BtaINT0152194 @ bosTau6
Intron Retention
Gene
ENSBTAG00000012020 | TRAF5
Description
Bos taurus TNF receptor-associated factor 5 (TRAF5), mRNA. [Source:RefSeq mRNA;Acc:NM_001105340]
Coordinates
chr16:73894532-73897325:-
Coord C1 exon
chr16:73897157-73897325
Coord A exon
chr16:73896499-73897156
Coord C2 exon
chr16:73894532-73896498
Length
658 bp
Sequences
Splice sites
5' ss Seq
TAGGTATGT
5' ss Score
7.76
3' ss Seq
GAATCTTTTTTTCTTTGCAGTTG
3' ss Score
9.04
Exon sequences
Seq C1 exon
GTTCTTGCCAGTCACATTGACAAGTCTGCTTGGCTAGAAGTTCAGGTGCGTCAGTTACTACAAATGGCTAACCAGCAACAGAGTAAATTTGATCTGAAGCCTTTGGTGGAAGCAATTGATACAGTGAAACAGAAAATCACCCTGCTGGAAACCAATGACCAAAGACTAG
Seq A exon
GTATGTCTAATGTCTTCTGCTTCCCTTCTCGTGCTTCATGACTTCTGCATGTGTTCACAGAAACAAGAAAACGGGCCAGTGGAGAGGCACAGCCATCCAGGGTCCACAGTGCTGAGTCTGGTATTTGTGAAGCAGAACAATATGAGGTTCTGGGCACTCAGACAAAAATGATGAAGGGCCCTGAGTGGGAACTGGAACAAGGACAGGGTGGAAACAGGCCAGGAAATTCCAAGAATAGGGAATGATGGTTTGTTAAGGAGAGCAGACAATGAGAAAGCTAGGGGAAAGATGTGGTAGGGAACATTGTTTCAAGTATAGAAAAGCAGAGACACGTTTGGCTATTTGAAAGCATCCCAGTTAGAATGTAGTGGGGCTTACCATGCCAAAGCCTGCTAGACGCGTGCTGAGTGGGTCTTCTCTACACTTCAGGGAGCTTCAGTTCAAGAGGACGCATTGGGGTTTTCTTGGGGCCAGTCTTTCCAAGACATGAGAATCATGGAGTCAGTATTATTAACATGGATGTCACATTGGTGGACATTGAATTCAGTTCGTTTTGGGAATGTCAGAATTCTATTGATTCTCTTTGGATAACCAAATTTCATTTTGGGCATATTTGAAAGACAGCTTTAAGGCCTTCAGAATCTTTTTTTCTTTGCAG
Seq C2 exon
TTGTTTTGGAAGGGGAGACTAACAAACATGATGCCCACATTAATATTCATAAAGCACAGCTGAATAAAAACGAAGAGCGATTTAAACTGCTAGAAAGCGCCTGCTATAACGGAAAGCTCATCTGGAAGGTGACAGACTACAAGCTGAAGAAGAAGGAGGCGCTGGACGGACACACAGTATCCATCTTCAGCCAGCCCTTCTACACCAGCCGGTGTGGCTACCGCCTCTGCGCTAGAGCCTACCTGAACGGGGACGGGTCTGGGAAGGGGACGCACCTGTCTCTGTACTTTGTGGTGATGCGAGGGGAGTTTGACTCACTGTTGCAGTGGCCGTTCAGGCAGAGGGTGACCCTTATGCTTCTGGACCAGAGTGGCAAAAAGAACCACATTATGGAGACCTTCAAGGCGGACCCCAACAGCAGCAGCTTTAAGAGACCCGACGGGGAGATGAACATCGCCTCCGGCTGTCCTCGCTTTGTGGCTCATTCCACTCTGGAGAATGCCAAGAACACCTACATTAAGGATGATACCCTCTTCTTGAAAGTGGCTGTGGACTTAACTGACCTGGAGGATCTCTAATCATTGCTTCTGGAGGGATAAAAGGACTCCTTGAATCCAGAACCTGTGGTTAATGTAGGGACTGAATCTGGGCTCAGTACATATTTGTACTTGGCTTTTTGTCCTTAACGTATGAAGTCATTTTAAGGTTTCTCAAGTGCTGTCTTCTTTTTACATTTTATTGTCCCAGTTTGAAACTTATAATACTCAGACTATCTTCTCATTATTTATATTTTTATATCTCTTCAAAGACGTTAACTTCCTTAAACGTAAGGACTGAAGCATACCTCTTTAACTGGTGCTTAGTGTGGGGTCTCAGGGTCTCAGTCTTCTATAATATTAAATGTCTTTGAGGACACAGATGTATTAGTAGAACTTCTAATCGAAAGTGTTTTGGTATTTTTATATTTGGCCTGTGGATTCTAGAACTGACCTTAAGCCTACAAAAGCTATCTTTTAGGGTAGGCTATTTCAGTTGAGTAGTTAAGTAGGGTGGTTGTTGTTATTTAGTCACTATGTCATGTCCAACTTTTTGCGACCCTGTGGACTACAGCCCACTGGGGTCCTCTGTTTGTGGAATTCTCCAGGCAAGAATACTGGAGTGGGTTGCTATTTCCTCCTCCAAGGGATCTTCCCAACACAGGGATTGAACCTGTGTCTCCTGCATGGCAAGCAGATTTTTTTACCTATGCCTCCAGGGAAGCCCAAGTAAATGGGTAGTGTACTTCAAAGTCAGTATACCCAGTTTGGATCAGACTTTTTTGGGTTAAATACTGTATTGTGGAAGCTACTACACTTTTAATACTTTCATGAAATTTACCAGTAGTCAGCAAGCACAGTTTTGCAAGGCTGCATAAGAACTTGTGAATAAAGTAAGTATTTTCATTCTTCCTGCTGAAGTAAAGCAGAAAACACTGCATAGTATATATATAGAGAGATACAGCCATCCAGCTAAAGTTATTAGGTCAAACCACATGACAGAACTATTTACAAACAAAATGATCAAGTGTTAGCAATTTCAGAAGATTCAACTTAATATATACATACATGTTTAAACATAGTTTACAGATATTTTGGTAATTATAGCAAATTAATATTAGGATGGGCAGAATTTAGTATATGATGGAGAAAGTGTCATATATGGATAAGAGGAATTAAAACCTAGGGATAACACCATTAAAATTTCCTCTGGAAATCAGAACTCCCATCTGAAATCGATGGCTAAGAAGAGTGTCTTTTTCTTTTTGAGTAGAATTTTGAGTTCATAAATTGGTTTGAAAATTGGCGTTTATGTAAACTTACGATGTTTCTTGTCAGAGCCCTGAGTACTTTGTGAAGAACAGAAAGCACGTGTTCTTCTATGTCTATCCGTATGGGTCTGAGAGTGTAAATACAAGTCTACACAAAGCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000012020:ENSBTAT00000015940:10
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.047
Domain overlap (PFAM):
C1:
PF059116=DUF869=FE(22.6=100)
A:
NA
C2:
PF059116=DUF869=PD(23.0=29.5),PF0091721=MATH=WD(100=74.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGCTAGAAGTTCAGGTGCGTC
R:
TGTAGAAGGGCTGGCTGAAGA
Band lengths:
342-1000
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development