GgaINT0126128 @ galGal3
Intron Retention
Gene
ENSGALG00000001910 | SNAPC4
Description
NA
Coordinates
chr17:8586721-8587692:+
Coord C1 exon
chr17:8586721-8586868
Coord A exon
chr17:8586869-8587585
Coord C2 exon
chr17:8587586-8587692
Length
717 bp
Sequences
Splice sites
5' ss Seq
AAAGTAAGT
5' ss Score
9.72
3' ss Seq
ATACACCTTTCCATTTCTAGTTG
3' ss Score
8.62
Exon sequences
Seq C1 exon
ACAAACAGGACAGCTTTTCAGTGCTTGCAGAAGTACCAAACCTATAACAAAGACTTGAAAAGGAAAGAATGGACCAGAGATGAAGATAAGATGCTCTTAGAGCTTGTTCAAGAGATGAGAGTGGGAAGCCATATCCCATACAAGAAAA
Seq A exon
GTAAGTGACCTACAAAGGGAATTGTTCTCCATTCGCACATGATGGTTTCTTGATTTCCAGCGTTGTGTGTGTTAATACCTCTGCATGCTGGAGCACCTGACCTGCTCTGCTCGAAGGAATTACTGATGTTTTATTTGCTATGAGTGTTTCCATTTCCATGATATTCCCATGTTTTATACCTAGATGAGATGCAACAGAACTATGACCCAGTATGTGTATGTATGTCAGTATGTATATAAGGTACAGCAGTGCTGTGGCCTGGGATGTGTGTACATGTGTGTACACACATTACAGTACCTATACTGGTTTCTAGAAGAGTTCTTTGTGAGCTCTCTGTGGGATTACATTGTAAGTAGTGAGGACTGAAGGTTAAAGTAGTAACAGAGTGTTTTCTGGAGTCCTAAATCCCAGCCCTTGTATAACAACATCCGATGCCTTGAATTTGTTGGGTGTGTATTAGAGCTGAAACGTTTCTTTTGGAGTTCTGTTGCAGTATGAATTGTTGGGTTGCTGTGTCTATATTGGTAATACCATTATAAATAGTAGCAATTTGTGTTTTCAGTTCTTGTTGTGTACCACTGTCAAAGCATTAAAGCTGAGATCTAGATGCATCTAATGGCAATCTACTGTTTGCTTGAAAAGATTGCAGTTCCAAATGTTAGTAAGTGAAGAAATATTGCTTGCAGCAGAGTTGAAAATACACCTTTCCATTTCTAG
Seq C2 exon
TTGCCTATTACATGGAAGGAAGAGACTCTGCCCAGCTGATTTATCGATGGACAAAGAGTGTGGATCCCAGTTTGAAGAAGGGGCCCTGGACACCGGAGGAGGATGCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000001910:ENSGALT00000002951:11
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:
PF139211=Myb_DNA-bind_6=PD(8.2=10.0),PF116263=Rap1_C=PU(23.5=48.0)
A:
NA
C2:
PF116263=Rap1_C=PU(32.4=91.7),PF139211=Myb_DNA-bind_6=PU(9.8=16.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAAACAGGACAGCTTTTCAGTGC
R:
AGCATCCTCCTCCGGTGTC
Band lengths:
254-971
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]