DreINT0128730 @ danRer10
Intron Retention
Gene
ENSDARG00000018334 | rpl35
Description
ribosomal protein L35 [Source:ZFIN;Acc:ZDB-GENE-020419-2]
Coordinates
chr21:5772844-5774259:-
Coord C1 exon
chr21:5774112-5774259
Coord A exon
chr21:5772981-5774111
Coord C2 exon
chr21:5772844-5772980
Length
1131 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGG
5' ss Score
7.61
3' ss Seq
ATGAGTAATTTGTGTTTTAGGCA
3' ss Score
6.88
Exon sequences
Seq C1 exon
CAATTATTGTCATCAATCGCCCCATTTAAGAGGAGAATGGAACGCTCCATCATCCCTCCCGCACTCGTTTAGTTTCTCCCGTAACCCGGCAGATTTTCCCACGTGACCGCTGCAACTTCCTTTCTTGTGGCAGCCATCGAGAAAAATG
Seq A exon
GTGAGGGTTTTGCTGAAACCGAACAATCTAAACCAATCTTGTCGAAAATACGTGTTAAATCACAACGAGAGCAGGTTTTATAGAAACTTTAAATTGAACGCTTGACTTTGAGTCCAGTATTTCAATCGATGATTTTAAAATAAATTGTTTTTTGAGTGATGAGGCGATGCATTGGGTGGCCTCCTGAAGCTGTTCAGACGGGTTAGCCTGTTTAGCCTAGCATATGATTTGGAGCAGCTTTAAATTGCGTTTCTAAATACTCAAAAATGAAATTATCGATCTGGATTTCCACACTTTGGCTTTCAGTTGATAAAAGCAGTTGGACGTAAATTAAATCTTGTAAAACACGTTTATTTGATCGCTTTGAGCTGACATGCGTCTCCAAACTGTCGACATTAGTGATATTTATCTAACACATTAGTGATATTTATGTAACAGTCGTGTATTCACTGTGCAAATGTCAAAAGCATAAGTTTAGTTTGGCACGTCTGTGCTTATGTTTGTGTCTTTCCTATCTATATACGAACACACACCAGTGTTGGGTGTAATCACTGTAATTAGATTACTTTTAGGTAGAAAAAGTGAAGTAAGGGACTACTTTTCGTTTCCAGGTAATTTAATTACAGTTCATTGTAATGTACTTGTGTTAATGTATAAAGGAAACAGTTCTGGATAAATCAACCATGAGAAGCAGAGTTATGAATGGATGAAGTCTCGAGAAACACTGTCAGTGAAAATTTGTATGAATATTGTTATTGACTTTGCATATTTTGTTACATGTTTATTATTCTTAAGGTGTTACCATTTTTAATACTGCTTAAATGACTTGTTTGGCTGCAAGTTGAGTTTATTTTCCATCATTTATATGGTATTGAGATTTATATGTAATGCACTGAATTTTAAGTCAAGTTATTTTAGTTGAGTGACTGAGTTACTTTTCAGACACAGTAAAAATTGAGTTTAAATACAAATTTAATGATGTAATTTTTGAAGTAACCCAGCACTGATATGTACAACTAAATAAACTTGTTCTTTTTAATACTTTGTACAAATAAATTCTGAGTACGTAACTTTACATTAGCATTAAAATGTTTAGTTTGCGTGAATGTTAATGAGTAATTTGTGTTTTAG
Seq C2 exon
GCAAAGATCAAGGCCAGAGACCTTCGCGGAAAGAAAAAGGAGGAGCTGCTGAAACAGCTGGATGATCTGAAGGTGGAACTTTCCCAGCTCCGCGTTGCCAAGGTTACCGGTGGAGCTGCTTCCAAGCTCTCAAAAAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000018334:ENSDART00000009241:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.087
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0083118=Ribosomal_L29=PU(69.5=89.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAATTATTGTCATCAATCGCCCCA
R:
GAAGCAGCTCCACCGGTAAC
Band lengths:
270-1401
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]