DreINT0049552 @ danRer10
Intron Retention
Gene
ENSDARG00000069093 | col2a1a
Description
collagen, type II, alpha 1a [Source:ZFIN;Acc:ZDB-GENE-980526-192]
Coordinates
chr8:21166129-21168507:+
Coord C1 exon
chr8:21166129-21166338
Coord A exon
chr8:21166339-21168490
Coord C2 exon
chr8:21168491-21168507
Length
2152 bp
Sequences
Splice sites
5' ss Seq
TCGGTCCGC
5' ss Score
0.78
3' ss Seq
CATGCGATGTGATTCAACAGGGT
3' ss Score
6.47
Exon sequences
Seq C1 exon
AGGAAGAGTTTGGCGGCTGTGTTCAAGATGGCCAGCAGTATGCAGACCGTGCGGTTTGGAAACCAGAACCGTGCCGTGTCTGCGTGTGTGATTCGGGGACTGTGCTGTGTGACGAGGTCATCTGTGAGGATCTGAATGACTGTGCCAATCCCATCATTTCACCTGGAGAGTGCTGTCCCATCTGCCCAGCTGACACCGACGACCCTATCG
Seq A exon
GTCCGCTCTCTGCTCACACACCTCTCTTTGCTTCTCACACCTGTCCTGCTCAATGTCTGCTTTGAGTTCTGTAACTTTGTCGTGCATACCATTAGACTACAGCCTGGTCATGTTGGTCATGTAATTGTGTTCAGAACTCAAAGCAAACGTTCCAAGTTTGCAACACTTTTAAATTTTATTGTTGATTCAAGTTTTAGACCAAATTATGTTTTTTTTTTTCTCAGTTATAGCTGTATTTGGATAAAATGTGGACACTTTTCATTTTAATTGAGAGGTTGTGTTTTTGGAAGCACATCTTGCTACCTGTTTGGCCACTACAATAAGAAAATATAAAATTATATAATGCACATAAATGCGTGATTTAAGTTTCTGTAAAATTATATATTATATCATATTATTCATTTTCCTTCGGATTAATATCTTTATTTATCATTTGTCACCACAGCGAAATGAATCGCCAACTTATTCAGCATATGTTTTACGTAGCGGATGCCCTTCCAGCTGCAACCCAGTATTGGGAAACACCCATACACTTTCGCATTCACACACTTACACCATGGCCAATTTAGTTTATTCAATTCACCAATACCACTGAAACAGTTCTCATTGGTTACACTACAAGTCTCTGAACTGTGGGGGAACCAGTGCACCCGGATGAAACCCACACAAACACGGGGAGAACATGCAAACTCCACACAGAAACACTAACTGGCCCAGCCGGAGCTCGAACCAGTGACCGTCTTGCTGTGAGGCAACAGTGCTAACCACTGTGCCGCTGTGTTGCCCTATATTATATTATATTATATTTTATTTTATTTTATTTTATTATATTATATTATATTATATTATATTATATTATATTATATTATATTATATTATATTATATTATTCATTCATTCATTTTCTTTTCGGCTTAGTCCCTTTATTAATATGGAGTTGCCACAGCAGAATGAACCGCCAACCTATTCAGCTCATGTTTTACGCAGCGGACGCCTCCTCCAGCTGCAACCCATCACTGGGAAACCTCCACACACTCTCATTCACACACATACACAACGCAAAATTTTAACCTACCCAATTCACCTGTACAGCATGTCTTTGGACTTGTGGGGGTAACCGGAGCACCCAGAGGAAACCCACGCAAATGTGGGGAGAACATGCAAACTCCTCACAGAAATGCCAACTGACCCAGCGGAGGCTCGAACCAGTGGCCTTCTTGCTGTGAGGCGACAGCTCTACTTACTGCGCTACCGCGTTGCCCCATATTATGTTATATTTGATTTTATTTCTATTATAGTAACAAGTAAACAAGCCAAAACCTCAATTAGTTTGGAAAAAGCTGCAAATCAAGACAAAGCGTCTTTGAATACGAGGTCATGGTGTGACCTCTTACTAACATCCTAATTAACAAAAAATTTAGAAGTGTTGTTCTTCCAACTTTTTCATCACTTCATGTTCAGTCAACCTTGACAGCTGCTACTGTTCATTTAAAAAAAACATTGTGTGTTGCTGTTACACAAATACACACAATAATGTTAAGATGAACAAAATGTGAAGAAATGTTTTTTCCCATAAACATTTGAATATATATTCTAGCTCACTGTAATCAGCTCATGGCTCTGATACAGAATGAGTTTTAATGAAATATTTATTTTCATCTTTGTATTTAATTTGCTTAGCACTGTACAGCCTAATAATGCTTCTAATATTTCAACAATGCTTCATGTTTTAAACTGATCATGAGCTTGCATCTTAATATTCTGCTTTTAACAATTTAACGAAGCAGACTGGGAAGGGAATGATGCTGATTTGGTACAGAACCTAGTGGGGTGCCATTGAGTTGGTATTTTCAGCCATGTGGCTTCAGAATAGCAGTTCATTAGTCGTTACAGTAACACTGAGTGTCTGACCAGTTTAACGTCCTCATTACGAGTCAGCATTAGCTTATTATTATTGCATTCACCAACTTTCTTCTTGACCCATTGGTGACCCTATAGTGAGCTAGCAGCATTGTTGTCAGTGTAAGATTTAGATGTCCAAATGTGTGTGTTATTGAAAAGTCAATTGATCAAATGCATGTAAAATTACTTCATCATGCTGTGTCTAACTGTCAATCTTTGTCTTTCCTTCATCATGCGATGTGATTCAACAG
Seq C2 exon
GGTCACTTGGTGCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000069093:ENSDART00000100234:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.070 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0009313=VWC=WD(100=78.9)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping 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]