DreINT0154683 @ danRer10
Intron Retention
Gene
ENSDARG00000004017 | spag1a
Description
sperm associated antigen 1a [Source:ZFIN;Acc:ZDB-GENE-030131-9443]
Coordinates
chr19:12087223-12087646:+
Coord C1 exon
chr19:12087223-12087349
Coord A exon
chr19:12087350-12087519
Coord C2 exon
chr19:12087520-12087646
Length
170 bp
Sequences
Splice sites
5' ss Seq
AAGGTTTGT
5' ss Score
7.81
3' ss Seq
AGTTTTGTTTTCTCTCACAGGAT
3' ss Score
10.61
Exon sequences
Seq C1 exon
AGCGCTGTGCTTTCTCAAGCTGGAACGTTTCGCAGAAGCCAAACAGGACTGTGATTCTGCACTTCAGATGGAGCCAAAGAACAAGAAAGCGTTTTATAGACGAGCACTGGCACACAAAGGCTTGAAG
Seq A exon
GTTTGTATTATGTCCTCAGATATTATGCCTGTGTAGTCAAAAGAGAGGTTTTACATTTCAAAATAGCATATGATGGCTTTGTGGTCATTTAAAGTGTGCAGTAAAGCATAGAAATCAACGTGTACTTCCAAACTCAGTGCCGTATTGCAGAGTTTTGTTTTCTCTCACAG
Seq C2 exon
GATTACCTGTCAGCCAGCACTGATTTACAGGAAGTACTGCAGTTGGATCCAAATGTGCAGGAGGCCGAGCAGGAGCTGGAGATGGTCACTAACCTGCTAAGAGAAAGTCTATTGGCTAATGCTCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000004017:ENSDART00000130537:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.047 A=NA C2=0.047
Domain overlap (PFAM):
C1:
PF134141=TPR_11=PD(35.7=58.1),PF0051523=TPR_1=PU(39.4=30.2)
A:
NA
C2:
PF0051523=TPR_1=PD(54.5=41.9)
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:
TCTCAAGCTGGAACGTTTCGC
R:
CTTGAGCATTAGCCAATAGACTTTCT
Band lengths:
242-412
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]