HsaINT0012420 @ hg19
Intron Retention
Gene
ENSG00000141748 | ARL5C
Description
ADP-ribosylation factor-like 5C [Source:HGNC Symbol;Acc:31111]
Coordinates
chr17:37317521-37319111:-
Coord C1 exon
chr17:37318964-37319111
Coord A exon
chr17:37317605-37318963
Coord C2 exon
chr17:37317521-37317604
Length
1359 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGG
5' ss Score
8.41
3' ss Seq
GGCTCCCCTCTGCTGCCCAGTTT
3' ss Score
2.71
Exon sequences
Seq C1 exon
CTTGACCAATGAGGTGGTCCATATGTGTCCCACCATTGGCAGCAACGTGGAGGAGATCATTCTGCCGAAGACCCACTTCTTCATGTGGGACATAGTGAGACCTGAGGCTCTGAGCTTTATCTGGAACACATACTACTCCAACACTGAG
Seq A exon
GTGAGGAGGGCACCAGGGCTGAAGGGTCTCCAAGGCAGGCGTGTGATATCAGACTGTCATGTAACCTTTCTGAGCCTTGGTTCCCCAACTTGTGAAATAGAGATTATAATGGTCGGTTCCTGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGTCCAAGGCGGGTGGATCACCTGAGGTCAAGAGTTCGAAACCAGCCTGGCCAACATGGCAAAACCCCACCTCTACTGAAAATACAAAAATTAGCTGGGCATGGTGTCAGGCACCTGTAATCCCAGCTACTCGGGAGGCTGAGACAGGAGAACTGCTTGAACCTGGGAGGCAGAGGTTGCAGTGAGCCGAGATCACGCCATTGCAACTCCAGCCTGGGCAACAGAGCAAGACTCTGTCTCAAAAAAAAAGTTTTATATATACATATATATAATGATCTCCCTAAGTTGTTGTGAAAATTAAATAACAAACCAATATGTAATGCATATATGTCAGATACTCAACACAGTGCAGTGCCTGCCTGTTAACGTGTTTGAATACTTCCTGGCAGCTGCTGGCAGCTTTCTGTTTGATGCACTGGATGGGTAGGCCCCTTCTCTCTAGGGGCCTTACTTTCTTACTCCAGCAGGAGTAGAATTCAGTGGTATAATTCCTGGACCGAGACAGAGCTGGGTTCCATTTCCAGCACTGCTACTCACCAGCTGTGTGGTCAAGAGCAAGATACATAGCCTCACTGAGCCTCAGTCTCTTCATTTGTAAAATGGGGATACTAACAGTACCAAGTCCACAGCGTTGTGGTAAGGCCTAAATGGAGTCATGAACACCCAATGCTTATGTAGCACAGCCTCTGCCACACAGTCAGAGGTGTGCTATTCCCATGTCTGGATAGAAAAGACAATTACAGGCCAGGTGTGGCAGCACACCTGGTGGTAATCCCAGCACTTTGGGAGGCTGAGGCAGGCAGATGACCTGAGATCAGGAGTTTGAGACCATCCTGGCCAACATGGCGAAACCCCGTCTCTACTAAAAATACAAAAATTAGCCGGGTGTGGTGGCACGCGCCTGTAATCCCAGCTACTTGGGAGGCTGAGGTGGGAGAATCGCTTGAACTAAGGAGGCAGAAGTTGGAGTGAACCAAGATTGCGCCACTGCACTCCAGCCTGGATGACAGAGCGAGACTCCGCCTCAAAAAAAAAAAAAAAGACAATTATAATGGAAGCAGGGTGGTGAAATCTTGAGGCTGCATGCTTTCATTTCTCTGGGGCTGACATCTGGGCAGTGCAGAGACCAGTGGGGAAAGAAAGAGGGCAGGAAACACATTTACCAAAGAGAAAGCCTGTCTCTCACGGCTCCCCTCTGCTGCCCAG
Seq C2 exon
TTTATCATCCTTGTGATTGACAGCACGGACCGGGATCGGCTGCTGACCACTCGGGAGGAGCTATATAAAATGCTGGCCCATGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000141748-ARL5C:NM_001143968:3
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF128032=G-7-MTase=FE(29.2=100),PF0002516=Arf=FE(27.8=100)
A:
NA
C2:
PF128032=G-7-MTase=FE(16.1=100),PF0002516=Arf=FE(15.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCAATGAGGTGGTCCATATGTGT
R:
TGGGCCAGCATTTTATATAGCTCC
Band lengths:
223-1582
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)