DreINT0013893 @ danRer10
Intron Retention
Gene
ENSDARG00000099137 | LTBP4
Description
latent transforming growth factor beta binding protein 4 [Source:HGNC Symbol;Acc:HGNC:6717]
Coordinates
chr18:49035767-49037983:-
Coord C1 exon
chr18:49037855-49037983
Coord A exon
chr18:49035887-49037854
Coord C2 exon
chr18:49035767-49035886
Length
1968 bp
Sequences
Splice sites
5' ss Seq
AAGGTATGA
5' ss Score
9.11
3' ss Seq
TAATTGGTGTTTGTCCACAGATC
3' ss Score
9.89
Exon sequences
Seq C1 exon
ACGTGCGTGTGTGTGAGTCGAGACCTCAGGTGTGTGGTCCGGGCCGCTGCATTGACCTGCCAGGCGGTCGACACACATGTGTGTGTAACACTGGATTCATCCTCAATCCTCAACAAGGCCACTGCCAAG
Seq A exon
GTATGAAATCACGACCGAGTGCATGACTTTAGACTTCAGAAGCACACTAGAGGAAGAGGAAATGAGCACCATTGCAGACCTCCGCTCTACAGAAGACAGAAATATATAAGGTGGTGAATGTGTGTGCTTCATAACAGTTGGCAAACCACTTGTAGACTTCTTCCACACCATTAAATGGCCTGACATATTTTAGCTTCTCCCCAGCCGGATATATCTGGCACTGTGGAAGATTTCCTTTTTCTTATTAATGCTTCCAAAGTTTTAAAAGGTCGAAGGTCAATTTCTGAGGCAGATATCTGTCTGTGTGTCTGTGTGCATCTACAAATGATGACTATGAGTTTCAGGGCTTCAGCTGTGGGACTGTTCTCTGTGCATGTGCATTATGTACTTACAGTTACTTATGACTGGGGAAACAGGTATTGCAGACAGCAGTAGGGTGCAACAGTTGGAGAGAAAGGGCAAACTCTCTAGGGAAACTGTTGTGTAGTTAATCATTTATAACAATAACTGATGAACATGATCTCATATAACTGATGATCTCATTATTCATTTTTTTGTCCTAAGATTGTTTTACTTATGTTGGAAATCAATGATCTGACGTTTCTCTTTGGCTTTCTGTCACTATCAGACAAAAACGAGTGTGTGTTGACGCCCCGGCCGTGTTCTGTGGGGGAGTGTGTGAATACACCCGGCAGCTTCAGATGTGTGTGTCCAGCAGGATACCAGACCAACTCCCAGCAGACCCTCTGTGTCGGTCAGAAACACTCATTCATTCATTCATTCATTCATTCATTCATTCATATATTTATTCATTCATTCATTCACTCACTTATTCATTGATTTGTTCGTTCATTTGTTCATTCATTCATTCACTCATTAATTAATTAATTCATTTATTTATTCATTTGTTCACTCACATGTTCATTCATTCATTCATTCATTCATTCATTCGTTTATTCATTCATCTATTCATTCACCCATTTATTGATTGATTCATTAACCCATTTATTCATTCATTCACTTATCTAGTCATTCGTTCATTTATCCTTTCACTCATTCATTTATTCATAAATTCACTCACTAATTTATTAGTTCTTTCATTAATTTACTCACTTACTAACTCATTCATTCATTCACTCAAACTATTTTTATTCATCCATTCACTCATTTATTCATTCATTCACTCATTTTTTCATTTAATCACTCATTAATTTATTTATTCACTTACTCACTTATTCACTCATTTATTCACTCATCATTCACTCATTCACAAATTTATTCATTTATTCACTCTCTCATTCATTCATTCATTTACTCATTCATTCACTCATTCATTTTATTAATTCATTCATTCATACATTCATTCAATAATTCGTTCACATATTCATTCACTCATTTATTAATTCACTTATGTATTAATTTACTCATTCATTTACTCATTTATTAATTCACTCATTCATTAATTTATTTTTTCATTAACTACTCATTCATTCACACACTCACTCACTCACTCACTCATTCATTCATTAATTTATTCATTCATTTACTCATGCATTTATTCGCTCTCTCATTCATTAATTCATTCATTTATTCATGTTTTTCATTCATTCACTCATTCATTTATTCACTCATTTGTTCATTAATTAATTTGTTCATTCACTCAATTAATTAATTGATTCATTCATTCATTCACTCATTCATTCGTTTTTTCATTTACTCACTTACTCATTTACTCACTCATTCATTCACTCACTCATTCATTTATTCATTCAATTACTCATTCATTCATTCATTCATTTACTCATTCATTCATTCACTCATTCATTCATTCACTCACTCACTCACTCATTCATTCATTCACTCACTCACTCACTCACTCACTCACTCATTCATTCGTTCTGTTTACTGACTGAACTCTCTAGCTTTTTTTTTTAAACATTCTACTTCATAATTGGTGTTTGTCCACAG
Seq C2 exon
ATCTGGACGAGTGCCGTCAGGTGCCCAATCCCTGTATTAACGGCCGCTGTGAAAACACACTCGGCAGCTTCAGGTGTGTGTGCAGGACTGGATACAAACTACAGGACAACAGCTGCATAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000099137:ENSDART00000160702:12
Average complexity
IR
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:
PF0764510=EGF_CA=PU(0.1=0.0)
A:
NA
C2:
PF0764510=EGF_CA=WD(100=95.1),PF0764510=EGF_CA=PU(0.1=0.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACGTGCGTGTGTGTGAGTC
R:
TGCAGCTGTTGTCCTGTAGTT
Band lengths:
246-2214
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]