RnoINT0082447 @ rn6
Intron Retention
Gene
ENSRNOG00000030666 | LOC108348140
Description
H-2 class I histocompatibility antigen, TLA(B) alpha chain-like [Source:RGD Symbol;Acc:11396749]
Coordinates
chr20:3118709-3119387:+
Coord C1 exon
chr20:3118709-3118911
Coord A exon
chr20:3118912-3119229
Coord C2 exon
chr20:3119230-3119387
Length
318 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
CAGTTCGTGCGCTTCAACAGCGC
3' ss Score
4.76
Exon sequences
Seq C1 exon
CAGGTGGCTTCCAAGCCCTCACCGTCCTGTTGAGAGCCGGTGCATAGAAAATGCCATAAAACTCTCTGTGATTGCAAGTTACAAAGTCTAGGACTTTATACAACTGTCTTTCGCTCGCCCTAACCAGAGGATGGGAAACATGGTGCCCAGCGCCCTCCTTCTCCTCCTGGCGACGTCGCCAGGCGAGACCCAGACCTGCTCAG
Seq A exon
GTGAGTGTGGGATCAAGAGGGAACCAGACTCTTCAGGCAGTGGCAGGGTCCTAAATCGGGAAGCCTCTTCCCAAGTCCCTGTATCCCCCACCGGACCCTCCGCCCCTTCTCCACCCAAGAGGCCTGAGTCCTGCTCCCTTCTTGTCGTGCGCACCAGGCCAGGGACCCGGGAGGAGCTCGGGGGTCTCACCTCCCGCCACCCCCAGGGTCACACTCTCTGCGGTATTTCTACACCGCCCTGTCCCGACCTGCACCCGGCGAGTCCTGGTACATCGCTGTGGGCTACGTGGACGACACACAGTTCGTGCGCTTCAACAG
Seq C2 exon
CGCAGGGGAGAGTGCGAGATATAAGCTACGTGCGTCCTGGGTGGAGCAGGAGGGCCCCGAGTATTGGCAGAAGGAGACAGAGATCGTCACAAGCAATGCACAGTTTTTCCGAGGAAACCTACAGACCATGCTTGACTACTACAACCTGAGCCACGACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000030666:ENSRNOT00000061395:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
NonCoding
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=NA
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
NA
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCCTCACCGTCCTGTTGAGAG
R:
TCGTGGCTCAGGTTGTAGTAGT
Band lengths:
344-662
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]