GgaINT0121812 @ galGal4
Intron Retention
Gene
ENSGALG00000027302 | TMEM52B
Description
transmembrane protein 52B [Source:HGNC Symbol;Acc:HGNC:26438]
Coordinates
chr1:77900956-77904963:-
Coord C1 exon
chr1:77904794-77904963
Coord A exon
chr1:77904351-77904793
Coord C2 exon
chr1:77900956-77904350
Length
443 bp
Sequences
Splice sites
5' ss Seq
CCTGTGAGT
5' ss Score
7.21
3' ss Seq
TTCTGTCTCCTCCTTTTCAGCTC
3' ss Score
10.95
Exon sequences
Seq C1 exon
GCTGGTGGTTGTGATTGGTGGACTGCTGCTGCTGTGCGGCTTGGTTTCTGTCTGCGTGAGATGTTGTCTCACTCACTGCCGTCAGGCTGGGGAGGAATCAGGTCTTCAACCCTATGAGGTCACTGTCATTGCTTTTGATCATGACAACACCCTCCAGAGCACCATTACCT
Seq A exon
GTGAGTTGGCTTTGTCAGATAGTGGGCACCTCAGCATGCCCTGCTGTGGCGGTTGCACCATAAAATGCCCAGACTGAGGCATATCAAGTCCTCCAATGGGCTGGCAAGGTGCTGGGAATGTGACATCTGTAAATACTATAAATTAAGGTACTCACCAGGCCTTATGTAGCAAATATGGTCAGATGATGAACTGTTTAAAGACATGTTTGGGTGGACTATGGGCAGCTACCAGATCCTTGATGGCATTAGAGGAAGGAGTAATTATGGGATGTTGTTGATGGGGCTTCATTCCTCCCTTTAGGGGAGGACTAAGGGGCGGGAAAACATTCAGGCCATGGTGAGAGAAAAGCGTGTGCATTGCAAATATACCTGTCTACCTGTCCCACTTTAATTGTACATGGCTTTCAGGATGAGGCAAATAGCTTCTGTCTCCTCCTTTTCAG
Seq C2 exon
CTCTTCATTCGGTGTTTGGGCCAGCTGCCAGGAGGATCCTAGCGGTGTCACACTCCCACAACACTGCGCAGGGCACGCCACCCCTCGCAGCATCAGACACCCCTCCAGTCTACGAGGAAGCTCTACACACAAGCAGATTCACAGTTGCCAGGGCGGGGCAGAAAGTGCTAGACCTGGATCCAGTGACAAAAGAAAAACTAGCAGACATCTGCCGAGGATAAGGATGCCCAGCCAGTCTTTGCAGAACACTAGTGCAGAACATTAGGAATATCAGATTAACCTCCTTAGTCTAATGAAAAAGGGGGAAAAAATGAGACTAAAATTCCAGATAGTTCTAGATCCAGCGTGTTTGGATAGCTCCTTTTTACTCCTTGAGATAACTGACCATTGGCAATCCCTGGATGCATCTGTTATACACACACATCACTAGATTCACAGATTGCATATACAAGCAGGCAGCAGGGTCAAAGCGCTGAGCCTTTATAGGCTGGTGCTGGATACCTACAGGGAGATGCTACCTCATTCTGATTGCCTACAGCCTGCATTTCCTGGGGATGGCAGAGATTTTCAGAGAAGGAAATGATAAGAAAGGGTCTTGCAACCAATATTAAAACTAAACTCCAGGAAAGCACCAACCATTCACAGTAATTAAAAAAAAAAAAAAAAAGAAAAAGAGGCTACATGTACACAATCTGCATGTAAGCAAAAGATAGCATAGTAGTATTTACAGTTCCCTAAATGCTCTACAGGATATATAGAGGGAGTACACTCTTGTCTTGAATATGATATATAGCAATTCTGAAATAGCAGTTATAAACTCTAGTATTTGAATTGAAACTATGATGTGTGCAATAACAAATCAAACAATAGAAGAAAGAACTCTATTGTTAAAATTTAATTATGTTTTAGTTGCCTTCATATTGTATCACTTATTAATTATTCCTACCACTGCTGTCAAAATCAGATCAGACTAAAGAAGATGATTTAAAACACTTCAGCCATTTCTCAAATACAAATAATTTGTGAGTCTTTCCTGATCCATAGAGATATGATTAATCACGAATAAATATCCATCAAACTGCTTGGATGAGCACTGCTATGGACTAACTGTTTAGTTCAGTTAGATACTCTTGACAAAGTGAAAGTTGAATTACATTGGTGTTGCCTGTAACCCAGGTTCTGCAACTGAAAACATTAAAGGAGAATGACATCAAAAACCAAATAATAAGCAGTCATTATTTATTTTATTTTTATTACTTTAGTTAATAATTACTTTATATGTTAATGTTGATGTGAATGCACAGACTGAACATCTATCTGAAGTGACGGCACGGCTCTTCCTACTATTCTACCCCAAACCCCACAGACTTTAATACATTGATGTTCACAACACTCCTTGTGAAATACACAGTAATACAGCCATTTTGTAGATAAGGAGAAAAAGGAGCAAGTTGCCAAATATGCTTAGGAATGTAACTGCTGTTGAGATTACAATCATCAAGGGATCTAGAAAGGAATGTTGATAAGATATCTCCAGGGATAGCGTAAAGCAGAACTGAACAACTAAAAGATCTTCGATCATTTCCCAGACTTTGGCTGGTCACAGAAATTTTGTATCCAAGAAAAGTATTTACTGCAGGTCTCAGTTCCCCAGCTCACCATTGTTTTTTTTTTCCTGAATTGCCTAGTCATTTGCTAATTGCATCAGTAATGGATGATAAACTTGAATAAAATAAATAAGTGACATATAAGGGTATGTCCCTTCTGCTACACAGTACTTGAAATAATAATAAGTGTTTGCGAAACATCCAGTTGAGTGACCTATTTCATCAGCTGATCTCTGAAGTTGAGTACAAGCCTGCCGTCTCTATCACACTGCAGAACATTTCCTGGAAGGCTTTTGTTTACTTCACAGTAAAGACGTGAAGCAAGCAGAGACATTTGCTGAAAATGTGTCTAGCCCTATTTTGACCAGAAACTTCTTGGAAGCCTTCGCAAACGTTTCCATTTGGAACATACCATTCCTGCACTGTCTCCACCCCTTTTTTCCTGCCGTAGAACACAGCCGGCCAAGTCCTGAGCTGTGCGTGCATTTAACATAAGATGGCAGTCGTTCTCCACAGGGGAGCAATCTCGCTGCTGGAATTCTCCCCAGACCCAGCAATACAAGAATGGATATCTTAAAAGAATTTTTATAATAACTACACTGCAATTTTGATAAGATGTGCAATAAAAAAGGGCAGTTTTAAAATGTTTTGTTCCCTCCCCCTCCTCTGCATCACACCACCTTTGCTACCTCTGATCTCCACTTCAAGGGAAAGCTAATGTGTCACTTGTACTGAGAGCTGGGTATCATCTGCTGATTCGAGTGTATTTCCCTCGACCAGAGTCACTACTGTCTAACTCTCACGTACTTCACCGTCTGCTCACATCTTTTTCCATTTGACTCACGCTTCATTGTGACTGACTGTAACGGGTCTTCTGCTGGCAAGAGATCAAATGATGTGACAATGATGATAGATACAACTTCATTCGTTAAGGGTTTCCTAAAGTGATTTCGGATGAGTGAATTCAGAGAAAATAGTCTTGCAACTGATCAGACACTCGAAGTCCACAGGATGTAATAAAATACCAGATTAGAGAAAAAAAAAGAAAAGTAAAAGCAGGCCAACAGACACTAAATCTCATGGGTATCGAGCCTTTTGGCTTGCCTGGGCCGCATTCAGTGAATAGAAATTGTCTTGGGCCGCGTAGGTCGCTCCAAAGTAATGCCTCCTACTCATTTCCATGGAAATTACAGCTGGTACACAGAGCTCGATAACACTGTTTGACAGAGCAAATCTCGGCTACAAAACATTAATTTTCAACATAGCCACCACCATTAACTATTCATTTTCACCCACGAGGAACAAGAGCCTGTGTGCTGCTCTTGTAAAAATCAGCAGCAGTGAAGGTGACCCACTGTTACCACAGCTGAAACACACCACCTCACCACGCTCAGTTTCACTGTTTGGTCTCCATAAACATTCAGCAAGTGAATGTCAGTGGGTGCAATTTTTTCCTCATGGATAAACTCAAAGAGACACTTTTGCTTCATATGTTCTTCTATGTCAGACACCATTTTCTCAGATGATCCCTCTGCTGCTACCTGCCACAGGTACAGGCCACATCCAACTCCCATACTCTGGACCAAAATAATAAAATAGGAGGCATTACTTTTTGAGCAGTCCTAATATTTTTAATGCATATAAGTAACACAACTTTAAAATTTCCAGTACTTCCATTACAACATTAAAAAGGTAAGCAACAAAAACATAAGAGCAGCGAGATATTTGACCTTGTTTTTGTGAAACTAATGCATCAGTCTGGTTTGATGGCAGTGGTTGCATTTCTTA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000027302:ENSGALT00000045030:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.096
Domain overlap (PFAM):
C1:
PF149791=TMEM52=FE(39.3=100)
A:
NA
C2:
PF149791=TMEM52=PD(45.5=89.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTTGTCTCACTCACTGCCGTC
R:
AGACTGGCTGGGCATCCTTAT
Band lengths:
346-789
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]