HsaINT0061968 @ hg19
Intron Retention
Gene
ENSG00000078098 | FAP
Description
fibroblast activation protein, alpha [Source:HGNC Symbol;Acc:3590]
Coordinates
chr2:163072408-163074650:-
Coord C1 exon
chr2:163074496-163074650
Coord A exon
chr2:163072512-163074495
Coord C2 exon
chr2:163072408-163072511
Length
1984 bp
Sequences
Splice sites
5' ss Seq
AAGGTATGT
5' ss Score
9.79
3' ss Seq
TATCTCAATTTTCTTGGCAGGCT
3' ss Score
7.47
Exon sequences
Seq C1 exon
AGGAAATGCTTGCTACAAAATATGCTCTCTGGTGGTCTCCTAATGGAAAATTTTTGGCATATGCGGAATTTAATGATACGGATATACCAGTTATTGCCTATTCCTATTATGGCGATGAACAATATCCTAGAACAATAAATATTCCATACCCAAAG
Seq A exon
GTATGTTGAATACTTTCAGCGATGCTTTCATTTTCCTGGTATCAAAATGAGCAATGATTTACCATGAGTAAAGGTGGGATCAACAAGTTTGGAGAGCTTCTTATCCTTGAGCATTGTAAGGCAAACATTGTACTGTGCTCTATTATTTATGTGGACATCTGTTGCTTTGGACATCTGGTTGTGCTGGATGAAGTAGTCTTTGCAAAATCTATTGCAGAATCTTTGAAAAACATATGGTCTTGATCATGGAGGAAAAACAAGCTTAACTTAATTTTAATTTTTTTCATATTTCATGCTCCAAATTCAGGGTAAAGTTCTGTTTTGCAATTCTCTCTTGAATTCTCATGTAAATGCAAACTAGAATATGAAATACAAATGCTGAATTTGATGTTCCTGTCAGGTAGAAGCAGGCATGGGTTATGGTCCTTTCTGGATGTACAAGATAGGTTAAATTTATAAGTCTCAATTTCTCCCTTGAAGGAAGTAGACATGGTGTGAACCCATAGTTTTTGGATATTTAACATTGTAGAGTTGTTATACATTCTTTTTATTGAGTTTCACATCTGGAGGGAGGAGACCTGAGTGTGCAGTAGGAGAATGGTCAGGTCTCAGTGAAGAAGCATTATATCCTAATTTCAATGTAAAAATGATATCAGAAAAAATGGAATCAAAGTACAAATTTACCTCTTGCACAAGGAATCGGATGCGATTTTAGAATTCACTTCTTTGTTCTTTGGATGCTATTGCTTTTACTTGCCAAGGGGAATATTGTCGTGGCTGGACACAGTGGGTCCCTGGGTGACAAAGACGGTTGGATGTGGTATACACACAAGTGAATTCTAAGCAAGCCAAAGTGGCCATAGAGAAAGAAATAGAATTGCAGACAGTGTAATATTTATGTTAAAAGTCTAAAAGCTGTGTAAAAACTCTAAAAGCTGGAGATGTTTGGGACAGGCCTCACATTTTGGGGGAACCCAAGATGTAAAAGAACTCAGATCTTTGGGAGGACCTATGGGAGCAGGAAGAGACGGGGAACCCAGAACTGAAGAGTGACTGACACTGATTGGGAAGTTGGGACCCACATTCTCATATTTCCTTGAGGCTTAAGGTTGCTAAAACATCTGGCGTTAGGTGGAGACGTGAGACCATCCCAAAAACTAAGGGAGTTTCTGATAAACTTGGGAGTGAAACGGAGGTCCTAAGAGACGTTGAACAGTTCTTTGGATGAATTCAAACAGCACTGAGTCATTACATACTGTGCACCTACATTTCATGAATTTAAATTTTATTACAACTCCAAGATTCTCTCTTTCTACAGCAAAATAACAGAGGAACTCTAAGAAACTGTCTAGGTATGAGCTATACTGTCATGTAAATTTTAAGCATACAGTAGTATAGAAAGCACAAAACAAGAAAAGTATAAATCTCATGGATACTTCATTTGGAGGTGAAATTTCCCTAACCTTTTGGAGATGGTGGCAGTAATAATGCAAGCAGGTAGGAGACTGAGCATTTGGTGATTGTCCTAGACCAAATCATATGGCAAAAGCAAAAAGTGTCTTTCATTTATTTTTCTTTCCATTCTCCTCTCAAATTAATCACCCTCTGAACTCTCCTTGGTATACAGATTATTATAATTATCCCAATAATAAAAATGAGAGAGATCTGTCTTGGAAATCAGAAAACAGAATATGGTTCACAGAACTGCATTTTCATATCCAAAATGATTTTCCCTATAAATTTTAAAGCTCTCTCATTAGGCAGTTAAAACACATAGTTTTGCTCTGGTTGACACAACATTTGTAATTGCCCTGCAGGTAAAATTGAAATGAGATTCCTTGTCGTGTTATAAATAGAATGTATTCCACAGTGATATACATAAGATTGTTCGCTTAGAAAAATATATCTAAATTCCTAAAGTTTCTTTAAAATGTTGGTGATAATTGGAATTTTATGAGCTTATATATCTCAATTTTCTTGGCAG
Seq C2 exon
GCTGGAGCTAAGAATCCCGTTGTTCGGATATTTATTATCGATACCACTTACCCTGCGTATGTAGGTCCCCAGGAAGTGCCTGTTCCAGCAATGATAGCCTCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000078098-FAP:NM_004460:9
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0093016=DPPIV_N=FE(13.9=100)
A:
NA
C2:
PF0093016=DPPIV_N=FE(9.2=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGGAAATGCTTGCTACAAAATATGCT
R:
TGAGGCTATCATTGCTGGAACA
Band lengths:
257-2241
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development
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)