RnoINT0157909 @ rn6
Intron Retention
Gene
ENSRNOG00000039777 | Ttf1
Description
transcription termination factor 1 [Source:RGD Symbol;Acc:1565673]
Coordinates
chr3:7657690-7660673:+
Coord C1 exon
chr3:7657690-7657867
Coord A exon
chr3:7657868-7658942
Coord C2 exon
chr3:7658943-7660673
Length
1075 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGT
5' ss Score
10.86
3' ss Seq
GTCACTCTGCTCTCTTCCAGCAC
3' ss Score
9.28
Exon sequences
Seq C1 exon
AAATCATTGACTACTTATATGAGAACAGTCTGCCTTTGCTGAAGGAAAAGTTAGCCAAGAAGATGAAGAAAAAAGACAGCCAGATCCAGAAGCCCACGGCTCCCAAACAAAACTTCCTCTTCAAAGACATCTTCCATTGCGATGATGACAGCGATGAAGGGGGCTTAGAGGAACCCAG
Seq A exon
GTAAGTACAGGTCACTGATTCCCCTCCTGTTCCTTAGGTTCTGCATGCACACGTGACAATCAGCTCCTCTTCCAAATTGCACCTAAGTTGCTCACCTTAAAACAAGAAGGGGTCGGGGTTGGGGATTTAGCTCAATGGTAAAGCGCTTGCCTAGGAAGCGCAAGGCCCTGGGTTCGGTCCCCAGCTCCGAAAAAAAGAACCAAAAAAAAAACAAAACAAAACAAAAAAAAACCAAGAAGGGGTCGCTTTGGCTTTCTGTAGCTCCAGTCCAGGCCTTGGTGCTCTCTGCCTGTGGAAGCAGCACACACGACAGCAGATCCTTTACCTCCTAACCAGGCAGCAGAAGAGAACAAGGATCCCACAGTCCTTTCAAGGCTCACCCCCATTGCCTGCAGAACTCCCATGCCCAACCATCATCTCACACGATACATGAAGGCCTTGGGGGAGTGGTTGAGATATGACCAGGCAGGAAGATTTTCAGTCCTGATGTCTGTTAAAAATGGCGTGATGAGACATGTGGATCTCTGAGTTCAAGGCCAGCCTGGTCTAGCAAGCAAGTTCCAGGACAGCCAGGACTACACAGAGAAACCCTGTCTCAAACAAATGGTGTGATGGGTGGGTGAGCAGTTGGGGGCTGGAGAGAAGACCATGCCATGTGCTTGCTTACAATGGAGTCAGATCCCCAGCGCTCACCCGGGCATGGATCTTCAAGGATAGGCAACCAAACTAGTCTAATCAGGAAGTCACAGGGCAGTAAACAAAGGAGGTGAGCAGAACAGCACTTGAGGAACACCACCAAAAACTGTCCTCTGGGCTGCACATGCACATACATGTGTGTTCACTGAACATCCATGTGCACACACACATCTTTAAAAGTATTAGCATTGACGTTAAAGTCGGTGTGATTGTGAGAGCACAGTGTGAGTGAGCTGACAATACTTCAGTACTGTGGTATTGAAGCAGTTACACTGATGGTCCCACTGAAGCAATGCAGCCACCAGCCCCAGTTTTAGCAGAGCCCGCTGTAAAATGAGAAAGCCAGCCTCCTGACGACTGTCACTCTGCTCTCTTCCAG
Seq C2 exon
CACCTCTGATACACAGTGACTGGATCTCCTCTTCCCGCAGACTGCTCTATTCTCTTGACCTCTGTTGTGCATTGGCCATAGATCCTGCTTCCTATGAAGCCTCTCCCATGTGGGCTCCTAATTCACACGGTGTTTTGCTGGAGCACTCGTGTTCTTCCTAGAAGCCCAGCTGCTGGTCTTGGAAGAGTCTGTCCAACTGCAAGAGTCTGGCAGCTGGAGCACAGCTCCCACTGGATTCTCAGGACTGGGTGAAAGGGGTCAGTCGGGAAGGTAAACCAACTGTAGGTGTTTCAGAGAGAGAACTTAGGGATTAGGTCCCATCCCACAAGGTCTATGCATGGGACACACACTATGCACTGGAGATAGGCAGAGGGTCACAGGATTAAGGCCAGCCCGGGCTCCACAGTTTCTCAAGCACCACACACCACGACCTGGAATGCTGGAGCACTGCCCAGAGAGTGGGCAGCCCACCTCCAGCTCTGCAGTCTCCGGTTCCCTGTGTTCTTCCAGCCGTTCCCCAGACCCAGGCTGGCAGCGACTGCTTCTACTGCTCTGCAGAGAAATGCATCTATGTGTGACCCTTAGCAGAACACTGTTGCAAGGAGTCTGGCCCATCTGTGCTGGGGAGACAGAGAAAGGAAACTGTGGCTAATGAAACAGTATACTGCTGCCCCCATCGGTGCCACTCGGCAGTCTACTGTATCCATGTGCCGACCTGCCCCCAGAAATCTCAGGCATAATTTCCATGGCACCATTAGAAGGTGGGCTAAGCCAGCTACTGTGAGAAGGAAGCACAATAACGGGCTTCTGCTTGCCATGTATCCAGCACAGACGTGCAGATAACAGAGTAATCGGTGGTACACACTAATGAACCCAGCATTCACATGGGGCAGAAGGATCGGGAGTTCTGAGTGGTCCTTGCAAGTAGCAGGTTCTAGGCCAGCCTAGGCTATGGATAACTCTGTCTCGAACACACACAAAGCATTGTATGAATGGTGTTATTTTAGAACATGGTTCTCTACCCAGCCCCCTCTATCCCTCAGGCATTCTAGTCTCTGTGCTAACAGGACTAAATGACTCCTACAAAAATAATAGTACTAATGTATAAACCAATTCTATGTTTGTAATAGAGAAAAAATTGAATATTCTTTAACATGAAGTATGGTCCTAGAAAGGAATATTATATGGTAAATTAAATTGATTACAATAGATCTGGTTGACATGAAAGTATATTTTTGTGAAATATTTCAAAAGAATGTATATTTTCTCAGTTTTATAAAAATGAAGAATAAATTGGTTGTTTATACAGATGTGCGGATTGACCTGAAAACCGGCCCATTACACATTTGACAGATTAGAACCCAGAGACCCAAAGCACCATGGGAGCTCCCAAAACTCACTTGGGCCAGGGCTACTGGGCTGACTTTCTGTGGTTTCTTTGAGGCTTTCTTACCCACACAGGATGGCCTCACTTCCATGGCTCTGGAGCAGCGGCAACAGTCCGTTCTGCTTCTGCCGTGGCCTTGGCGCCATTTCTCAGATCCGGATCTACCAGGCACAGCTGTTAGTGTGGCCAGCAGGGTCTGGGTGGCTCAGCTTTGAAGGTGGCTGTGGCTGAGAAGGCAGTGCCCCAATAGAGTCAGTGCATCCGTAGCAGATTGGACTGATGGGCTCCTAAGAAGCAAGCCACAGGCATGTAATGGCCGAAGGCACAGCGTTTCCAGGGAGCTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000039777:ENSRNOT00000061029:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.233 A=NA C2=1.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg19)
No conservation detected
Mouse
(mm9)
No conservation detected
Cow
(bosTau6)
No conservation detected
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:
TGAAGGGGGCTTAGAGGAACC
R:
GACCTTGTGGGATGGGACCTA
Band lengths:
356-1431
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]