DreINT0049900 @ danRer10
Intron Retention
Gene
ENSDARG00000052061 | col4a6
Description
collagen, type IV, alpha 6 [Source:ZFIN;Acc:ZDB-GENE-101001-2]
Coordinates
chr7:50698228-50700712:-
Coord C1 exon
chr7:50700596-50700712
Coord A exon
chr7:50698288-50700595
Coord C2 exon
chr7:50698228-50698287
Length
2308 bp
Sequences
Splice sites
5' ss Seq
CCTGTAAGT
5' ss Score
7.52
3' ss Seq
CTTTTTTCACTTGCTTTTAGGGA
3' ss Score
10.42
Exon sequences
Seq C1 exon
GGACACCCTGGTCAGGAGGGGCCCAGGGGGCCTCCAGGTCTGGATGGGTGTAATGGCACACAAGGGGACACTGGTTACAGCGGCCTTGATGGGTATTCTGGTATTCCTGGTTCTCCT
Seq A exon
GTAAGTTATAGGCTATGTTTGCATTTGAAGAACATTTCTGAATAATCAATATTAATAATAGTTGCAGGTTCAAATGATAAAATAGAAATTAACTTCTCTGTTTTTATAGCAAAAATGGAAAATACGTTTTCGGATCACATGTGTTTTTATTTAAAGAGGCCCTATTATGCATTAAAAAGATCATACTTTGGTTTTGGGGGTCTCCAACAACAGGCTGATATGCATGCAAGGTCAAAAACACTTTCATTGTCTTATAATATGCATTTATTTTTACCTAATTACCACAACAACTCCCATATGACTCAGCGATTCATTTGCTCCCAAAGCCCTCCTCAGCACAATGCTATGCGCTGGTTGGTGTGATGAACCAGTCTGTTGCGATTAGCTAACTGCTTTCAGCATGAGACAGAGAAAAATGCCCAGCAAGAAGTCAGAGCACGGAGTGTATGTGCGAGCCCATTGCAGGAGTGCATTAAAGCAAAGCAAATTAACACCAGCTTATACTGACACACATTCAGTATTAATCCACACAGCAGCAAAAGCTGAACTATTTTAAACATTGACTGCCACATGTGTGTAAAAACAGCCAATGGTGGCCATTGCAATGACAAACGGCAGTAAATTGTGAGCTCACAAACACGTTTAAATCCATAAATAAAGCAGCACGCGCTGCGTTTTCAACGTGGTTTTAGATCCAGTATGAGAATATAAAGAGTTAACCAGATACAGTACAAGCGGTTATAAGTAACAAAACACAATTCCATACATAATTTGCAAACTAAAGAAAACAAGGAGGCAACAATTTTTATCGCACTTAACTTACTTACACTTCTGAAATGGAGGAAGAAACTGATTCATGAACTCTGTACTTTAACGTTCCTGTAAAGCTCTGACAAAGTCCTACACATCAATAGTCTTTTCTGATCCTTCCTTTAACAAACCGCACATGAATCCCCCATTGTAAGCGTGTAGATTGCTGAAGCACTCATCAGAAAAAAGATGGGAACACAGCACAAGGCTGGGTCTATAATACTGAGGTATTTTTTCAAAAATAAACTTGAACCACTGACTCTTCACACCCTCATCTTTGGGTAGGCAAAACAACACAAACTTTCCCTCACACTTCAGAGCAAAGCATCTTCGCGACATAATTCAACCGGGACCTGCTATAGTGTTTGTCTTCCTATTTTTCTTTCTACAGTGTTTGTGGGCGGGCCCGGGGGATTCAATTTTTCTGAGTCTGCGTGCGCAGCAAATGGGTGGGGCTTGAGATCCATATTAATGTCACGCCGACACGGCTAAGGACTCGTTACCCCCACAATTCATTTGAACCACTCTGAATCGACTCTTTTATAAATGAAGCATTAGTTTTAAACACTGTGCACTTTCAGATTCAAGGCTTAGCTGGATATTTCACTTGACTGTAGAGCTGTATTACACACTACATGGAAGGTCATTTTCAAAAATCCATAATAGGGGCTCTTCAATATAAATTCATATATTAGAGATTTAAACACTGCTCATAACTCTGGGTTATTGTTGGTCTAAAGCAGGGGTGTCACAACTTTTTCATATGAAAGGGCAAAAACAAATCTCATTGATAGCCGTGGGCTGAAGATAAATATACCAAACTACATAACATTAAAGCTGCCATGGGTACTTTACTAATTCATATAATTTTTTTATAATATTAAAAAAATAAATAGAAAACATTACTTTGAATTATATTAACTAATGCAGTGTAACTTTTTAAATGATAACTTATAACAATAAAAACATAGACAATTACATTTGTAACACAGTGGATTTCAATGCTGAATTTACTAGGCAAGCAGAATCTGCCTTTGCCTTGATTTACTCACCAAAGTCTCTGCATTGACCCTTTTTTCTTTCATTTGTACATTTTAAACTAATTCTGATTAATTTATACCATTTAAATTGAAACATTTACTTTCAGAAAGCCTTTTTGTAGCTTAACAATAAGACAAACAAATAAAAGGTACATCAAATTTGATATGACTCTAAACCATTCTCAGATGGGATGGCGGGCCAAATCAAAGGTTACCAACTTTGGCCCATGTTCTGAACACTACTTTTAGCTCTAGGTAAATCAATGTTTTTCACTCAAAATATGTAAAAACACAAAGTTTATGTATCATAAACTCAAAAATATAAACTCAAATGCCTGCTTATGTAATAGTGCAATTCTTGGTTACTGATTTTATAGTTGCACAGCTATAAAATAGATGTCTGTAAAGTTTTACTGCACATCAGTTTTTATATTTACACTTTTTTCACTTGCTTTTAG
Seq C2 exon
GGATTTCCTGGTCTAAAGGGTCAAAAAGGAGAACCATCCTATCTAAATATTCCCAGCCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000052061:ENSDART00000121574:7
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(0.1=0.0),PF0139113=Collagen=FE(62.3=100)
A:
NA
C2:
PF0139113=Collagen=PD(21.3=65.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping 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]