GgaINT1010115 @ galGal4
Intron Retention
Gene
ENSGALG00000008266 | COL4A6
Description
collagen, type IV, alpha 6 [Source:HGNC Symbol;Acc:HGNC:2208]
Coordinates
chr4:14057525-14058541:+
Coord C1 exon
chr4:14057525-14057641
Coord A exon
chr4:14057642-14058349
Coord C2 exon
chr4:14058350-14058541
Length
708 bp
Sequences
Splice sites
5' ss Seq
AAGGTAATG
5' ss Score
8.99
3' ss Seq
AGTTCTCTTCTTCCTTCTAGGTG
3' ss Score
11.25
Exon sequences
Seq C1 exon
GTGCAAAGGGTCTGCCAGGCAGATCTGGTTTGAAAGGACGTGACGGTTTACCTGGATCACCTGGCATTGCTGGTGACCCGGGACCTGTGGGTGCCCCAGGACCTCAGGGATTTGAAG
Seq A exon
GTAATGATATGGTTTGCAGAGCACAGATCATTCGACTTTTCTTTGTCCACAAATTCTGAAGAAACCAACTTAGTTACCTTAGGAAGGCTGGGGGATGTACATGATTTTCTGCTTTGTATCTGCAATGAAGTAAATCTTATCTTCAGTGAGGAAGGTTGTCACATGTCATTGCTGTCTGTCACTGCTGATGTTTCCCTAGGTACAATTCTGAACATCTTTTGGTTTCAGTATTCTGTGGATGTAGGAGCCATCTTGGAGGTTTGAAGGAGCAAAATGGTATTCACAGTGAGCACAGCTGTGAGGGTTGGGTGGTAGAGCCATAATGAGAGACAGAAGGGGATTCTGCCACAGATTTGTACAGCTTTTGGCCTTTCTGTGTCAAAGAAATATCAACATTAAAGCATTAGAGTGAAAATGAATTTATTATGTTTTGGCTGGTGCTTTGAGATCCTTAGAATATGAGAATGTGAGTAGTGTAAGATAGACGCTAACATTCTGGCATTAGAGTTGTTGGGGAAAGACAGAAAATGAAATGAGGTAGGAAATGAGTGGTTGCTACTGCAAAGCAACTGCTTTTGGAACAGGTATGCCTCATGGGTCACACAGCCCTCCAAACTTGGCCTCTGTCATACAAAGCAATGCCAAAATCAGCTGTAGAGCCAAGTGATACCCACCCTGCCAATGAGTGAGTTCTCTTCTTCCTTCTAG
Seq C2 exon
GTGCGGCTGGAAAGCCAGGCGCGCTTGGCTTGCCGGGAATGCCTGGTCGGAGCGTGGGTGTCGGGTACACCTTAGTGAAGCACAGCCAGTCAGACCAAATCCCGCCTTGTCCCATTGGCATGAACAAGCTCTGGGATGGCTACAGCTTATTGTACGTGGAGGGGCAGGAAAAATCACACAACCAGGATCTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000008266:ENSGALT00000013447:42
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=0.246
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(46.7=70.0),PF0139113=Collagen=PU(63.9=97.5)
A:
NA
C2:
PF0139113=Collagen=PD(34.4=32.3),PF0141314=C4=PU(39.8=66.2)
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:
GTGCAAAGGGTCTGCCAGG
R:
CTGGTTGTGTGATTTTTCCTGCC
Band lengths:
302-1010
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]