HsaINT0170729 @ hg19
Intron Retention
Gene
ENSG00000236236 | TNXB
Description
tenascin XB [Source:HGNC Symbol;Acc:11976]
Coordinates
chr6:32024363-32026167:-
Coord C1 exon
chr6:32025835-32026167
Coord A exon
chr6:32024681-32025834
Coord C2 exon
chr6:32024363-32024680
Length
1154 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
ACGTGTCTGTCCAACTCCAGAGG
3' ss Score
7.25
Exon sequences
Seq C1 exon
CCCCACAAGAGGATGTGGACGAGACCCCCAGCCCTACAGAACCAGGCACAGAGGCCCCAGGGCCCCCCGAGGAGCCTCTCCTGGGGGAGCTGACAGTGACAGGATCCTCCCCTGACTCGCTGAGCCTTTCCTGGACCGTCCCCCAGGGCCGCTTTGACTCCTTCACCGTGCAGTACAAGGACAGGGACGGGCGGCCCCAGGCGGTGCGTGTTGGGGGCCAGGAGAGCAAGGTCACTGTGAGGGGCCTGGAGCCTGGGCGCAAGTACAAGATGCACCTGTACGGCCTCCACGAGGGGCGGCGCCTGGGCCCGGTGTCTGCCGTGGGCGTCACAG
Seq A exon
GTGAGTGAGTGTGGGTGGGGCAGGGTTGGAAGACAGCCCTAGAAAATGTGCCCTTCTCTACCATTTTCCTATACATATTTCTGTCTTGATGGGGCTCACAGTGAAAGGAATATAGCAACATTATGGAAAGACATGTCATGGAGAGACAGGCTGCAATCCAGCAAATGAAGCAAAGGCGGGTGAGCATGTGATAGGGAGGCCCAGGGCTCAGGTCAGGACCAGACAGGGACGCCTAAGTCACCCTGCCCATGGGTACCCAGGGGACAGCCAGGACCTGAGGCCAGGCATGCCTTAGCTTGGTGACAGCTTTAGAGAGAAGGTGAAGTGTGTCAGATAATCACAGCTGGTGCAAAGGCCAGGAGGCTAGAAAGAGCATGGCACGTGAGAGGCACTGAGGATTGAGTGGGGTGTCCTTTACGGTGAGTATCTCATCCTGAAGTGTGGGAGCAGAGGAGGGGACCACTCACCAGGCCTGGGGTCTCCCAGGGATGAGGATGTGGTTGCCCAGGTCTGTGCTGAGATGGCCCCAGCAGCTGTGCCTGTGTGAAGCTCATCCGTGGGGGCTGAAGATGGGGATGGGGTGGCAGGGAGCCTGGAGGCAGCGAGGCCAGTAGGCAGTTGGTGGCCCTGGTGAGAGGTGACAGTGGCTCAAACTAGGATCGGGGACTGGAGGTGGGGTAGGAAGGTATCCAGGGGAATTCAGGGTAAAGATGCTCTGAGGCTGCTGGCAGCTGGTGAGGAGCTGGATCCAGGAACACACCCCAGGCTCTGGCCTCGGGAGGAGTGTGCTGAGCTTGTTGCGGAGCAAAGACAGAAGCCCAGTGAACAAAAGATGGCGAAGAGACCCCAGTGCTGGGAGGCCAGGGGTGCAGAGGCCGAGTGGGGCTGTGCTCAAAAGAGAGGCGGTGCTGGAGGGACAGGGAGAGGTGGCCTGGGTGTTGGGAGGTGGGGGTGAGGTGGGGGCTGAGGGCAGGAGGGTCAGGGTGAGGGATAGGAAAGGCCACAGGAGAGGAGAGGATGAAGAGCTGTGCTGGAGGGGCTGTGGGCAGCATCGTCCTGCTCTTGGGCACTTTGTGTTTTGTGACACATCCTTTCTATGCTGAACTGAGGAGCCAGGGACCTCACTGTCCCCACACGTGTCTGTCCAACTCCAG
Seq C2 exon
AGGATGAAGCCGAGACCACCCAAGCAGTGCCTACCATGACCCCTGAGCCCCCCATCAAGCCTCGCCTGGGGGAGCTGACCATGACAGATGCCACCCCTGACTCCCTCAGCCTGTCCTGGACGGTTCCCGAGGGCCAGTTTGACCACTTCCTGGTCCAGTACAGGAATGGGGATGGGCAGCCCAAGGCGGTGCGGGTGCCGGGGCACGAGGACGGGGTCACCATCTCAGGCCTGGAGCCAGACCATAAATACAAGATGAACCTGTACGGCTTCCACGGTGGCCAGCGCGTGGGCCCCATCTCTGTCATTGGGGTGACGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000236236-TNXB:NM_019105:22
Average complexity
IR-S
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
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGACTCCTTCACCGTGCAGTA
R:
TCCCCATTCCTGTACTGGACC
Band lengths:
351-1505
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)