DreINT0154678 @ danRer10
Intron Retention
Gene
ENSDARG00000004017 | spag1a
Description
sperm associated antigen 1a [Source:ZFIN;Acc:ZDB-GENE-030131-9443]
Coordinates
chr19:12065986-12068510:+
Coord C1 exon
chr19:12065986-12066481
Coord A exon
chr19:12066482-12068410
Coord C2 exon
chr19:12068411-12068510
Length
1929 bp
Sequences
Splice sites
5' ss Seq
CTGGTAGAG
5' ss Score
1.5
3' ss Seq
TGCTGCGTTTGTATTCGCAGGTA
3' ss Score
9.61
Exon sequences
Seq C1 exon
CGGAGACCCCTCCTCCCAGTGATGTCACAGCAGGAGGTGTGTCCTCTGAATCTGTTTCAATCTGCGCAGGGAACAGGAAGAGTGTGCATGAGAGTGTGTGTGTGTGAGAGAGGACGAGAGCTCGCTGTACTGTATCGGGCAGCCATGGGCAATGCACAGAAGAAGGGCCCCGGTTACAGAGAAGGAGGGGGCCCAAACTCTCAACCCGGGACACCGGGACGCAGGAGAAGCCATGGACTAAATAACGCAGCCAACTCGAAGGAAGTCCCAGGCAGCAGCCCGGCAGCGAATGGCAGCCTTCCAGCCGGCAAGAGCCAGGATGAGCCTCAGGGACCCGGATCTGCTGGGGAAAGCTGTAATCTGGACGCCCCGTGTGGAGCCCTTCCTCCTCCACTAGCCCGGCTCAAAAACCAGGGCAATATGTTGTTCAAGAATGGACAGTTTGGGGACGCGCTGGAGAAATACACACAGGCCATTGACGGATGTATAGAAGCTG
Seq A exon
GTAGAGTACCAAATACTGCTTTTTAATGTTATTTAAATGAGATATCCTTGAGTAGCTGTGATTATATATCATCTTTAGCTGTATAGAAGGATGTGTTGAAGTGCTTTAAGGGTGTTGAAGGATGTCCAGAAGCTGGTAGAGTATGAATATAGTTTGTTTAATGTTATTTAAACGAGATACACTTGAGTATCTGTGATTATATATCATTTTAAGACGTATAGAATGATGTAATGAAGTGTTTTAAGGGTGTAGAAGAATGTATAGAAGCTGGTAGAGTATAAATATAGTATGTTATATATTAAATGTTATTTAAATGAGATATATTGGAGTGGCTGTGATTATATATCATTTTTAGCTGTATAGAAGGATGTATTGAAGTGCTTTAAGGGTGTTGAAGGATGTCTAGAAGCGGGTAGAGTATAAATATAGCTTGTTAAATGTTATTTAAATGAGATATACTTGAGTATCTGTGGTTATAAATCATTTTAAGGTGGTATAAATACAGTTCGTTTTTTTGTTAAAGTTATTTAAATGAGTTATTCTGGAGTGGCTGTGATTATGTATACTTTAAGGTGGTTGTTTTTTATTCTTAATATATTGAGTTAAAAGTGCTGGACTTAATCGAAGGAAGTGTTTTGTGTGAAGGACATTACATGTGTGTAAAACAATATATTTAACATTTCTATAATATAGCAATATTTTATTATAATTTATGGATTTAAAAGTACTCATGTAACCTACTAATTTCAAAAATTTTAAAGAATCAGATTGAGTAGATGCATGTATCTTGGAATAATACATAATATATGTTTAAATTGTGTATTACAGTTTTTGTTGTCATCTTAATGACATTTTTACAAGCTGAAACTGGCTTAAAAATCGTATCTATGCAACACTATTTTGGTAACGCTTAATTATATTTAACATTTATTACATATTTATTGTATTTTTTTATATAGTGTACAGTGTAGTGACGTAAAAGAAAAAAAAAACATTTCAAACATTCTGCTTCATGGTGGATATATAAGTATTATAATTTTTAGGTATATTTATTTATTATTATTATAAATTTTTTATATATTTTGGTGTTTGACATTTTTTGGTTAAATACTTTTGGTGTTACCAAATAGATGTTTTGGTAAGGCAACCTTTGCCATTGATAATTTTTTTAAATCCTGACTTAAAGGTTTTGGGTTTTCATTTACTCTACTGGATACAACTATTTTGTCTATTCGAAACTGTGTATGTATGTTTGTGTGCTAAAAATCTCATATTTTTTGAAATTACATTTCTGCAAGGTGACAATTTATAATATTCTGACTAACACCAAAATATCTTAATGACTTTGATGAGATATAAGTATTAATCTTGAAATAATAGATTTAACAGCTTAAATCTAGATTTAACAGCTAGCATACAGTAACAGCATACTAACCTACAAGTTCCCCATTAGCAAGTTTACATCACGTGTAAATGAATCATCTGGTAGTATTGCGCAAAACATTGCATGGATCCTGTTCAGCAGCGTTGAGTAATGCAGAGGTTCATTCAAAAACTCAGGCTTGACCGTCTAGAGTTCCTATTGAAACCAAGCATGTATCAACCCATGACATTTTGAAAGCCAGCAGCTGCATTTTTGGTTTAATTAGTAGTGAAAGTGTTTCACGAGAGCCCTCACTCGTTTCTGACACATCACATTGTAGGTGTGCCCGGTAGACTTACGTAACGAACAGCCGTGATGTGTCTCTCTAAACCGAGCTGTGTTTATTCTATGACTAGTTGTGTTTGTAACATCATATCAGGTGACCAAACGGCAGGTTTTCCACAATGAATGGCCACCTGCACTATGAACTCTTCCTCCCACGTGTCTCCATGCAGAACTAAAGCTGCTTTCTCAGGCTATTTTCAGTGCTGCGTTTGTATTCGCAG
Seq C2 exon
GTATCGACAGCCCAGAGGATCTCTGTGTTCTGTACTCCAACAGAGCTGCGTGCTTCCTCAAAGATGGAAACAGCGCAGACTGCATTCAGGACTGCACCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000004017:ENSDART00000130537:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.482 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF134141=TPR_11=PU(46.7=21.1)
A:
NA
C2:
PF134141=TPR_11=FE(44.0=100)
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:
CAAACTCTCAACCCGGGACAC
R:
CGCAGCTCTGTTGGAGTACAG
Band lengths:
353-2282
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]