Special

RnoINT0092392 @ rn6

Intron Retention

Gene
Description
MHC class I polypeptide-related sequence B [Source:RGD Symbol;Acc:1564508]
Coordinates
chr1:79770133-79771920:+
Coord C1 exon
chr1:79770133-79770241
Coord A exon
chr1:79770242-79771398
Coord C2 exon
chr1:79771399-79771920
Length
1157 bp
Sequences
Splice sites
5' ss Seq
CAGGTACTG
5' ss Score
9.04
3' ss Seq
TCTTTCTCCTCTTCTCCCAGGTT
3' ss Score
10.94
Exon sequences
Seq C1 exon
GAGCCACGTGCACCCAAAGCTGACCTAGTTAAGACGTTCTTGGATGAGACATGTCCTGCTCGGCTCCAGAGACACCTGGCTTCCTTGAGTAATGTTCTGCCGGATACAG
Seq A exon
GTACTGACACGGGGCTCCCTCCCTCCATTAGCCTCTTTCTCAGGGATGTTCTGAACCCAGAAGGAGACACAGTTAGTTATGAACAATTGGGCTTGGGTGGTAAGATGTTTTCTCAGAGTTAAGACAAGACAGAAGGATCCGGTTGTGGACCTGGACTACAGATTCAAATGCAAGCTACCCATGTTCCATAGCCAGGGTCCTTTACCTGAAGCTCAGCTCGTTCGTTTGTTTGTTTGTTTGTTTGTTTAAGATTTATTTATTTTATGTATATGAGTATTCTGTCTTCATGCACACCAGAAGAGGGCATCAGATACCATTGTAGATAGCCAAGAGCCACCATGTGGTTGCTGGGAATTAAACTCAGACCTCTGGAAGAGCAGCCAGTGCTCTTAACCACTGAGCCATCTCTCCAGCCCCTCTGCTTTGTTCGAGAAAGGTTAAGCTTTCCGTTTTTGATACAAGGCTGGCTTGGAACTCAAGATCCCACATTCACCTCTTGAATGCTTGGATCCCAGGTATGCACAGCTCTACAAGGCCCTGTTAGGGTGATAGTCAAAGTTGCTCCTTGGCTAAGTCTCATGATTTCAAAAAACAAAAAAAACAAAAAACAAAAAAAAAACCAAACAAACAAAAAAACAAAAACAAAAAAACAAAAACAAACAAACAAAAAAAAAACAACAACAAAAAAAAGAAGAAGAAGAAAGAAAGAAATCCCCCTTGAAATGGGGATAGGGTAGGCAGTGAAGATGCTGGGAACCGGTCAAAAGTCCTCATGAGCAAGGTCAAGGGTCAAGCCAAGAGGCAAAGAATTAGAGCCGCAGTCCGGCAGCACCTCTCTGTCTCCTGGAGTGCATGACACAAGCTTTGGGGGTACGAAGTCAGATTGTCAGCCATCTGTTGACTAGAGAAGCCCACTGTCCCTACCAAGCCATCCCTGGAAGGTTGATCTTCTGGCCTCTAGCCGTCCCCTGGCAGATAGGGGCCTGATAACTCCATGTTATCAGGCATCACTGGGACTGCGTGCTGTACTCCCCAGTCCTCTCACCACTGGCACATCGTCTGGGGGGGGGGCACAGGCACACGGCGTGGTTGTGTAGTTGTGTAGTTTCTGCCCTCCACACCCTACCTTTCACCAGCTCTTTCTCCTCTTCTCCCAG
Seq C2 exon
GTTCCCCAGTGGTGATTGTGACCTGCAGGAATTATCCCGTGGGCAGGATCACGCTGACATGCCGGGCTTTTAATCTGAGTTCCCGTGTGGCCACCCTGCTCTGGCTTCGGGACGGGAAGCCGGTACAGCAGGATGTCTTTGGGCCTGGGACCATCCTGCCCAGTGGGGACGGGACCTACCAGACCTGGGTGTCCATTCGGGTTCTTCCTGGACAGGAACCACAGTTCGCCTGCAACCTGAGGCATAGCAACCGCACCATCATGCAGACCGCTGTCTCTGGCGAGAGCATGGGATGGCCATCTGCCTCATGGGCTACGAGGCAAGAGGCGGAAGGACCCCATAGGACACACAATGACCACGTGGTTGATGGCGGACTGGTTACGGGGAATGCTAATAAGGACAGTCCAGATGCTTCCAGCTGTGCTACAGCCTCAGCCATATCTGCGTTCCCCGTTGTCGTGTTGTCTGTGGCACTGCCCAGAGCCAACTGAATCCAGAGCCTAAAGGATAAGAAGCTTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000057645:ENSRNOT00000083211:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact

ORF disruption upon sequence inclusion

No structure available
Features
Disorder rate (Iupred):
  C1=0.027 A=NA C2=0.307
Domain overlap (PFAM):

C1:
PF0012913=MHC_I=PD(18.2=86.5)
A:
NA
C2:
PF0765410=C1-set=WD(100=47.6)


Main Inclusion Isoform:
NA


Main Skipping Isoform:


Other Inclusion Isoforms:
NA


Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
Mouse
(mm9)
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:
GTGCACCCAAAGCTGACCTAG
R:
TTGCTATGCCTCAGGTTGCAG
Band lengths:
352-1509
Functional annotations
There are 0 annotated functions for this event


GENOMIC CONTEXT[edit]

INCLUSION PATTERN[edit]