GgaINT0124402 @ galGal4
Intron Retention
Gene
ENSGALG00000004767 | ODF2
Description
outer dense fiber protein 2 [Source:RefSeq peptide;Acc:NP_001012817]
Coordinates
chr17:5112583-5114287:+
Coord C1 exon
chr17:5112583-5112736
Coord A exon
chr17:5112737-5114161
Coord C2 exon
chr17:5114162-5114287
Length
1425 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGA
5' ss Score
9.79
3' ss Seq
TTTCTCTGTTTCTTTTTTAGCAA
3' ss Score
11.9
Exon sequences
Seq C1 exon
GTTTCCTTTCATTGTATTCTCCTTTCCCGTCTGCGGGAGAAGAGCCATGAAGAACCGTTCCTCATCTCCCCCTTTGCACGTCCATGTGGATGAAAACACCCCTGTCCATGTCCATATTAAAAAGGGTCAGAAAACCACACCTGCAAAATGCCAG
Seq A exon
GTAGGAGTGTGCAGCTGGGTGTTTGTGAGGGCTGCAGGGAGGAGGCAGTCCTGGAAGCACCACGGAATCTTTGAGGTCTGTTTTACCATAGTATTAGAACTGAGACCTGTTGCCTTTTTAACTACATGCTTAGCCACTGGTGAATTTTCAGTGACGTGTTTTCTGTGTTTAAGATGATCTAATTATGCTACAGAATATATGGCTTGTTTTCATGTTTGATTAAATGACTGGGGCTGGACTCAATCATCTCTAGAGGTCCCTTCCAGCCCCTACAATTCTGTGATTATGAGAACTGTTGCTTTCAGTGAGATGCAGCTTGGGGGATTTTTTCCTCTTATGTCGTGGATTTGTATTCTCATACTGTTATTTCTTTAGCTTTGTCCCTGTTTTTGAAGGAAGGGTTTGGGGTAAGGAAATAACTGAATGTTCCGTGTTCTGTCTCGATTGTATTAAAATTCACACGTTTAGAAGAAGAGGGACTGGATTCAGACCATCTTCTGGCATTAAGCACCTTGTCAATCTGCGGAGCTGCACAGCAGAGAAGGATCTCTTCATACCCTTGTCAGCAGTAGATAGAAGGCAATACTGAAACTGTGTTGTAGCTGTCTTGCATCCTTTTGAGGTTGGATGGTTATGTAAAGCTTTTCTCTACTGGTACTGGAAGTTGCTAGCTCATTCTTGTGTCTGCAGACATGCTGGTACCAATTCTCCATTAATTTTCTCTTTCTTGCTAATGGCAAATCAGGGTCTGACAGTGAAGTCGCTGCCTCCTATTAATTAATTCCCCATAGGGTACTTTAGAATGGCTTTTCTTCCTCATCAGATATTAAAGTTGTGCAAACACACTTTGACTTTTCATCTTTTAGAGCACCTCGAATTTAAGGCAAGTAAATGTGGATGTACTTTTGACTCTAAAACAAGGAAAATGCTTCAGGGGCTTTTCATAACCAATCACACTGTGTGATGCTTTTTCCTCTCGTAGTGTTGTCAGCTGATACAGTTGCTGTACTGTGAGATTCATCTGGAACAGAGAAAAAATCTACTGGGTTGTTCCCTCTGCACCCAAATGGGTTACATCAGTGTTCTTTGCATATCTCCCTTCAGAGGAGACTTCCTTCCCCATACCCTGTGCCCAAATCTTCCTGCTGGCTGAGTAAGGCTTTCATCACATCACAGTTGTGATTATTTCAGTCATACAACAATCTTTACATGATAAGCAGCAAGAACACATCAGCTGAACGTGCAATAACCTTTCCTTCTGGCTAGTGTTAGCCTCTCTGGTGGTTCACCTGATCTCATGTACCATGTATAACACTGACTTTTTTTCTGTGTGTGAATGATCTTCCATTTCTTTTTGCAGCCATAAAAATTGTAAATAGTTCTTAGAAGATCTTAGCGATCTTATTTTCTCTGTTTCTTTTTTAG
Seq C2 exon
CAAAAGCACAAACAGAAAATGAAAGGGAATACTGTGAACGTGCGCCGAGCAGTCCAGGTGAAAACAAAGGCCCCCTGGATGCCCCCAGGAAAAACATCTGTCCTTGATTCCACCTACAAATGGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000004767:ENSGALT00000007603:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping 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:
TTCCTTTCATTGTATTCTCCTTTCCC
R:
CTCCCATTTGTAGGTGGAATCA
Band lengths:
278-1703
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]