DreINT0115983 @ danRer10
Intron Retention
Gene
ENSDARG00000099954 | plekhm1
Description
pleckstrin homology domain containing, family M (with RUN domain) member 1 [Source:ZFIN;Acc:ZDB-GENE-030131-2752]
Coordinates
chr12:4909891-4912014:+
Coord C1 exon
chr12:4909891-4910365
Coord A exon
chr12:4910366-4911845
Coord C2 exon
chr12:4911846-4912014
Length
1480 bp
Sequences
Splice sites
5' ss Seq
TGTGTGAGT
5' ss Score
5.84
3' ss Seq
GTTTTATTTGTGTCTCTCAGAAA
3' ss Score
8.86
Exon sequences
Seq C1 exon
AGAGAGCCTGATGAAGGAGGACATTGATGTGTTCATACCAGCTCCAGACAATCTGACTGACACGCATTCTGTCAACGAGCACACGCACATACCTGACGCCTCACTGACATCAGCACAGGACACGCATCACTCGCACATCACAGAGCAATCTGTAGAGAACATATCAGTGGAGACGAAAGAAGAAACAATAGAAGAATCTGAGATTATAGTTAAAAGCACAAGACTTAAAGCTAAAAATACTGTGAGTGAGACTGCAGAGAAGGAGAAGAAGAGGGAGAGCAGAGACTCATCTGTTGATCCTCCTTCAGTTTCTGCTTTAACAGAGACTGAGGAGACGCCTGACCCTAAAGACACTGTTCTTTCAGAAATTTCTGCTGCTCCTAGTCCAGTGGAAACACCTCAACATGCTGCATGCAGACGCACCACAATGAGCGTCAGCAGGAAAATATCCACAGACTCGCTCTATTCCTCCTGT
Seq A exon
GTGAGTGATTATTTCATTTCTATCAGTCTTGACTTGCATTACAGATGAGCGGAATCAACTTTGATGATGAATCTGTATTAAAAATGATAACAAAACACTTTTAAAAACTATTGTTTTGAATCCCAAGATGTATTATAGTCTGTTTTGGTAACACTTTATTATAAGTAACCATTGACACCATTTATTACCTGCCTATTAAACAGATGTTAACAGTTTATTAGCACTTTCTAAAGTATGATCTTATATTACATCCATAATCCTACCCAACATCTAAACCCAAGCAGTACCCTACTAATTATTTATAAGCAGCTAATTAGTAGACTGGGGGCGAAGCAGTGGCGCAGTAGGTAGTGCTGTCGCCTCACAGCAAGAAGGTCACTGGGTCGCTGATTCGAGCCTCGGCTCAGTTGGCGTTTCTGTGTGGAGTTTGCATGTTCTCCCTGCATTCGCGTGGGTTTCCTCCGGGTACTCCGGTTTCCCTCACAGTCTAAAGACATGCGGTACAGGTGAATTGGGTAGACTAAATTGTCCGTAGTGCATGTGTGTGTGTGGATGTTTTCCAGAGATGGGTTGCGGCTGGAAGGGCATCCGCTAAGTAAGAACTTGCTGGATAAGTTTGCGGCTAATTCCGCTGTGGCGACCCCAGATTAATAAAGGGACTAAGCCGACAAGAAAATGAATGAATGAATGAATAATTAGTAGACTATTGAGCACTGTTGAGTCGTAGTTAATAGTTTAATGATTTGTCAATAACATAAATTGTACATTAAAATAATGCTGCGGTCACACTATAGTAAGCTTGTTATGGGGAGAAAAGTGCAGTGTGATTGCAGCTTAAAGTGTGACCTTGTTTTCTGAAGACATGTGAGAAAGCGTAACAGAAATACATGTAGATTGGCCCCTGTCAAATAATTGCAGTAAGCTCTCAGGTGGAAATTTCATAATTTCTTGCCAATTTTATTTATAAAGAAACATGTTATTTAGAAACAGGCTAACAACATATGTTGGCATGTGGCAGTGTTATAAATCATGTTAGAAGCATGTAAACAGTGTGTTAAAACATGCTAGAAATGTGTTAACAATGGCATAAGTCATGCTACCAGTGAGTTTATCTATCTCTGTCTCACTTTTATAATCATTTTAACTCTTTTAAACTAGGCTAGGCTTAGGCCCAAGCCAAACAGTTGAACAAAATTGATCATCTTTTTATATATATAATATATATATATATATATATATATATATATATATATATATATATAAATAAGTAGTCTAGCAATTAAATTGAACAGATTAGATTCATTTACAGAGATATTAAAATTCATTTACAGAGTTGAATGAAGGATTTTTTTCCCCTTAGGATAATGACGAATGCTGTACCTGATATGTATTCAAACTCTCACCAAATTCGTGTCAACACCTAGAGGATTGATGCTAACAGATGAAAAACTGGCCTAACAGTTTTATTTGTGTCTCTCAG
Seq C2 exon
AAATCTACATCTTGGATCTCAGAGGAGGATTTCCACAAACCCGAAGACTTGAGTATTTCTGAAGCTTATGCCATCATTGACGTCACTCCGATGAACGGGCAGGTGTCTCCTGTGTGTGAAGCAGACGAGCTTCAGCCTCCTCCCAGTGTTGTGCACCGGAGACACAACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000099954:ENSDART00000171525:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.862 A=NA C2=0.316
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Human
(hg19)
No conservation detected
Mouse
(mm9)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGGAGAAGAAGAGGGAGAGCA
R:
CGTCTGCTTCACACACAGGAG
Band lengths:
342-1822
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]