MmuINT0167451 @ mm9
Intron Retention
Gene
ENSMUSG00000026803 | Ttf1
Description
transcription termination factor, RNA polymerase I [Source:MGI Symbol;Acc:MGI:105044]
Coordinates
chr2:28940157-28943170:+
Coord C1 exon
chr2:28940157-28940334
Coord A exon
chr2:28940335-28941626
Coord C2 exon
chr2:28941627-28943170
Length
1292 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
GTCACTGTGCTCTCTTCCAGCGC
3' ss Score
10.28
Exon sequences
Seq C1 exon
AAATCATTGACTACTTATATAAGAACAGTCTGCCTTTGCTGAAGGAAAAGTTAGACAAGAAAATGAAGAAAAAAGACGGCCAGATCCAAACACCTGCAGCTCCCAAACAAGACTTTCTGTTCAAAGACATCTTCCATTGCGATGATGACAGTGATGAAGGGAGCCCAGAGGAGCCCAG
Seq A exon
GTGAGTACAGGTCGCTGACTCCCATCTTGTTCCATTAGGTTATGTGTGCACGTGTGACAGTCAGCGTCTCTTCACAATAGTGCCTAAGTAGCTCACCTCAGAATGAGAAGAGGTCGCCGCTTTGGCTTTTCTTTCTGCGGCTCCAGTCCATGCCTTGGTGCTGTTGCTCTGTGCCTGGAGGTAGCACACATGACAGCAAATCCTTTACCTCATAACCAGGAAGCAAAAGAGAACAAGGGAATCCCACAATCCTTTCAAGGCTCACCTCCATTGGCTGAAGACCTTCAGTGAGCAACCACCATCTCACACTGACGCTGCCCAGGGGACCTGGCCTTTAATGTGTAAGCCTTAGGGGAGTGGTCCAGAGCTGACCAAGCAGGAGGATCTTCAGTCCTGATGGCTGTTAAAAATGGTGTGATGGGCACATTTCTGAGTTTGAGGCCAGCCTGGTCTACAGAGTGAGTTCCAGGATAGCCAAGGCTACACAGAAAAACCCTGTCTTGGGGGGAAAAAATATTGTGATGGCTGGTGGATCTCTAAGTTGGAGGCCAGCCTGGTCTAGAGAGCAAGTTCCAGGACAGCTGGGGCTACATAGAGAAACCCTGTCTCAACAAAGCAAATAACAAACAAAATGTAATGGAGCTAGGTGGTGGCTCACACCTTACTCCAGCGCTCAGAAGGCAGAGGTGAGCGGATCTCTGGGTTGGAGGACAGCCTGGTCTGCACAGTGAGTTCCAGGATAGCCTGGACTACAGAGAGAGTTCCAGGACAGTCTGGGCTGCACAGAACCCCTGTTTCAAACAAACAAGCAGATGTGCTGGGCAGGTGAGCATGAAACACATTGGGGGCTGGAGAGAAGACCGTGCCAGTGTGGTGCCTGCTCACGGTGGCATCAGATCCCAGCACTCACATAAAGAGCTGGGCCTGGCCATGGTGCTGCGTGCATGCTATCCACGTTTGGGCTGAGGAACAGGAGGATCTTCAGGGCTAGGTGACCAAACTTCAGCAAGTAAGCAAAGGAGATGACCTGAAAAGCTGAGGACCACCACCAGAAATTGTCCTCTGGACTCCACATGAACAAACACACACACATCTTTAAAAGTGTTAGTTTCATGTTGATGTTGGTGTGCTTGTGAGCTGACTGAATACTCTGTACCATTGTATTGAAGCAGTTACACTGCTGGTTCCATTGAACCAGTGCAGCCACCAGTCCTAGGTGCATCAGAGAACATTACACCCAGTAAAATGAGAAAGCTGCCTCCCCTGATGGCTGTCACTGTGCTCTCTTCCAG
Seq C2 exon
CGCCTCTGATGTGCAGTGACTGGATCGTCTCTTCCTCAAACTGCTCTCTGTTCCCTTGGACCTGTGTTGTGCATTGGCTATAGATCCCGCTCGCATGTGATACCTCTCCTGTGCTGGGCACCGAGTCACACGGTGTTCTGCTGGAGCATTGGTAGTCTGCATCGGAGCCCAACTGGTAGCCTTGAAGAGTCTGTCAGCTGAACACAGCCCCACTGGATTCTCAGGACTGGGTGAAAGGGGTGCTCTTTGGTCAATCAGGAGAGTCAACCCAACTGTAGGGGCTTCAGAGAAGAAAACTTAGGGTTTGGGTAAGAAGAAGTATTCCATGAGATCTGTGCACTATGGAGATAGGTGGGGGAGTGGGAAGTGGGGTCACAGGATTGAAGCCAACCTGGGCTACATAGTTCCTCCAGCATATACACACACAGTGGGATGCTGGAGCATCCTCCAAAAGGAGAAGTGCATTGCCCAGAGAGCAGGAGAGTACTGCAGAGAAGCTCTAGCTCTGCAAGCCCCAATTTCCCTGTGTTCCTTCTAGCTGTTCCCATACTCAGGCTGTCTGTTGTTGCCCTGCAGAGAAATGTGTCCATGTGTGACCCTTAGCAGAACACTGCTGCAAGGGAGTCTGGGACACCCAAATGTTCAGACATTCAGACTTCTGCCCCATCTGTGCTGGGGAGACAGAAGGGAAAGTGAGGCTAATGAAACCGCCCATATACTGCTGTCTACGTTGGTGCCACTCAGCAATCTTCTGTCTCCCGAGAACTCTCAGACATGATTTCTGTGGCACTATTAGAAGGTGGACTAGAGGGCTGGTGAGATGGCTCAGTGGGTAAGAGCACCCGATTGCTCTCCCGAAGGTCCGGAGTTCAAATCCCAGCAACCACATGGTGGCTCACAACCATCTGTAACAAGATCTGACTCCCTCTTCTGGAGTGTCTGAAGACAGCTACAGTGTACTTACATATAATAAATAAATAAATCTTTAAAAAAAAAAAAAAAAAAAAAGAAGGTGGACTAGAAGGAGCTTCTGCTTGCCATGTACCTAGCACTTCCCCAGATGTGCAGATAACGGAGTAGTCAGGTGGAATGCACTAATGCACCCAGCATTCATGTGGGGTAGGAGGAGCGGGAGGTCAAAGTGGTCCTTACAAATAGCAGGCTCTAGGCCAGGGTGGCCTATAGATGACTCTGGCTCTAACAAACACACAAATAAAACATTGTGTGAATGATGGTATTTTAGTACATGGTTCTCTACCCAGCCCCTCTGTCCCTCAGGCATTCTAGACTCTGTGCTGACAGGACTAAATTGCTCCTACAAAAATAATAGTACTAATGTATAAGCCAATTCTATATTTGTGATAGAAGAAAAAATGAATATTCTTTAACAGGAAGTATGTTCCTAGAATGGGATATCATATGGTAAATTACAGTGATAACAATAGATCTGGTTGACATGACGTTATATTTTTGTGAAGTATTTCAAAAGAATATATATTTTCTCAGTTTTATAAAAATGAAAAATAAAAGAAATTGGTTGTTTA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026803-Ttf1:NM_009442:11
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.250 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
Other assemblies
Conservation
Human
(hg38)
No conservation detected
Human
(hg19)
No conservation detected
Rat
(rn6)
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:
AAGACGGCCAGATCCAAACAC
R:
CCCTTTCACCCAGTCCTGAGA
Band lengths:
345-1637
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: