DreINT0049515 @ danRer10
Intron Retention
Gene
ENSDARG00000099930 | col27a1b
Description
collagen, type XXVII, alpha 1b [Source:ZFIN;Acc:ZDB-GENE-100119-2]
Coordinates
chr5:64499681-64501112:-
Coord C1 exon
chr5:64501059-64501112
Coord A exon
chr5:64499744-64501058
Coord C2 exon
chr5:64499681-64499743
Length
1315 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAC
5' ss Score
7.82
3' ss Seq
AGAGTTTCTGTCATTCAAAGGGG
3' ss Score
4.79
Exon sequences
Seq C1 exon
GGTGATGCTGGTGAACAGGGATTTCCTGGAGTTCTTGGAATATTTGGACCACAG
Seq A exon
GTAAACTCAAAAGAAGAATAGCGGTGTAACTCCGGTCTCCTGGCCAAAGTTCCCCATTTGGTCCTTACTTATCATGGCCTCCTAATCATCCCCATCCACTGAATTGGCTCTATCACTGTCTCTTCACTCCACCAGTACCTGGTGTGTGGTGAGCGCACTGGCGCCGTTGTCTTGTGGCTGCCGTCACATCATCCAAGTGGATGCTGCACACTGGTGGTGGTGTGAAGAGACTCCCCTCATGATTGTGAAGCGCTTTGGGTGTATGGCCATACACAATAATTGCGCTATAAATACACATTACATTAAAAAATAAAAGTCAACCTGTCGCGTTTTTATGGCCCTGTTTACTTTAAAATATGTTACTGATCTTATTATGATGATAACGAAAGTCTTATTATTCTGTGATGTTCCCATTTTTTTTAAAGAGGACCTATTATGCCCCTTTTTTACAAGATCTCAAATAAGTCCCTAGAGTGTGTATGTGAATTTTTAGCTCAAAATACCTCACAAATAATGCTTTAGAACTCTTTGCAACCGCCCCTTTTATGTTTTGATTCTAATTGGGTCCTTTTGGTTAATTTCGCTTTAAATTCAAATGAGATTGTGCTTTTTTCAAAAGAGGGTGGAGCTACAAATGCCTGTGTGTCAGCATAGTGGCAGATTCATATACAAGACATTGAAGTCCTATGCTAATGAGGGAGAGATCATCACTAATGGGCGGGGCTTTCCTTCTCTGATGACACGTACATTGGGAGAATGTCAATCAAAGTGTTTCTGCAGACTGTTTTTATCAAGTGTGATTATAAAAGAATAAAATTGATCAACTTTTTCCATTAGAATCTGGTTATATTTAAGGACTGATGCCACACAACTGTGTTTAAACCCCTTATTAAAGTGATTTTTGCATAATAGGTCACCTTTAAAAAATGCTTGTTTCAATTCAGAACCTTCTAAGTACTTCTAGTATACTGTTTTTTAAATACTATTAATTCAGACATAGTACTCGGCTAGCATACTACTTTTAACATAACATATAGTAGGTATATATGCAATTTTTAACACAGCCCAAGTGTTTTTTATGATTATACATTAAAAAATGTTGAACATAACCCAGCATTACAATCTAAAAATCTTTTAAAATAATAATAATAAATCAAATGTATGGCTAAAAATTTATGGTGAATGAGAGCAGAAGTCTCGAGCCAACAAGCTGCCAATGGGTGTGTCTTCTCGTACATGAAAGAATAAGGGCAATAGTAATAAACAGTCAATTGTTCTTCCTTTCTGACTCCTAAAGAGTTTCTGTCATTCAAAG
Seq C2 exon
GGGCCTCCTGGAGACTTCGGTCCAGTGGGTGTGCAAGGACCTAAGGGTCCTCAGGGTTTAATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000099930:ENSDART00000167886:43
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=PD(11.4=50.0),PF0139113=Collagen=FE(20.0=100)
A:
NA
C2:
PF0139113=Collagen=FE(23.5=100),PF0139113=Collagen=PU(12.7=38.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
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]