DreINT0091499 @ danRer10
Intron Retention
Gene
ENSDARG00000035682 | ltbp3
Description
latent transforming growth factor beta binding protein 3 [Source:ZFIN;Acc:ZDB-GENE-060526-130]
Coordinates
chr5:36961305-36963078:+
Coord C1 exon
chr5:36961305-36961457
Coord A exon
chr5:36961458-36962964
Coord C2 exon
chr5:36962965-36963078
Length
1507 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
AATTTGCTTTGTCTCTTTAGCTT
3' ss Score
7.9
Exon sequences
Seq C1 exon
CAACAGTTGAGCTGGGGTACTGTTTTCGCATGGTTACGGAAACAGGGAAATGTGAGCACGCTCTTTCAACACGCCTTTCCCAGGAGATGTGCTGCTGCACTGTGGGTAAAGCATGGGGAAGCAACTGTGAGAGGTGCCCACAGGATGGCACAG
Seq A exon
GTGAGTGAGTGAGTGAGTGAATAATTTAGTTAAATTTACTTTCATTTAATTTTCAATCGGCTTAGTAAATGAACTACCAACTTATCCAGCGTATGTTTTACACAGCGGATGCCCTCCCAGCTGTAACCCAGTACTGGGAAACACCCATACTCTATTACGTTCACACACATATAATACGACTAGTTTACTTTATTCAGTTCACCTGTAGCGCATGTCTTTGGACTGTGAGAGAAATCGGAGCACCTAGCAGTGCCAACTACTGAGCCACGGTGTCGACCCTCAATTAAATTTCTGTAGCTCAAATATTAGAGCATGGCATCAACAATGCCAAGCTCATCTGTTTAACAGATTATTGAAATGCTACATTTTGGCCAGTTGTTCAGTGGTCCAAGGTCCCACTTTGTAATATTTTTGAGTTTTTTTATTTTTATTCTTATTATTATTTGATATTTGTAAGATAATGTTTTTTTTAACCCTTGAAAAGGTGTGGGGGCTAATGTTAAATGTTAACTTTTCTGATTTTGTGTCATTTTTGTGTGGTCTTCACTAAAGCTATGTTTCCATCCACCTATTTTTCTGCTCATGTTGGATATGCACATAAAAATGGTCATTCTTAACCATTTTAGTATTAGTGTCATTATATTATTAATTACCTCCAGAAATATCAAGAGCGTCTGTGCTCTGCTTCTCACGCCTTCAAACGCTACCACACATTTATTGTGTATCGGCATTGCCTTCGGAGTCATTTATTAAATGATGAAAAGATTCACGCAGCCTCTCCTACTGCAGCAAATTCCATTTTAACTTTTGATATTTGGCGCCAGTTAATCAAAAAGTGACAATTTTGTTCTTTTTGACAGGAGGAAAACCCTGCTTTAAGCGCACGTCTTTTATGCGATATTCCAGTTTTGCGCATACATTTAATTTGCATCTTTGGATGGAAACATAGCTAATGTGATTTTTTTGGGGATTTATTTGATCCACATTATAGACCATTTTTAAGAATGTAAACAAAAACAATTGTCCTAACGTATTTCCTATTGTCATCATGTCATGTTAACATTAAGTTATAATTGAATTGCCTCTTGTTACAGTTATGAATAGTTTGATGATAAGCAGGAAATGTTCATGGGTCAATCACATGACCACATTAAAATGGTCTATAAAAGTTGTACCAATATTTTGAATGTAACCAAAAGGGCAAAATAAACATTGTTCCTCACAGTTTTTTTTGCAAAGTTTAAAAATACCAGAGAATGAAAGGTATATCTGCGCTATCAGTGATATTTACATTATCAGTACTGAGCATCATCATGAATTGTCTGTTTCCCCTGTTTGTTTAAAGGCAGGCTTGCCATATGGCAAAACTCTCATACACTGAAATGGAGAAAATTCTTTCATTCTGACTTTTGCCCAATTTGAATGTGCTCCTATATCTATAAATAGGTCTTTGAATAATGAATATCTCTTCTCTAATGTTTCCCTTCAATTTGCTTTGTCTCTTTAG
Seq C2 exon
CTTCCTTTAATAAGATATGTCCAGCAGGAAAGGGAATGTCTTTACAGACCTATCACGGTACTCTGACCTTTCAGCCCTTCCTGACCAGCATTGAACACATTAATCCTGACACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000035682:ENSDART00000048107:9
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=0.103
Domain overlap (PFAM):
C1:
PF0068312=TB=PU(85.7=69.2)
A:
NA
C2:
PF0068312=TB=PD(11.9=12.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAGTTGAGCTGGGGTACTGTT
R:
GTGTCAGGATTAATGTGTTCAATGCT
Band lengths:
262-1769
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]