DreINT0049518 @ danRer10
Intron Retention
Gene
ENSDARG00000099930 | col27a1b
Description
collagen, type XXVII, alpha 1b [Source:ZFIN;Acc:ZDB-GENE-100119-2]
Coordinates
chr5:64497671-64499443:-
Coord C1 exon
chr5:64499408-64499443
Coord A exon
chr5:64497707-64499407
Coord C2 exon
chr5:64497671-64497706
Length
1701 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAGA
5' ss Score
9.48
3' ss Seq
TTTTTTTTTGTTCCCATCAGGGG
3' ss Score
10.37
Exon sequences
Seq C1 exon
GGACCGCAAGGAGACAAAGGAAACAAAGGGGAAATG
Seq A exon
GTAAGATGTTTTTGGAAACTTTTAATTATGTCAGCCCCTATTTAATTTCTCCAATTTCCTATTTTATATAATAAACCACTTTATAAATCAAAAGGTATTGGAAAATCTCACATATTATTCACTTTGTTATTGCAAATTTTGGATCAACTGTTATTCATTCATGCTATTTTTTAGTGTGGAATGAAAACATGCTTATCCATAACAGAAAAATTTAAACTACATGTTATTTCACACTAAAGTCATGCAAACATCATGCTAATTCATACTTGAAACTATACTATATTATACTATACTATACTTTACTATACTATACTTTACTATCATAATCCATACAGGAAACATGTTAGAAGATGCTAATTCATACTAGAAACATGCTAGTAACATGCTAATTCACACTACAAGCTATACTAAACTATACTATGCTATAATATACAATACTGGAGACATGTTAGAAGATGCTAATTCATACCAAAAAAATGTGAATAACATGCTAATTCATACTAGAAACTATAGTATACTGTGATATACTATACAATACTAATCCATGCTGGAATTATGTTAAAGGATGCTAATTCATACTAGAAACATGCTAAAAGTATGCTAATTTGTACTAGAAACTACACTATACTGTGATATACAATATATACTATACTATACTCTAATATACTAAACTAATCCATACAGGTAACATGTTAAAATATGCTAATTCATACTAGAAACAAGCTAATAACTTGCTAATTCATACTAGAAACTATACTATATTAATCCATACTGGAAACATGTGAAAAGATGCTAATTTACACTAGAAACATGCTAATAACATGTTAGTTTATACTAGAAACTATTCTATACTAATCAATACTGAAAACATGTTAGAGGATGGTAATTCATACAAGAAACATGCAAATAAAATGGTAATTCATACTAGAAACTATACTATACTGTGATATATTATACTATACTAATCCATGCTGGAAATGTTAAAGGATGCTAATTCATACAAGAAACATGCTAATAGTATGCTAATTCTTACAAGGAACTATACTATACTGTGATATACTATACTATAATATAATTTACTATACTCATCCATGAACATGTAAAAATATGCTAATTCTCACTAGAAACATGCTAATATCATGCTAATTCATACTAGAAACTATACTATACTATAATAATCCATACTGAGAGCATGTTAAAGATGCTAATTCATACCAGAAACATGCTAATTCATACTAGAAACTATTCTATACTATACTACAATGTACTATACTATACTAATCCATACGGGAAACATGTTAATCAATACTAGCAACATGTTAATAGCATGCTAATTCATACTAGAAACTATACCATACTATGATATATTATAGTGGAAACATGTTAAAACATGCTAATTTATACTAAAAACATGCTAACAACATGCAAATTCAAAAGAATTAATGAACACAAGATCCAGAAGAAAATTTTAACTGAACTGGCAGGAACAGTAATGTATTCTTGATGACAACTTCTAAGTGACTTTATGGTTTAAAAGTGTTCATTGCAGAGTATAATTCTGTGGTTTTTCTTTTATTTTAAACAGGGTGTTCAGGGACCCAGGGTATGTTTGATCCAATCGCCTTAAATATTACTTACCACCTTTTTACATAAGTTAAGTGGCATGTTTTTAACAAACCATTTTTTTTTTGTTCCCATCAG
Seq C2 exon
GGGCCTCCAGGTCCTCGTGGACCACCGGGACCTCCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000099930:ENSDART00000167886:46
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(17.5=100)
A:
NA
C2:
PF0139113=Collagen=FE(17.5=100)
Main Inclusion Isoform:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]