DreINT0049546 @ danRer10
Intron Retention
Gene
ENSDARG00000069093 | col2a1a
Description
collagen, type II, alpha 1a [Source:ZFIN;Acc:ZDB-GENE-980526-192]
Coordinates
chr8:21171457-21173277:+
Coord C1 exon
chr8:21171457-21171510
Coord A exon
chr8:21171511-21173232
Coord C2 exon
chr8:21173233-21173277
Length
1722 bp
Sequences
Splice sites
5' ss Seq
AAGGTACTG
5' ss Score
8.56
3' ss Seq
TCTCATCTCTTTTCCTTCAGGGT
3' ss Score
12.02
Exon sequences
Seq C1 exon
GGACACCCAGGTCTGGATGGTGCTAAAGGAGAGGCTGGTGCTGCAGGTGCCAAG
Seq A exon
GTACTGCAACAAAAATACTGCATTTTATGCCAAAATATCCTACTTTGACAGGAAATAACCATGTCTGAAACTGCACACAAAGGTTTTGTCGGGCATCATATTTCTACCATAATTTATGATCGCATTATTGTTTACACATCTGCTTTGGAACAATATATGTGATGAATTTATTTAATAACATTTACTGAAGATATTTTAAAATATAAATACAGCTGAAAACAATAGACTTTGTTCAAAATGGAGTATACAATAGCATCCATTACCTACTCATTTGTATTTATTTATAGTATGGCATTATTGTTTGCAAATTTGCTTTGGAAGAGTTGTAAATTATATTTAATAATTAAATTTTTGGTTTAATATAGAAAGCTTACAGCATATGACTAAATCGTAAAACAACCCCGAACCCCCCCCCCAGACGTAAACAGATTGTTAACAGACGTAAAAAGATTGCTGTGTTAAAAAAAACAAAAAACAATGAAATAAAAGAGAGTAATTTTAAGCCATATGCAGAGTAGAAGTTAGGTAAGTACAAATAAATAACTATTACATCATGAGATACATAAAGTACAAATAAACAGACAAGCCGAACATTAGAAGGTAGAAACAAGATTTGACAATAAATGTTTACAGATATGTTAAATAATAGTTTGTTTTTAAACTATGACAAAATGTTACATTTTAAGGCTTTTTAAAAAAATAAATGCTCCTGTTAAGTCCACAGACATATCAGAAACTGAGAATATTATAACATTCTTTACCCTCTCATTCACATTTTATGTAGTTAGTTATGTAGTATGGCAATATTGTTTTCGAATCTTCTTTTTGGAATAATTTATATAATTAAATAATACAACTTCAATAAATGTGTATACAAATAAAATTTTATTTCATTAAAATCTTATTTCTAGATTAATATGAAAGTAGGGGGAACAATACGAAGACTTTTTAAATGGAAAAAAGAGGTGTATAATACTCATATTTGACAAATTAAATGCAAGCATAAATTTGACAGGTTTCACAGGACATCATAATAGACCCTTTTCATGTTTCCAGATTAGTCAGGGGCGGAAGCCATCATAGTTGGGAAAATTTTGAGTGCAGTGAATGAGAAAGTACAACAAATAATTGTTTTTACGATCTTATTTGCTAAAAAAATAAAATAAAAACTTCATGATGATGTTCAGAAAAATTGTGTGAGACTGATGACGGCAGCCAGAGGAGAGAATAATGTCAGATTTACTGTCCTTTCCCATAGACACTGCATTAAAAAAACACTTCGTACAAGCCGTAATTAGTTTTTTGTCATTTGAAGCAAAGATGATATAATACATACATAAATACGTATAAATATTCATACCGTTTTTTAATGTAAATATTAGTGTCATAACTGGCTTGTAAAAAAGGGTCCATTCTAACAGACATTTATCAGATTTGTGTATTTGTGAAGCTTTATAGATTTCAAATCTACTTTGGAAACATTTGTATATTTCTTTTTTAAAGATAAGGATTTTTGAAACTATAAATATTATAAAGATATAAATATAAAGATATATATATATAAATACTATAAAGATATGAAAATACTAAAACTAATAATAACATGGATCTGGTTATAGGCTCAGTAATTCAATAGTTTAATTGATTTTATTTGGCTCGGAACTAATTGATTTTACATCATGCAATTTTAAAGTTTCATCATTCTCATCTCTTTTCCTTCAG
Seq C2 exon
GGTGAGGCAGGTTCTAACGGTGAGAGTGGCGCTCCTGGACCAATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000069093:ENSDART00000100234:14
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=FE(21.8=100)
A:
NA
C2:
PF0139113=Collagen=PD(10.3=53.3),PF0139113=Collagen=PU(16.7=73.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
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]