BtaINT0154683 @ bosTau6
Intron Retention
Gene
ENSBTAG00000018710 | TTF1
Description
Bos taurus transcription termination factor, RNA polymerase I (TTF1), mRNA. [Source:RefSeq mRNA;Acc:NM_001102083]
Coordinates
chr11:102503830-102505679:-
Coord C1 exon
chr11:102505446-102505679
Coord A exon
chr11:102504016-102505445
Coord C2 exon
chr11:102503830-102504015
Length
1430 bp
Sequences
Splice sites
5' ss Seq
AGGGTGAGC
5' ss Score
7.75
3' ss Seq
CAACCGCCCCCCAATCCTAGGTG
3' ss Score
8.14
Exon sequences
Seq C1 exon
TTTTTCTCCATAGGTCAGAACCTACAAATGACGACGAAAGCAATTCGGCTAAAGATTCCGTAGCTAAATACTTATCTGAAGATTCGCGAGATTCCGAAGATCCGGAGGTGGACTTGGAGTCTGCAGTGAAGCAGCTGCAGGAATTCATCCCGGACATCAAGGACAGGGCTGCCACCACCATCAAGCGGATGTACCGAGATGACCTGGGGCGGTTTAAAGAGTTCAAAGCCCAGG
Seq A exon
GTGAGCTTGTGGCCTGAGCCTGAACGTTGGTCAGACGTCTTCGCTATTAATATGTGTGTAAATTGCCCGGACCTCCTTGGTGCACAAGTTCCGCTTTATAGGTTTACGGGAAGCGTCCCTTAGCTGCTTTCAGCTTCATCTCCTTCCAGAACCATCATCTGTGCTATAAAATTAGCAAAATAAAGTGCAGTGGTTTTCCTGTTTTTTGACGCAAGTTTTGGTAGGGGAGATGAGGGAAGAACAAGGCTGAAAGAACCCGGTGAACACAGATGAAGCCTTGAAGATGTGGGGAAAGAGGTTAAGTGGCTAAGAGGCTGGGAAGGATGCACCAGTGAGATTAAATGAAAATACTCGTATCAAATATCATCGGCTTTGATGAGATGTAATTTCCAGGGTGTTAATTGGAGGGTGAGCTGGTGGTAGTTGCCATGGTTTCAAGCATTACCCGGCTTGGTCTCCTCGTTGATTTCACTGTGTTACAAGAACCTCTCAAAAAGCCTATTGGATTTCAGAATGAACTGCAAGTGTAGGGCTTCGTGCTGCAAGTGAGTGGTATTTACTCATGACTGTCTGCCGTGTGACACCCGGTGCCACTGGTTACTGACAAAAGTAAAAGGGGGCGTTAGCCTTGTAGAATTCATCATGTTGATAAGATTAGTTTTTTAAAAAATAGACAAACTAAGCAAGAAGAACAATTCATTGAGCAGTATCTATAAAGGACCCCATTTTATTTCTGTATTTTATGCTGACATTTTTATTAGTGTGTATTTTATGAAAAGATTTTAAAAATAAGTCTGGGACCTCCTTGGCGGTCCAGTGGCCTCCTCACTTCCACTGCAGGGGGCACAGGTTCAATGCCTGGTTAGGAACTAAGATCCCACATGCCATGTGGCTTGGCCAAAAAATAAGTCTAAGAATGGGAAGGTGTACTGTGTAACGCAGTCATTAATAATGAGACTTGAGTGCTTGGAATTATGACAAGGAATAGAACGTGAGTTGCAGTGACCTTGACCCCTCCATCCCCCAAGGCCCACACACACAATACACATACGTGTTCACGTAAGCGCAAGCCAGTTGGCAGCACTGCTTTAGGGCACTGGCTGGCAGAGGAGAGTGAAGGGGGCTTCTTTTAAACTTCTGTTTCAATAGTTTGAATTTTTAATGTATGTTACTCTTAATATTTCTTTAAAGTAACTGTATAAGAAGGGATTGATGGCACAGCAGAGGCCACACTGGAGTAGGATGACCAGGGGAGACTTGGGGAGGACAGAGTGGCTTGAGCTGAACTCTTTAGGGGAGCAGATGTCCAGGGCCCAGGCGGGGGCTGCTCCCTGGCCCGAGGGGAGGGGCTGACAGGCACTGTGTCATAAGTTGCTAAAGACTTAACATTGGTGCCTTTTTCTCCCCCGCCAACCGCCCCCCAATCCTAG
Seq C2 exon
GTGTCACTATTAAATTTGGCAAGTTTTCCGTGAAGGAAAATCAGCAGTTGGAGAAGAATGTGCAAGAATTCCTGTCCCTGACGGGAATCGAGAACGCAGACAAGCTGCTGTACACAGACAGATACCCGGAGGAGAAGTCTGTGATCACCGACTTAAAGAGGAAATACGCGTTCCGAGTGCACATTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000018710:ENSBTAT00000024905:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.513 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion 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:
ACCTACAAATGACGACGAAAGCA
R:
CCTCCGGGTATCTGTCTGTGT
Band lengths:
347-1777
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development