RnoINT0152906 @ rn6
Intron Retention
Gene
ENSRNOG00000058653 | Tmem52b
Description
transmembrane protein 52B [Source:RGD Symbol;Acc:1586337]
Coordinates
chr4:163271661-163274028:+
Coord C1 exon
chr4:163271661-163271827
Coord A exon
chr4:163271828-163272217
Coord C2 exon
chr4:163272218-163274028
Length
390 bp
Sequences
Splice sites
5' ss Seq
CATGTGAGT
5' ss Score
7.83
3' ss Seq
AACTCTGTCTTCCTTCACAGCTC
3' ss Score
11.01
Exon sequences
Seq C1 exon
GCTGCTGGTGGTAGTTGGCGCGCTGCTACTCCTATGTGGTCTGACTTCAGTATGCTTCCGATGCTGCCTGAACCGTCCGGAAAATGGGGAAGATGGGGCCCCGCCGCCTTATGAAGTGACTGTCATTGCTTTTGACCACGACAGCACTCTCCAGAACACCATTACAT
Seq A exon
GTGAGTCTATTCAGAACACCAAGTTAGGGTTCACGTTTAAAGATGTATTAAACGGTTTGAAAATGCATGTAGGGCAACTTGCGAACTAGCCTTGAGTGTTTGAGAACTGGGTGTAGTTTTCATTTCCAGAAACTAAAGAATGTGGTGACCTGGGCTATCACTGTTGCCTATATTCTCAAGTTTTTGGCTGACGATAAATCGATGAACCAAGTAAAATATTGGAACCAGAGTTTCTTGAAGGATTTTTGTAAAGTTTTTCAAAGGTCACGGTAACAAGCTTGAACGTGTGTGAAAGACAAAGAGACGTTAGGTGTGATGTAGATCTCTCATGTTTGAGGACATGGCCTTTGGATGTCATCATCTCTACACTAACTCTGTCTTCCTTCACAG
Seq C2 exon
CTCTGCAGTCTGTGTTTGGCCCCGCAGCACGGAGAATCCTGGCAGTGGCTCAGGCACACAGCTCCCTGGGCCAGCTGCCCTCCTCTGTGGACACACTCCCGGGCTACGAGGAAGCTCTTGGCATGAGCCGCTTCACAGTGGCAAGGTGTGGGCAGAAAGCTCCTGATTTACCCTCTGTCCCAGAGGAAAAGCAGCTGCCTCCCACAGGGAAAGAGTCTCCTGGGACAGAAACCCCATCACACTGATGGGGATGACGGTGTTCCTCATGTCCAAGGCATCCTCGGGTCTGGAAAGATCCCCAGACACATGAAATCTTTTGGACTACCCAGAAAGGTTCAGGGTGCCATCTAGACATTTTTCTATGAACAAGATGGGTTTTCACTCTTCATTCACGACAATATGCTTTTTCTGATACACAGATTTCTAACTGAATTCTAACCCCTTATTCAAAGTTCAAAGTTTGCAGCTCATCTTTAGCTATATTGATTACTACCAGAGCATGAAACATTAAGGTATCTTGAATTCCTTCAACTATGGCATGCATATAAGGTTCCTTTAACCCTAAGATCCTGCAAACTACTCGTCCCTCTGCTTAACTGTTATTCTTGAAGGGAAACACACTTTGAGCACAGCCACTAACATCAGTGCACCGAATCCATGCATCTTTTCTTCTAGGGAACAACCACCTTTATGCTGAATCACCATGGCAACTTGGTACGCCATATAATCCCCACCTGGACTTGCATATTGTAAAGCTAGAGGTGCTTGCTGATATGAGAGGGGAGACACTAATATAGTATATGCCACACATCCAAACCTTTCTAACATTTTGGTCTAACCCACAAGTGTGAGACATTGTATAGAGTGCAGAAATGGTCCTAGCAACTTTCCAGTGCTTTGTCCTGCAAACACTCGTGCGTGTGTATGCATGCACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACGAGCACACACTCCTTTTAGCTCTGAAAGAAAGCATGTCTCTGCTTCTTTCCTTCTTGTTCTCAGGATGCAAACTTTCACCATGTAGTCTAGAGAGACTCATCCTGGCTCTTGAGGTGGGCCATGCTGCCATCTAGTGGAACTATAATGGAAAATGCACTCACTCCTTTGAGGTCCTATGTATGTTCCTTTTCTCAGTGCTACCCTAAGCCTGGATCTTCTTCTGATGGAAGCATCAAAAGTGAGTGCCGGGCTGGAGAGATGGCTCAGTTGTTAAGAGCACTAACTGTTCTTCCAGAGGTCCTGAGTTCAAATCCCAGCAACAACGTGGTGGCTCACAGCCATCTATAATGGGATCGATGCCCTCTTCTGGTGTGTCTGAAGACAGCGACAGTGTACTTAAATACATAAGATAAGTAAATAAACCTTTAAGAAAAAAAAAAGTGAGTGCCAAGCTATTCTGGTCATGTACTACTTTCCACAGTACTGCTATTACAATCAAAGGAGTGAGATGTACTCTGGAAAAAACTACTGAGAGAAGTTATTCAAATCCTGGAATAATGATTTTCTCATCTGTAAATTAGACATTATGGTGCACATCCAAGAACACAAATACCCAAGGCACGATTTGTAAAGATATTCCATGCATCACATATTACTCTTTCTGTTGTTATCGTCTCTTCAGTGCCCTGTGGTGACTTCACTGAGAAGTATGTTCTGGTCTGTCCTTTGCCTCTCCGCTATGTTATTGTAAAGCCATAGCTGAAGAGCCTTTATTTTATCAATAAAGATGTGTTGCTTGAGATAAACAGCTGAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000058653:ENSRNOT00000079337:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.018 A=NA C2=0.346
Domain overlap (PFAM):
C1:
PF149791=TMEM52=FE(39.4=100)
A:
NA
C2:
PF149791=TMEM52=PD(45.1=78.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGGAAAATGGGGAAGATGGGG
R:
GAACACCGTCATCCCCATCAG
Band lengths:
352-742
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]