RnoINT0155205 @ rn6
Intron Retention
Gene
ENSRNOG00000008145 | Traf3
Description
Tnf receptor-associated factor 3 [Source:RGD Symbol;Acc:1304633]
Coordinates
chr6:135705659-135708783:+
Coord C1 exon
chr6:135705659-135705751
Coord A exon
chr6:135705752-135708642
Coord C2 exon
chr6:135708643-135708783
Length
2891 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGGC
5' ss Score
10.08
3' ss Seq
TGAAGAATTTTTTCCCTCAGGTT
3' ss Score
8.16
Exon sequences
Seq C1 exon
GGTACAAACCAGCAGATCAAGGCCCACGAGGCCAGCTCCGCGGTCCAGCACGTGAACCTGCTGAAGGAGTGGAGCAACTCCCTGGAGAAGAAG
Seq A exon
GTAGGCTGGGCCTCTGGCTTCTGTCAGATTTGTAATGCTTCCAACTATTTGTAGAGTAAATCTATGTTGTAATTATCAATGGTTTTTAAATGAAAGGGCCAGCGTGAAGAGATTGCCAGGAGTCAGTTCTGTTCTGGAATCTTGGCCTTCTGTGTAGAAGTGTTTGCTCCTGTTGAGCTACCAAGCAGCATGCAGTGGCCACGCTCCCTCCTCCTCCTTGTGGGTCATCCTAGCACTGATCTAGGACAAAGATTGTCCCAACTCCCGTCCTCTGGCCCTCAGCTCCATAGTTGTGTGAAAAGTGGCCACCCTACAGGTGAATTACCTCTGGTTGTTTCGGCACTGATCACCATGGAGACGGGTACTCAGGATGGGTTAGCCCCAAGTACTGGCTAGCTCCTCAGAGCAAGTCTGCCAGTCCCGTGTGTCCGGTTACTAGTGTCACACGAGCTACAGCATGCCTTTTGTGAGCCCCAGGTAGGAAACCTTTGCCTTCTCCATGTTGTTTGCCGTTGGTTCTCTTGGCAGCTGTACTGGCTGCATAGACAGCACCGCTACCAACCTCCTCCCCGCCCAGGGCTGAGCCTGCAGCCAGGTTCTTCCCGTCAGAGTGCGCCCGGCTTGAGCACTTGTTGGGTGGTGTTCACCCCACAGCAGGATGTGTTTCCATGAGAGAAAGGTGAAACGAGAACCGACAGGAGGAATGGTTATGGGCCCACACTCACTGCGGCTCACTGACGTTCAGTACACGTTGATTAAAAGCTTGTAGCAGAAGAGTATCAAGGACTGATAAGGGGGAAAAGAGCTGACAAGAGCCACTTGGTGGTGGCACACACCTTTAATCCCAGCACTTGGGAAGCTGAGGCAGGCGGAATTCTAGAACACAGGGCTACACAAGGAGACCTTGTCTCAGAAGCTCTTCCTTTTACCTGGTTTCACCCAGGTGGTGCAGCACATAGCAGTAATCCCAGCCCTCAGAGGCAGAGGGAGCAGAGGTCAGAAGTTCAAATCTAACTGCATAGCAAGTTCAAGGCCAGCCTAGGCTCCCTGAGAGCCTGTCTCAAAAGAAGAAGTCGTTTTTGCCTTGTTTTGTTCATCCCTTGCTTCATTCACGGCAGTGTAACGGCAACACAGGCGTTTAGTGGCTCTTGAGGTGTGTGCTGGTTGGCCAGTACACCAACCCAGGAGGTACTGAGGAAAAGGATGTTTTAAAGCTGTGGAAGTAGGTCCCGGTTTCCCCATAGGACTGTTACTCTGCGTGTCTGGAACACCTGCCTGCTAGCCTGTGGCGCTCATTTGAGAGCCAGATGAAGGCAGCTGCATGCAGGGCCCCCGGGGCTTTGCTCTCTAATGTGAGTGTGAATTCATAGTTCAATGAGGGAAATTCTGAAGGGAGGGAACCAAGACTACTTGATATGATGTGTGCGCATCACTGTTAGCTGCTTCTCTTCACCCAGTGCCTGGCTGGTGCAGGAAAATTGGCATTTTGAGAAGGATCAGTGATGTTCTTGTTTGAGTGACAGCTGCACTCAGGTGAGGGTAAGAAGAGTCTGGGGACCTCAGTCTGGATCTCCAGATGGACTGATGGGACAGTGCCTGTGAAGAGTTTTGTGACGCTGCCACTAACACAAGTTACAGGTTGGTAGTGTAGGAGCTTAAGGCCTTACATGGCGAGAAGAAAGCTGGTTTTCCCGTAGTCGTGGAAAACGAAGGCATGTTTGCCTGTGGGATGTGCAAGCTTGGTCTGCTCTGCTTTCTTCCTGTTTTTGTTGGTTTGGTGTTTTTGTTTGCTTGGTCGGTTTTTGGTTTTTCAAGACAGGGTTTCTCTATGTAGGTTTCTCTATGCCCTGGAGTTCAGAGATCCGCTTATGTCTGCCTCCCAGTTACTGGGACTGAGGGCGTCACACCTGGCTGACTTGGCTGTTTCTGCATCAGAGTCTCTGGGTGTGAGCTCTGTTTCTGAGGCCCAAGGATGAGTGCCTTGGTAACCAGTCCAGCCTCGCTCCTTGTGTGTGGGGTGCAGCACTACTGGGCAGACGGGGCCTTGCAGGGCATGAGCTCACATTCATTGGGCCATCATTGGCCTTTTAAAGATCCGTCGATAGTGATTGTATATCTTGTATTGTATATGGGGCGCAGATGTTAGAAAATGGTTTTGAAAGTTAATTGAAAGGCCTTTACTGTCTACGGTGTGAACATTTCAAACCTGTCCTCAGCAGCTCGGAGTGCTCTCTACGTTGTCACGGTCAGGAACTTCTTTAACTGAAGCTCTGTGTGGCAGGGGCTCCCATAAAGCCCCACTGTCCCCGCACCCCTCCTTTTGCTTCTGGGCTCACCTTTTAGGCTCCAGTCGTGAAAACAGGCAGGGTCTTCCTGCCATGCCCATGCAGTTTGAGCCTCTGATGCCCTCTGGGGACTAGCTTTTTATTGTTATTTTTATATCAAATGGAAAGAATAAAACAGAAAGTATCAGGTACATTGTGTTTTTAGAGCAGATATTATTCTGTAAGGACCATGTTTGCGTGTACACACAGTGCTTGTGCAAGCTGGATAAAATGAAAAACTGTTTTTTATTATGTGTCCTGGCCAAAAGTTAGAATCTTCACTGGAAAAAGGTTTGTTTTCAGTAAGCACTTTCAAAACCAGCCCCTTGTTCTGACATTCAGTTGACCCTGGCCCAGACCTCCCCCAGCTGCAGGAGAGACAGAAATAGCTTACAGGGCTCCCTGCTAGCTCTCCGGAGTTCCCCTTTCTGTGTAGAGGAATTTTTCTCCTGGGCCTTTCAAGAAGCCAGTGGAAAGCTTATATTGTGAAAGTTTAATTACTATCATTATTGTTAATTAATGCCAAACCACTTTTTGTTAAATTAATTGAAGAATTTTTTCCCTCAG
Seq C2 exon
GTTTCCTTGCTGCAGAATGAAAGTGTTGAGAAAAACAAGAGCATACAAAGTCTGCACAACCAGATATGTAGCTTTGAGATTGAAATTGAGAGACAAAAGGAGATGCTTCGAAACAATGAGTCCAAAATCCTTCATTTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000008145:ENSRNOT00000010906:9
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:
PF041569=IncA=FE(13.7=100),PF101744=Cast=FE(19.6=100),PF0205011=FliJ=PU(13.9=61.3),PF0149614=V_ATPase_I=PU(4.5=25.8)
A:
NA
C2:
PF041569=IncA=FE(21.0=100),PF101744=Cast=FE(30.1=100),PF0205011=FliJ=FE(33.6=100),PF0149614=V_ATPase_I=FE(26.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]