAATGGTAAGTGCTTTTAACCACTGAGCTATCTATTCAGCCTTTACCTATAGTTCACGTCCTTTAGGTTGTGAGCCATCTGTCCAGGCCTTAGGTGGAACCCAGGCCTTGTGTTTGTCACAAAATGCCAAGTCATGGAGTCACATCCAAGTCACAGCTCCAAGGAAGTTGGTTCTCGCGTTGATCATATGAATACTAAGTGAAAGAATTCTTCCATGTGGGGGTGGCGTATGACTGAGTGGCGTACATGATGTTGGTTAACAGTAGGCAGCACTGGTCTAGAGGACATAGTATGATCCAGGGGTCCATAGATGTTGACTGCAGGCTTAGAGCAGCGCAGAGGAGACTCAGCAGGGGCACTCAGTGTTCCCTGCAGGGTACCATCCAGATAGCAGTACCAGTGGGTGGAGACAGCCATCCATGTTCAAGCCAATGCAGGCTGTGACGTAAGAACAGGCCTAGATGGTTCAGCATGGCCTATGAGAGACTGAGTAGACCTTGGCTCTTTCAGCCGTGATTGATGGCATAATAACCACTGAAGTGTACAGACAGACAGTGAAGGGCTCCAGCCATGGGTGGGAGGGGCTCCAGCCATGGGTAGGAGAGGCATGGCTTCCTATCAGTGCTGCCATTAGCTTTTCCTATGTTCTACCATGAGATGCCGTTCCTAGTCTTAGACTTCATTAAACCTAGCAATCTTTTTCCTTCTCTTCAG
Seq C2 exon
GTACAATGAGGAAGATACTAAGAAGCTGAAGGCCTACCATTCCCTCCATGGAAATGACTGGAAAAAGATTGGGGCCATGGTAGCCCGAAGCAGCCTTTCAGTTGCCCTCAAGTTCTCTCAGATTGATGGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000039777:ENSRNOT00000061029:5
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=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF139211=Myb_DNA-bind_6=PU(74.1=95.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGAAGGGCATTGCTCGGC
R:
ATCAATCTGAGAGAACTTGAGGGC
Band lengths:
206-1771
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]