HsaINT0139677 @ hg19
Intron Retention
Gene
ENSG00000131378 | RFTN1
Description
raftlin, lipid raft linker 1 [Source:HGNC Symbol;Acc:30278]
Coordinates
chr3:16357352-16364964:-
Coord C1 exon
chr3:16364883-16364964
Coord A exon
chr3:16358740-16364882
Coord C2 exon
chr3:16357352-16358739
Length
6143 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGA
5' ss Score
10.57
3' ss Seq
CCATCCTTTCTGATTTCTAGTTT
3' ss Score
7.51
Exon sequences
Seq C1 exon
CGAGGGGAGTGTATCCACCAAGCAGATTGTCTTTCTTCAGAGACCTTGTCTACCTCAGAAAATCAAGAAGAAGGAATCGAAG
Seq A exon
GTAAGAGACTTTGATGGCCTTCCTAGGTTTTCCTCAGCAGGGCTTCATCTTCAGTGGATTTTCTGCAGCATTTGAGGGGGCAGCCTGCTCCAGCTTCCAAGGGCTCGCAGAGCCCAAGGAACACCTGAGCCCCTGGCAACCCGAATCACATCTCAGGCTGCTAAAACGGGACAGCTGAGGGGACTGGAGGGCCTTGTCTGCCATCGTCCTGCTGGGCCGGCCAGAAGGATGGAGGAGAGAGGCTCTTCTGGAGGCTTCAGCCTGCTAGATATTCCCACTAGGATGAAAAGAAGGGCACGAAGTCAGCTGCAGCCTGACCATGGGGTGGGGATGGCTCGAGCTCATGGCCAGTTTCTTTGTGTCTTAATCTCATTATCAGCTAGTTGGAGCTCTGGCCTGCCCTGTTAAGATTCCTTAGGACATTAAAAGTGTGGGGATCTAAGCAGAGACCCTGCCAAAATTTCTTCATGACAGGCCTAGACCCAAAGGCCTCTGTGTGACAGCTGGTGATGCTAGCTGTAGCCTGTGGCAGCAAGTCCTCAGGCCAGGCTGTCCTCAAGAGATCCCCAGGGCCCTTTTCCCCCTCTCCGGACTCTGAACTACCCTAGAAACAGTCGCACAGAGACTGGCCTTCTCAGAGAGTCTTCTCTGTGATTCCTGAAGGTTGAGCACAAGGGCTGTACGAGGTGCAAGTGTCGGCAACCCTTGTGCCAGATGATTCTGATGCTTCCCACCCCACCCTGAGCAGCCTGTGGTGCTTTTCCTGAGGACATTTTCACCAGTTGCTGGGGAAGAGGCCAGTGAGTCGAGTGGACACACCAAAGCCTGAGTCAGGCATCACCTGGATTCAGCTCACTGCACCTTTGATGGCTGAGGCCACATTCTCGGCAGGGCCTGCCTGACCTGCTCGGCTCCTCACTCCTGGCATCACTCCTGCATTCCTCACGCTTGGTTCCTCATGTTCTTTGGACACAGAGCCCTGGGAAGGAGCATCAAGTAAATGAACAGATTGGAGCAGCCCCTCACCAGCCAACAACTCCAGGGGGAGCCCACTTGTGGAAGGAGTGCCAAAGCAATGGTGACTTGAAGCCAGATGGGCTGGAGTGTGGAGGAAGGTCTTTCTCCAGGCTCTGAAGGTGTAATGTGACAGGTGACGGCACAATGGACCAGAAGGGAACTGCCAGCCCACCATCAACCACCAGGAGCAGGCAGCCACCAGCTGGAAGATGGATCGGCTGCAGAGCGCTGTCAGTTTCAGCTCAGCCACAGGCTCACGGGAACTGCATGCATTCAGCAAGTGCAACATTCAACACACAGCACGCAAAGGGCCCCTGTCAGATGCTGACAGACACCCGCTGCAGCCTTACAGAGGGAGATGGTGCCACCTTTGCCTAACAGGTTCCTGGTGGTGGGGCACACAGATTCCAAAGGAGAGACATGTGGTTGGATGTTGGTGTGAAGGTCATGGCATCGCATGCAGGGGGACAAGTCAGTGGAAACTTGAGTCGGCAGGGAGACTTTAGAGATAGATTTGTAAAAGCTGCTGTAATAAGGTTGAACTGACTCTCCTCAGGGAAAATTCAGAGAGGATGGGACCCACTGTTTTTTCAGTCAGTAAAAACTTCTAATCCCAAGCAGCTGTACTCATCTGGGTGGACTGCTTTCTCTTTCCATGTACCTAATTATTTCCTGCCTCATTCCAAGACTGTAGGTGACTGGTGTGGAGCACTTGTTCTACACAAGACCCTCTGGGTCACCTCACAGATGGGAGTCCTCCAGAGAGGGGGGCTTCACAGCCAGACTCCTTGGAAGAATCTTCTGCACTGGGTGTCCCCTCCTCACTCCTCAGCTGACAAGGGTCAGCGTCCTACTCCCACAGGCCTGTGTCCCCTGGTGACCGAGAGTCACTCCATCTAGTCCTCATCATGCCTGAGCTCTTGCAGCCCGGATGTTGGGACCACCCCCACTCCCTGAAGCAGCTTTTCTCTTGGTTCTTTCCCACCTCATTCTCCTGGTTTCCCACTAAGTTCCTCAGGGTTCAGACCCAGCCCCATTTCTCCCTTCACTCTTGCCTCTTCCTTAGAAAATCTCCTTCACCACCTCTGTGCCAATGACCATTCCGCCTGCATTTTCAGCCCTCACTGCACCCCAAGACTCCAGCTCCATCCATCCTGTGGCTCGAGGAAACCTATGACTGTCCCCCTCCCCATACCTCGCCCACCTGGCCAACCGCCACCCTATCTAGAGGAATGGCATTGCACCTTAGGGGCTATCCCTGCTGACCCTCCCCTCTCCTTCCCCTATATTCAATCTATCCTTAAGACCCATCTGTGTTAGGTCCCGGAGGCTCTGGAATCCCTCCACTTCTCTCTACCATCACTCGCCTCAGCTATTCTAATCTCCTAATAATAGATATCCCCTTCAAATAGGTTCCCTATTCAGAGCCCAAGTGATCTGTTAAAAAGGGAACTTGAATCCTGTCATCCCACTGCTCAAAGGAGTTCTAGTTTTGTATGACTCTGAAGACAAAGATGGAAATCAGTACTGTGGCCCTCAAGGCCCCAAGGGATCTGGTCCCTCTTACCTCCTCTGCCAGCCTCCCATTCTCTGTGGCCTCCAGCTCCTCTGTGGCCTCCAGTTCTTCCGTGTCCCCTCTGCCAAGGACATTCTCCTCCTTTCTAGCTCTACTCGAGCATCCTTTTCTCAGAACAGTGCTGTCTCCTTTTATACCAAACCAGACTCCTTTGTACTACCCTGGAAAAGAACCACGTTCTTCTCCTTCAGAGCTCTCCTTTGGGCTTTTAGTTATTTGTGATCATTATTTTATCCTTCCCAGGCAGAGTCAGACATAGTCTCCACAAGAGCAAAGACCTTTTTCCTGTGTTGTGTACCCAGATTTTAGTTGGTGCTCAACAGATACTTGTCGAATCAATGAATGAGTAATCAGCTTCTTAGCGAGGACACACATAGTATGTCTAGCATTAAAACTTAAGAAAAGAAACTGCAAGATTGGCACACCGAGGATGTGGCATATTTAGTCTTCTTTTAATCAGCAACATGGATAGATTTTTCTAATCAGGACTTTTCAGCATTGGAAAGAAACCTCTGTGTACGTGCGTGTGATTTTCAAGGCAAATATTAAACTTCTTCAAAGGGAGTAGGTGATTTCTACAACTCGGGAAGACTTCCTTCCAGCTAAACTACTTGAAGTGGACACATCATGGGCAGTTTTTAAAATGTGCAAATTAAATCCATTGGCTCCTGCTGACATGGAACTCTGGACACACACTGCTGTAAAGTGAAGGATTTCTTTTTTTCTTTTAGACAGTTATTTCTGAATTGGGCGGCTAATTGGATTTGGTGACACACCCAACTGCCACAGATGCTCTGGCTTGGGAAGGCCCCCAACTCAGTGCAACCTGTTTTATCTGCGGCTTGCTGGTTAAGCTCAGAGACTCCCCCGGTCCTACTCAAAACCTGGAGTCCATTCCCCAGGCTGGACTTGCCTGCCTTTAAGTGGTGTGGATGTCAGAGCTCACCTCAGAGGCTCAACTGAAATCTGGCACAGTCCAGGCCTCCTCTTGCTTTCTGAGACGTCTCCTTTTTGAATTGTTGGGATCTGAAACAGTTTTTGTTGTTTGTTTTCTACCATTTGTGTTCTCGTTTTGTATTATATCAGCAGATCAACAAGATGTGATCTTCTACAGGAAACTGGATGTGGCCAGGCATCCAGGGGAAACTATGGAAGCTCTGTTATTTAGCAAGAGCAGCCCCGGAGAGAGTATCTGGGCTCATATTAGATGGAAGGTCTAGCACGTGGTGGAATTGTCCTCAGTTGTACACTGCACAACAGCAGAGGGCGCTATTCACATCAAATACAATATGAATGGGGCCCTGGAGGTGTGCACCGCAGCCCTGGAGGTAGAGACAACCATTTTAGAGATGAGTAACTTGAAACTCAGATTCATAACCTGCCTAAAGACTGACAGCTAATGAGTGCCAGCACTAGGATTTGAACCCATACTATAATGCTTTGACATTTTAGCACTTAAGGCCTCTTAGCCAAAACAATCACCACTTTTTTGGCAACAGTAAAACTTCCTCTGACTTCCCTGAGAGCCAACTGCCTCTCGGAGTACTATACTACACAGGTAGGCTTCACTGGTCCTTTTCTAAAAACACGTAAAATGATATAAAATGTGAAGAGGCTCTGACTGTTTTGGAACATCCATTAAAAAAAAGGAGAGACTCTTACATTTGGGCTGGAATTAAAATGCAACGGCAGCTGCCTAACACAGGGCAGCAGTTACGAACCATAACACGGTGCCTGGAAACTATGGAGGCTTGGTGGAGGCAGCCACGGTCATGCTGAGGGCTAAAATCAGGGGCCTCCTCTGGTGGGTTTGGAGCCTCGAGATGCCTGCCTGGCAGGCTCGGCTTAAGTAGGAGGTGGGTCTGAGACACCACTTAGCCTACAGAGTGATTCCATTATTGGGATCCTCACAGTTTGGGTGGAAGAAGCTCCACCCATCTCCTAAGGGAAGTCTGTCAGCTACAGTACGAGACATTTCAAAAGAAGTCAAAGGAGAAACCCATCCAACATTGTAAGTGAACTCATTTGGGTTTTTTGGGGGATACAGGGTGGGAAAGGACCAGATAAATGTTAAATCCTAACCTCAACATGTATTTCACTCATGTTTCTCTACTTTAATGGAACATTCCATTACCATTCTTATCTAAAAGGTGCTAAATCCAAGAATCCTATAATGTATTAAATCTCAGAATTCTGTGTTTGGGCAAATGTTTTATCTGAGGAAACAGATCTCTACCGTGGAAAACTACAAAAATGGCAGATTTTTAAACATTTACATAGCACATTTTTGGTTTTTCCTAGCAAAGCGCTCAGAATGATTTACAACATACTAAAGCCTTAAGAAATCATTTCCCACTGATGGTGCAACTGCATTCCTGGGCTCCTCTCTCTAGCCCAGCAAGAAATCATAGGAACTGAGAGCTCCCTTTTTCTCTCAATTATATAATGTCTAAGATTTAAGTGCGTATTTGGTGAAACCAATGAGATAACAGCTGAAGCACAAGGAAGTGGCCATGGTGGGAACTGAAAACTAAAACCCCACGTGCACTCTGGGCCACCGAGATGAGAAATTCAGATTGAGAAACTTGGCCGGTCAGTGACGGAGCTGGGGCTCGCTCTCGGGTGGTCTTGCTCCAGAGATTTGATGAGACCCTGGTTGTTGCCCAACTCTATTACTGGCCGCGTGACCTTGGGACTCTGAGCCCCTGACTTCCCTGTCACACCAGGAAATGCTTGGTTGCAGGTTGGGCCCCCGGGAAGCGGCCTCTGAGATTGGAAGTTTTTAGAGGGAGTTACCTTAGAACACTTGTCGGTACAGTAGCGGGCAGAGGGAGAATTTGGGCTGTGATGCAGTCACAATCCCCCAGGTTGGCTTGGAGCTGGGATGGCATTTGCGTTATCCCAAATTGGGATCAGGAAATGGGTTGTTGTATCCCACCTGGGGCAGTCATTGGTTGTAGGTTGCCCTGGTGTGACCCTTCTGTGAGGTGGTGGTCAGCAAAGGGCTATCGGCCTAGCTGGGGAGCGGGCCCGCCAGTCCTGTGGGGGGATCTGAGCGGTACAGCACAGTGTCTGCCCCATGTTCTGGGCCCTGCCTTACTCAGGTGACCTAGTGAGAGAATGCCAGCCCCGTGCCTGGTAATCCTCAGCCTGCTCAGAATGGAAATGAGTAGCTGCAGCTCTGGCTCTTACTGGGGGCAGGCCTCACATCTCCTCTCCATCCTGGCCCTCCAAATGATAGGACTTTAGGAGCCCTTTCCTATGTGGGCCTTTGGTATAGAGCCAGTCAAAAGAAATACTGCTCTGCCCCAACAGAACCTGAAATCTACATCTAAAATACACATCCTGGAAGGTGTGGTGCAGGCTCTTGGGGTGGGTGTGATGTGATAGTGTGCGATTCAAGTTTGGTGCCTGTACTGCCTGGCTGGGGGATGCTGGGAATTGTATGTCTCACTCAGACATGGTGTGGGTATGAATGCAAACAAGGCTTTGGGTGAAGCTCTGGGTTCCCGGAGGCTTGTTATTTATCCCCATCCTTTCTGATTTCTAG
Seq C2 exon
TTTCAGTGGCGATTCTCCAGAGAAGAAATGCACAACAGGCAGATGAGGAAATCAAAAGGTAAACTCAGTGCCAGAGACAAACAACAAGCAGAAGAAAATGAGAAGAACTTAGAAGACCAGTCTTCCAAAGCTGGAGACATGGGAAACTGTGTTTCAGGACAGCAGCAGGAGGGTGGAGTCTCCGAGGAGATGAAGGGCCCTGTCCAAGAGGACAAGGGAGAACAGCTGTCCCCTGGTGGCCTGCTGTGTGGGGTGGGTGTGGAGGGTGAGGCTGTGCAGAATGGTCCTGCCAGCCACAGCAGGGCCCTGGTGGGGATTTGCACTGGGCACTCCAATCCTGGAGAGGATGCCAGGGACGGGGATGCTGAGGAAGTCAGAGAGCTTGGTACGGTTGAAGAAAACTGAGTCTTGGGCAATTTGTGCTAAAACTAGGTGAGTTGCCAAACCCAAGGCATCTTACCAACAGCTGGTTTGGGGGCTGGTTTCCCTGGTGTTGTGTGTTACCTACCCTTTGGCTTGGCTTGACCTCTCCTTGTGAGCTCACCTGAGCCCTCCCAGGGCCAGGTTCCTGACAGTGTTGGTTTTTGCACATCCACTGGAAAGGTGTCATTAATGACCCAGTGTTAGAATGCAAGAGGTCAGGTTATTCTAGCCCTCATGGCTGAAGGCCCAGTCCTGGCTCCACCACTCCTCCAGCCAGAGGGTCTGGACCATCCAGTGCCTGTCCTCGCCACAGGGCCTCCAGGGAGCATTCGGGTCAAATCCATGGACACCCTGGGCTACAAACCAAGGCTGCTGTTCATCCCACATCGTGTGGGGCAGTGTCCATCCCCTGCAGCTACTTGGTGACTTAACAACTCCAGGAGCCCTGTCAGCTGCCCTCCTCCACCTAAACCCCTTCGACTCTTCTGCTTTGACAAAGAAAATGACATTGGGGAGGGGAGGTGCTCCGCCTCCCAGCTTTTCTCAAAATAGTCCTATAGATACTGGTAATCTGGAAATGAAGAAGTAATTCTGTCTCTGCACCTACTTTTGCAGAATGTTCAAGGAAGTATTCTGTGTTAGTATTAATGCCAAAAAGTTGTTTTTAAAGGTTTTGTACTCAGCACATCATACAAACCACATTACTTCTGTCACTTCAGGGCATCGGGACTGGCTGGCGCCCTTGTTATGTGCTATTTTAATCAGTGTAACATTGGTCAAGTTGTTACCCATGTATGCTGTGTTTATCATGTGTATATCGTCCAGAAAGTATTAAGGCTTTAGGTAGATGCAACTGGCGAACCTTGGAGAGGGAATGCTGATTGTCTTGACCAAACCCACAGCCTGTCTCTTCTCTTGTTTAGTTACTTACGGCAATAAATCATCTATGAGTTAGTGCACCGTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000131378-RFTN1:NM_015150:9
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.970
Domain overlap (PFAM):
C1:
PF152501=Raftlin=FE(5.6=100),PF137831=DUF4177=PD(27.8=53.6)
A:
NA
C2:
PF152501=Raftlin=PD(8.6=28.1)
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- 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)