DreINT0048848 @ danRer10
Intron Retention
Gene
ENSDARG00000026165 | col11a1a
Description
collagen, type XI, alpha 1a [Source:ZFIN;Acc:ZDB-GENE-070209-167]
Coordinates
chr24:28759933-28762035:-
Coord C1 exon
chr24:28761979-28762035
Coord A exon
chr24:28759987-28761978
Coord C2 exon
chr24:28759933-28759986
Length
1992 bp
Sequences
Splice sites
5' ss Seq
GTGGTGAGT
5' ss Score
8.95
3' ss Seq
TTGGTTTCAACCACATTTAGGGT
3' ss Score
5.83
Exon sequences
Seq C1 exon
CTCGCCATGAGAGGTCCACCGGGTCCAATGGGTCTCACTGGACGATCTGGACCAGTG
Seq A exon
GTGAGTTTATGTGACTCGCATATGTCCCTATCAGTCAGAGCATTTTAGTGGCTAAAGGAATTTTATACAAGTATTTAACGTTTTTCAATAGTTTTTTTTAATTTAGTTTAGCATTAATTATATGCAGTAAACCAGTATAAATATCTGAATTTTCATTAGTGTCAAAAATCTGGAAAAATTGGTTATAAAAAAACTTGTTTTTAGCAAACATTCAAATACATCAATAATAAATCAATCATTTAAAAAGTGCCCTTTGCTTTTAAAAAAACATTAATGACAAGTGCAAAATGTGGATAAATGGGGAGTTTAAGTGTTGGCTGACATTTTAAATGACAATTTAAGTGCCATTTTTAGAAACAAAACACATCCATGTCAAACAAAAGTAATGTGTTGCTAAATACAGTGTAATGTGAGAAATTGCACTATCTATATCTCATCAGATGACCTAACTTTTGTTTAATAGTGCAAATTCGACATTTCCATTCCTCACCACCCCAAATTATCTAATTTCAAATAGGATAAAGCAAAAAAATTGTGCTGGATTGGAGCAAAGTAAGCACATGCCTCACTGTTCAATCATCTTTTAAACATATCTGTATCAAATCATCCTATTAGCTTTTATTTTCTTTTCTGGAAACTAACATCCTCACCCATTTCATTGAGTGTTGTCCAATTATGGCAAGCAAATGTCATAAGCTGACTGGGACGACAATAAGAAACTAACTGAGTGTCATAAATATCGGCATTTCATTTCAGACCATCGCTAAAAAGACGATTAAGATTATGCATAAGAACATGCGTTTATCAAGTAGTACATCCCACACCTTTTATTGCGTACACACAATATGAAATGGAGGTGTATACAGAATAAATTCTCTCCAGGAATGAATCTGGAGTAGAGTCCCGGACTTTGAGGGCAGTGTTCTATAAAACCATATTGTATAAACTAATTTAAAAATAACTATGTAATAAAATAAATGTTGACTGAAAAAAATCTAATAACATAATATAAAATACATATTAATTTTAATTAATTGTAATATATGTTAATAATAAATGTGTAAAAATGTATAAACTTAAATGAAAATGAAAATAAAAGGTTTAAACTAGTTCAAATAGTTAATAAAAATTACAATATTATCTTAGGTGTGTGTGTATCTAACCAACATATGTTCAAATACCCAAATGAATACTAATTGTGTAAAGTTTTGTAATTGTGTGGTGTAGAAAAGCACCAACAGATGTTACAGAAAGCATTATCATTCATATTCTGACAGCAATATTTCTAACACTAAAATCAGTATAATAGATTTAATACTGCATTTTGGAATCAGCACACCAAAATGAGTAAGAAACAAGAGCTGGATGTACTGTAGGAAGGTCAGTATTTTTTTACAACACAAATTATCCAACTAAAAGAGTCCCTAAAAAATCTATAGCTATATTAAACATCTGAGACATGTAAACCACAGCCATGTCATGTCGTATTTACCCTGTGTGACTGATTGAGCGTGAAATGATGAGACGCTGAAATCATAATCTTTATATAAGTTAAGAACACAGCAACTGTTTAATGGCTGGTTGTGAATCCTCAGATGTGCAATTCAAAAAGCAGACAAATGAGAATCTTGGACTTTCCAAATCAGTCTTTATGGCAGGGTGCAGTTTTAAGAAAACATGCACAAGTCAACTCTCAAATTATCTTTTAAATTAGCTAAAAAAAAGAAGACTGTCTGTCTAAAATAGCAGCAATTTTAAAATCATCTGTTTTTTTTTTTTTGCAGTGTTAAAGAAATGCAACGTCTGTGTTTTGATTTTTTTTTCTCTAAGGAAGTGAAGAGCAGTAGGGACATGTATGTTGTGAAAATATCGCCACCTGCTGTTTGTTTATATATAGTGCAGATGTTTTTGGATTGCCGTAACTGTTAAAAACGTCTTGGTTTTCTGTATTCTTAGTCTGATGCATCTCTTTTTGGTTTCAACCACATTTAG
Seq C2 exon
GGTCTTCCAGGTCCTCCTGGACTGAAGGGAGAAAGTGGGGATCATGGTCCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000026165:ENSDART00000003503:14
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=PU(25.8=84.2)
A:
NA
C2:
PF0139113=Collagen=FE(26.6=100),PF0139113=Collagen=PU(16.7=77.8)
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]