GgaINT0124585 @ galGal3
Intron Retention
Gene
ENSGALG00000001187 | STRBP_CHICK
Description
NA
Coordinates
chr17:9617283-9619226:-
Coord C1 exon
chr17:9619086-9619226
Coord A exon
chr17:9617407-9619085
Coord C2 exon
chr17:9617283-9617406
Length
1679 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGA
5' ss Score
10.77
3' ss Seq
ATTATTATTACTCCAAGCAGACT
3' ss Score
2.23
Exon sequences
Seq C1 exon
GTAGAAGTAGATGGCCAGAAATTCAGAGGTGCAGGCCCAAATAAGAAAGTAGCAAAAGCAAGTGCTGCATTAGCAGCACTTGAGAAACTGTTTTCTGGACCTAATGCAGCAAACAACAAGAAAAAGAAAATTCTTCCTCAG
Seq A exon
GTAAGAATTGTTGCTTGCTTTTCTGGTACATTTTGTTACCACAGCGCTGTGTCTTATGATTCAGGAGTCTCTACAGGAAGTAATTTCAGTGTTTTGTCTGATGGGCTCACAGTAAGGCTTCTGATTTTTATTCGACAGTAACTACAGTAGCGTAACAACACGGTATGATATTTGGGACCACACTGTACTAATGCCACTGAAATGTTTTCATATTGTTAAGGAGTTTAAGCTGAAGGAAATACAGTAGAAAAGGCAGCACAAAGAGGTGGTGATGAGCTGGAGGAAATACAGTAAGTTCAGTGGTTGAATGATGACATGGAAATCTATTCTTTGTCAGAGCCATACTGTGCTCCTCCATCACTTACACACATAGAGAATAAATTATGTATAGTTTGGCAAAGGCATTATTTCTAGGTTCTGGAGTAGGCTGAAATTTCTGTACCAGACTTGGCAAGTGAGACATTTCAGTTAGTGTGGAGCACTTCTAAAATTAAAAAAAAAAATCAAACAAAAAATAATCTTGGACTTTTCCATTAGGTTTAACAGCCCCAATAATCACTCAAGTTTAAGGTTGAACAGAACAGAAACTATCAACAGTGTCTTTCCCACAGAGAACTGCTGACAGAGAAAAACAAACAAACAAACAAAAAACCCTGAGGATTACCATCTCGGTCTCTTCTGTACAAATACATTAACATTAGGATTTTCTTGTCATTTCAGGAGCAGAATGTATCATAATATAGAGTTAAATGACAAGTCAACTCTTTTTGTCTTTGTTCTGTTACTAATAACAATCCTTGTTTTACTAAGACTTCTGGTTAGGAGTATTTCAATTTCCATTACTGTGCTGAAAGTCTACAAGATCAGAAAAACACTACCTCATAGGATAATGTTCCACAGGCAGCCAAGATATGAAGACTTACGATTCAGGCAGTTTCTAAATTGACTTTTTTCCTTTTTTTTTTCCTGTTTGCTTGTTCTCTTTTTTGCAGAAGGCAATGATGGCAACAACTTCTCTTTGAATTAATGGGATATGCATGATTTTACAGTGTTTCCAGAAGACAGCCGGGGGGGGGGGCATCTAGTAACACAAAGCTCTGCTCTGATGCAGTAAGCAGTAACAGCTTCTGCAACTCCTTGCAGTATTCTGAGATCTTTTGACAGTGGAAAAGAAAATGCTGATCTAAAGCAGTCTAGTGTTTCTATGAGGTGGTTATTTGTCTTTGCAATGAAGTCCTGGCCCTGCTGAAGATATATGGGTTCAGGGTGGTAGGAGAAAAGCAAAGGCCTTTTTATAGATCAGTGAGAGGCAGTTTGTAGGAAAAGACAACAGAGAGGCATACCGAAGAAAGGTGCAGAAACCAATCTACCACTGGGGTAGATCATGACCACACAACCAAAACTCCAGTAAATGAAACATAGCCTGATCATGCAGACTGCAAGGTCTGAGTAAGGTGAACATGAACATCAGAACTAGAACTTGTTTGCTGAAGGGACTTGGTTTCTGTCAGTCATTCTTTTCACATTACTTTTCCATTCTGTACTCTGCCTTAAGCAAGGACAGCACATCAAGCATGCTTAAAGTGATTCAGGAAAGATAGTGATTTAATGTACATGGCCTTTTGTATTTCCAGCAACATTTTAACATTCTGAATTGCTATTATTATTACTCCAAGCAG
Seq C2 exon
ACTAAAGGAGTTGTCAATACAGCTGTTTCTGCAGCAGTCCAGGCTGTGCGAGGTAGAGGACGAGGTGCTTTAACAAGAGGTGCATTTGTTGGGGCAGCTGCTGCTACTGGATACATAACGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000001187:ENSGALT00000034915:14
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.340 A=NA C2=0.006
Domain overlap (PFAM):
C1:
PF0003520=dsrm=PD(46.0=61.7)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Cow
(bosTau6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGAAGTAGATGGCCAGAAATTCAGA
R:
TGGCGTTATGTATCCAGTAGCA
Band lengths:
262-1941
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]