GgaINT1010116 @ galGal4
Intron Retention
Gene
ENSGALG00000008266 | COL4A6
Description
collagen, type IV, alpha 6 [Source:HGNC Symbol;Acc:HGNC:2208]
Coordinates
chr4:14058350-14059057:+
Coord C1 exon
chr4:14058350-14058541
Coord A exon
chr4:14058542-14058770
Coord C2 exon
chr4:14058771-14059057
Length
229 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGT
5' ss Score
8.73
3' ss Seq
TGCTTCCCCATTTCTTCCAGGTT
3' ss Score
9.73
Exon sequences
Seq C1 exon
GTGCGGCTGGAAAGCCAGGCGCGCTTGGCTTGCCGGGAATGCCTGGTCGGAGCGTGGGTGTCGGGTACACCTTAGTGAAGCACAGCCAGTCAGACCAAATCCCGCCTTGTCCCATTGGCATGAACAAGCTCTGGGATGGCTACAGCTTATTGTACGTGGAGGGGCAGGAAAAATCACACAACCAGGATCTGG
Seq A exon
GTGAGTTGACGTGCTTTTCTCAGGAGTAAACAATGTAGGCCAAAACCCAGTTTCTAATGTGCAGTTTTCACTGGTACTGCTGGCAGCTGCTGTAGGGAAAGTCTCCTTGGCCAGAATCTGTGCTGTGGAAGCAGTGTTACTTGTGCCATACTATGCTACTCTTGGCTAGTGTGTATGAGCTGGAACATTTGGCAGATGCTTGGTATGACTGCTTCCCCATTTCTTCCAG
Seq C2 exon
GTTTTGCTGGCTCTTGTTTGCCCCGCTTCAGCACTATGCCTTTTATTTACTGCAACATCAATGAAGTGTGCTACTATGCCAGCCGAAACGACAAGTCCTACTGGCTGTCCACCACCGCTCCCATCCCCATGATGCCAGTGGACAGCAATCAGATCCCACAGTACATCAGTCGTTGCTCCGTGTGCGAAGCACCTTCCCAGGCTGTGGCTGTGCACAGCCAGGATATCACCATCCCACAGTGTCCCCTCGGTTGGCGCAGCCTCTGGATAGGATACTCCTTCCTAATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000008266:ENSGALT00000013447:43
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.246 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(34.4=32.3),PF0141314=C4=PU(39.8=66.2)
A:
NA
C2:
PF0141314=C4=PD(59.3=66.7),PF0141314=C4=PU(25.9=31.2)
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:
TTGGCATGAACAAGCTCTGGG
R:
GGTGATATCCTGGCTGTGCAC
Band lengths:
308-537
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]