DreINT0108116 @ danRer10
Intron Retention
Gene
ENSDARG00000028900 | odf2a
Description
outer dense fiber of sperm tails 2a [Source:ZFIN;Acc:ZDB-GENE-091117-46]
Coordinates
chr21:13046223-13047964:+
Coord C1 exon
chr21:13046223-13046486
Coord A exon
chr21:13046487-13047863
Coord C2 exon
chr21:13047864-13047964
Length
1377 bp
Sequences
Splice sites
5' ss Seq
AAGGTGTGT
5' ss Score
6.64
3' ss Seq
TTCTGGTGGATTGGGTATAGGCA
3' ss Score
1.87
Exon sequences
Seq C1 exon
AACCAGAAGACCCGTGCTGAAGCAGACGAGTTTGCTGCACGTCTGCAGATGGCTTCAAGTGAAGCTCAAGCTGTACGAGATGAACTAGACCAGGAGATCCAGCAGGTCAGGAAGCAGCTTCAGGGTCGACTGTCAGAGCTGGAGCCCCTTCCTGAAGCTCTGAGACATGCTGAACTCCAACTGCAGGAAGCTCACGAGAAAGAGAGGTTACTAGAGAGAAGAAACACAGAGCTTGGCACTTCCCTTACAGAGCTACGCATCAAG
Seq A exon
GTGTGTGTTCTGCTGTTGGCCAAGTATATTGTTGTTTTATAGTTAGATCTTAAAAACTTGGCAAAACCTTTTATAGTTCTGAAAATTGCCTATAAAAACGCATTACCATTAGATGAGTATACATTTTTTAAATGTTCAAATCACTGGTGAACACTGGTGGGGTTGCTTTTATAAGATAAGTCCTCTAAAGCTCTTTGTATTAAAATTACGACAATGAGAGGAGAATGTGAGCGTGCCTCACACAGGTGAGTGGGCTTCACAAACCATCTGTAGAAAACACTTTTTCATCTCTCTCTCAGTTTAACCAACACTTGCACTAGTTTTGCACATTTGCACTAGACACTTTTTTTTATTTACAATTACTCAACGTCTCATTAAAAAAATTCAAAAATGTTTTGCATTTATGGAGTGTACTTCACAGGTCAGTGGGCTTGACAAACCACCTGTAGAAACACTTGTTTCTATAAAAATAAATCCCCCTTTCTTACTTTAGCACTTAATTCTCTGAGCACAGTTAATTTGTAAGATTAGCACTTCTTATGTGTAATGCCTCTTCTGTTGAATCCCTGAATGCATGCTCAATTGTAAGTCGCTTTGGACAAAAGCGTCTGCTAAATGTAAATGATGTGACCAACTGAACCTAGAATATCAATTGCTAATCAGTTTTCAGCAAGTTGGCAGAGCCGTTATTTCTTCCTTCGAATGCAAATAGGTCAGCCATTTGAAACAGGTCTTAACATTTGCATACAGAAGGTGTAAATGTAAGAAATTTCTATTCCAAAGGTCAGTGAAAGGGAAGATAAAAGACAACGGGCCTTAAAAGAGTAGAACAGAGTACAGGTAACCCCCAAAACACATTTAAAGTTTTCGCATTTCAGGTCCATGTGGGTTGAAAAAAAATAGATATTTTATAAAACATTCAGAAATAATATTTTTATAACTTACTGGGGGTCTTGAGGTATGTCTATGCAGATTTTATTGATTTGTAACACTTCGTTGTTAAACAATAAATAAATATATTAATTTATTAATTTTCCTTTGGCACATCAATACACCTTCTCATTCACACAGACACACTTGTACACTACGGCCAATTGAGTTAATCCAATTCACTTATAGCGCATGTCTTATGTCTTTGGACTGTGGGGGGAAACCGCAGCACCCGGAGGAAACTTATGCAAACACGGGAAGAACATGCAAACTCTACACAGAAATGACAACTGGCCCCTCCCAGACTCAAACCAGCGACCTTCTTACTGAGAGGCAAAAGTGCTAACCACTGAGCCACCGTACAACTATAAGTAAATATAATTGTATTTTATTTTATTGTATTGGATTATAAATAAATCATGTTGTATTCTGGTGGATTGGGTATAG
Seq C2 exon
GCAGAGCAACAGGGAAGCTTGGCGGAGATGTTGAGGCACAAAAACATGCTGCTACAGGAGGAAAACAAACAGCTTCAGCACAAAATGGAGAGCCTTGAACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000028900:ENSDART00000081426:15
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.670 A=NA C2=0.824
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Human
(hg19)
No conservation detected
Mouse
(mm9)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AACCAGAAGACCCGTGCTGAA
R:
GCTCTCCATTTTGTGCTGAAGC
Band lengths:
357-1734
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]