HsaINT0126263 @ hg19
Intron Retention
Gene
NA
Description
NA
Coordinates
chr2:159533251-159535166:+
Coord C1 exon
chr2:159533251-159533379
Coord A exon
chr2:159533380-159535092
Coord C2 exon
chr2:159535093-159535166
Length
1713 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGA
5' ss Score
9.45
3' ss Seq
CATAAAATATTTTCTTACAGGCT
3' ss Score
7.97
Exon sequences
Seq C1 exon
TCGGCAGCACCTCTTCCTCACCAGCACTGTTAGGAATCAGAGACCCTCGCTCTGAATACGATAGGACCCAGCCACCTATGCAGTATTACAATAGCCAAGGGGATGCCACACATAAAGGCCTGTACCCTG
Seq A exon
GTAAGACGCCAGTTGGGTGTGTGATACAGTCTCTTGAAAAGCCGCATTTCCAGGCGCTTGGCCAGTGGCCTGGGAAGTAGCCTGTGCTTGTATTGAGACAGTCCCCCAGCAGCAAACCATGTTCCAGTCATTCCCTTTCCTACTTTGGGGATTGTTGCCTTTTCTGCTTGTTTAAAGTAAAACAAGCATGTACTTGTTTGTATGTATGTATGTATGTAGTTGTACGGTGGGCACAAATAAAAAGAGGGCTGTATCCAAATAAATCATTTCTGGCTGCTCACTGGCACAGTCCCTTTGCTCCGTCCCCTCCTGGCTCGAGCAGTCTCTGTGTTTTCCACATGCATCAGAACCGTCAGCCCAGTGTCACTTTGCAGGGGCCACATCTTCTAGACTGGCTCATCTCTTAAATTCAAACCAGAGAATGGAGATCAATTTCATTTACATTTTCATGGAGAAGAGTTTGAATAAATAGCAAAAGGTATAATGTGATTCTTCTCAACGTGATTATTTTTTAAGAATAACAAAAATAATGTTACATAGTGTTAATATTTTTATATCCTATTCAGAAAGCTGTGCATACAATTTATTTAAAGGATACCAGCCCAAAGGGTTACTAAGATTTCATACTGTTCCCATTCTCAACCGTCTGGCGATTATAACTACTTTAGATGTTCCAAATAAGTCAGTGTGAGCTACCCCACAAAAAGTACTCTTTTCTCAAACCTGTCTATTAAAAATAAATAAAAGCTGGTGGCAGCTTTACTCCTGCTGGGGGGGCAGTCTCCATTGTACTGTTGTCTTTGAAATTGTGATTTCACAGGACTATTTACTAATCGACTGTTGTTACTATGGCAATTAATAGCTCAGAAAATTGCAGATGCTACATTTCAACACCAAGCTCTGGGCAAAAGGAAATGCACATACCAACTGAAGTGCATGGTTGCTTCCGATTTGCAGCAGCCTGCTTTATCTTACAGATCACCTCTTTAGCATGCATGCCCTTCTGTATCTTCTTCGCTTGCTTCAATAAACTAATTTGCCTCAACTACGTTTCATTTTCCTCATTAAAAAAATAAAAATCTTTGCTAGCCTTAATAATAATGGAAGGGTAACATCATCAGGAGTCTACTATGGACTTTTGAAGACAATTATCTCATTATTACCAAGTTCCTTTTGTATTAAAACATACTTAAATATGCCAGGTACAAGACTGTGCCTCCATTGTTGCTCCTTCCTTGACCTGAGATTTTGAATCCCAGTTGTTTGTTTGGAAGGCATGGGGCTTGTTCGAATATTGTGTTTCGCTTCTCCTCTCTGACCCACTGCCGTAGCTCAGAGCCCTGGAAAAGGAGTGTTCCTCAGCTCAGGATCCCGTGCTGCTGTCCAAAGCCAGCTGGAGAAACCCTCCCACATGTGAGCAGAGCTTGAGCAGGAACCTTTGCGCATGGGCTCTGCACTGGCATTGCTTTTTGGGGAAACACACACAGCCTGTTTCTGCCATAGTTTTGCCATTAGCCCCCACCAGCCCTGAGGTAAGCAGCAGCCAGGCCAGATCCAGGGACCCTGAGCTGCTACCTCTCCCAGCCCGCATTGGCACTGGGGAAGACAGGCCCTGTCGGGGACAGTGCTAGCCCTAGTGCAGGGGAGACCACCCAGCCTAATGGACCAGAGTAATAAGCACTAGTTTTAATTTCATAAAATATTTTCTTACAG
Seq C2 exon
GCTCCAGCAAACCTTCACCAATTTACATCAGTTCCTATTCCTCACCAGCAAGAGAACAAAATAGACGGCTACAG
VastDB Features
Vast-tools module Information
Secondary ID
-PKP4:NM_003628:20
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
No protein impact description available
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
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCGGCAGCACCTCTTCCTC
R:
AGCCGTCTATTTTGTTCTCTTGCT
Band lengths:
199-1912
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)