GgaINT1010120 @ galGal4
Intron Retention
Gene
ENSGALG00000008266 | COL4A6
Description
collagen, type IV, alpha 6 [Source:HGNC Symbol;Acc:HGNC:2208]
Coordinates
chr4:14028883-14030495:+
Coord C1 exon
chr4:14028883-14028951
Coord A exon
chr4:14028952-14030459
Coord C2 exon
chr4:14030460-14030495
Length
1508 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGA
5' ss Score
10.57
3' ss Seq
GGTGCACTTTTCATTTTTAGGGA
3' ss Score
9.09
Exon sequences
Seq C1 exon
GGTCGTCCTGGTCCAAAAGGTCTTAAAGGAGAACCTGTTTATGCTCAAGGCAGCCTTAAAGGAATGAAG
Seq A exon
GTAAGATTTGCTATAGGAGAAAACACAGAATGAGAAACACTTTGATGTCTTAGAGGTTTCAGGGCTGATGCAACAGCTTAGGTTGCTCATAATGTTAAATGTGGGTGTCCTAGATAATAGGTCTGAAGGCAGAGCAGAGAAAAAGACCATTCATTCCTTAATGGCAATGCGGAGTACTCTCAGAATTTGAAATTGCTTGATCTTTGCAGCACTCAAACATCTTGTTTATTGCATGCTGTACTGCTGGGACATAGCTCATCCCGTTACCATTCAGAGTAGTTGCTGGTCCTTCATCTAGACAGCTAGCACCATTCATTTGTTGGTGTCAAACCATAGATATGAGGAATTTCCTGTAAGCTTATCCTGATTTACGTGAGGTAGCATATTTGTTTTTAGATGCAGAACTTCCCTGTATGTGGCATCTCACACATGCCAGGTCTGTTGAAATAAAAGCCCAGGAGACTCTCAAGCAGAGATTAAGATTTCTCCTGTGAAATTCCACTTACCCCCCAGTGCTTTTTGTAGTGGGAGATACTAATAATTGGCCAGTTATATTCTGGGTTTAAATGCATGAATACCGTATTCCACTCATAGTATTTCATCATTTATTGCTATGAAGTCAGAATTTAATTCTCTACTTAATAAGATAATAATAATAATTTTGCCCTGAAATGTCTGTATCATGTCTGTAATTTTATTTCCTATAAAGAGAATACAGACTATGGAAACATGATCTCAGTTTATTGTTCCAAACAGCGAGTAGGTTTTTCAATACCCTCATATAAAAATTCAGTTCTTTGCTGCAAAGAACAAAAACATTCACCAGCTTAGAGTGGTTTTGATTTTTGCCAATAGCAGTAGGCTTGGGAAAAAACTGTAAAAGATTTGATGCCTCTTCTACATTCAGCAGCATCATTACTCATTAAATATAGAAAATATTAAGGTTTTTTGTCTGTCATGTAAGGCCCCTCACTCTGACCTTTTTTTTTGTCAAAATTATGAACTTTTAAAAAATCCTACCTATATATATATTTATATAATATTGTTTAATATATTATAATAATGTATAATATAATATAATTATATAATAAAATAATAATAAAAAAATAATATTGTTGTACATATAACAATACATCGGTAAAAATTGAATAGATCTTTATTTAAATAAACTTCACTATTTGTGGAAAATACAGATTGTTTGAAATAACGTTTTATAGTGTTTGTAATGAAAGTTTTTGTAGTGTGTTTCCCAGATTTTTTACAGTGAACTTTTTAATGCCACTTCAGTTTCTCTTGCTACCTGTAAATAAAATGGTTGTTGTTATTCCAGACTTTTGGAGCCTTTCCGTTTCCCAATTTAAACATGGAAGCACAGGTGTCAGAACTAAAAGTGAACAATAACTAAAAGCAAATACTCCTGTTTAGACTAAAAAGTATGTATTTATAGCCCTTCATAGTTTCTTGCAGTAATACAATGGTATTTTTACTGGTGCACTTTTCATTTTTAG
Seq C2 exon
GGAGAAAATGGTCTTCCTGGATTGGATGGTATTTCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000008266:ENSGALT00000013447:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.974 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(25.8=73.9),PF0139113=Collagen=PU(13.3=34.8)
A:
NA
C2:
PF0139113=Collagen=FE(18.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
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]