GgaINT1010098 @ galGal4
Intron Retention
Gene
ENSGALG00000008266 | COL4A6
Description
collagen, type IV, alpha 6 [Source:HGNC Symbol;Acc:HGNC:2208]
Coordinates
chr4:14046746-14049055:+
Coord C1 exon
chr4:14046746-14046907
Coord A exon
chr4:14046908-14048884
Coord C2 exon
chr4:14048885-14049055
Length
1977 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGT
5' ss Score
9.8
3' ss Seq
TATTTCTTGTATTGATTCAGGAC
3' ss Score
8.11
Exon sequences
Seq C1 exon
GGCTGGATGGGAGGCCAGGCCTCCTAGGTATTAAAGGCGAGCTGGGTAATCCAGGATATTCGGGTGTCCCCGGATTGCGGGGTCCTCCTGGTCCTGGAGGTCCTTTTGGCATTAAGGGAAAACCAGGACCACTGGGATCAGTTGGCCTTGCAGGAGCACCAG
Seq A exon
GTATGTAACTTCTTCAAATGAAGACAGGTAGCTGAGATGAACACTGCAGTGTTGAGGAAGTGTGGGAGAGATTGCCAGTTGCTGATGGAGAGCTCCTACCACTATTTAGGGGTAACTGAGTGCAGAATTTGAGCTTTTTACCTCTAACTGCTGGAATCCTCCTGCACTGAAATGGTGCCCCAAGGTTGTAAGAAGTACAGCAAAAAGACAGGAGAAAGCAGTTTGATATCTTTTAACATCTCTCATTTACAGGCTGGCTGTATACACTGACTAATCTTCATTTCCCATTTTTGTAACAATTGATTTTTTAATATATGAGGTTGCTTGAAACGCAACTTCTATAGGTTGGAAACTTGTTAGGTTTCTGAGAAGAAGCACTTATGTGCTACACCATCTGGGTCAGAAAATAAATGAACTTCCCTTCACTTTACAGGAAAAAAAACACTTGAATACAACAGTATCTCTGAAGCTGTACTGACTAGAGTGTTTCATGATAACAGTGTATTTGAGACTTGAGAACCGAGCAGAGAGGCATCTGGGAATTAGTAGATAATTCCCAGGCCTGTGATGTAATTCTGTCCTAACTTGCAGAATGACAGTGCTGAAACACAGTGACAACAAATGAATGAAAGCACTAACTTCATCTGAGAAGAAAATTATAGTTTTTAAGCTTCTTATTAGAATGCTAACCTGACTTTCACTTCCCTGTTATTTTATGGTTTTGGACTGTATGCCATATAGGACTGTTTCCTTCAACTGTTTTTAAATACCTTCCATTACTAGGACGATAAACTCCCAGTGACTATGATATTTCAGCTGTATTCTCTGAATCATTAATTTCTTTATATCCTTATTCTTTCTGTTTACATATTGTATCTGTTTTTTCCTTCACCATGTTTCTATTCCATTTATCAACTCCCCATTTCTGATGTCACACTGTTTGGTTATGGGTTCTTCACATAGGCTGTCAAGGTGAGAAAATGCAGTGTAGCATAAAAGCTCATGGACTAACAACCTAGCTTTTAATGCTACAAGAATTGCATTGACTATAGGTGATACCCCTTATTATTGCTAATCAAACCAGAAGGTAAAGAACTGTTGTAGTGAGAATGCTCAGATGGCAGCAAAGCCTGAAGCTTAAAAGGAAATGCTTAACATGCCCAAAATTTAAGCCTGAATTTTCTTTGTCTTTTTAAATAAAGCAGCCATTTCATCTACTTTAAAAAAAGTACTGGATCATAACATAAAATGTTTGAATACAATGAAGCTTATATGTTGGGTGCTGCTGCTGCAAATGTCATTTTTCAGAAGCCACTTGATTTTTTTTTTCTTTCCTTCCTTACTTTGGATCTAAGCATTCTCTTTTCAATAGTTTGAGCCTTTATTTAAAGTTGTAAATCATTACAAAGCTTCAGCTAGAAACATTCTGAAGCATCTAGAGGCAAAACTGAGTATATGGTGTTGGTTTCATCACAACACTATCAGAAGCTTGTTTCCTTAGTGAGCAATTTGCTTTTGAGAAGTAACGCTTTAACTGCCAAGGTGGAAAAGAAACTTGTGAATACAAGTCTCTCAAATTGATCTCTGCTTCGCTCTGAGGATGGGGTAGGTAGATGTAGCTGACATTAAAGATGCTCCCCATCCTGGTTTGGCTGCCTTGATGATAAAGGTAAGACTGGTGCTCTACACTGTGGTGTCTGGTAAAGGAGACAAAAATGGATACATCATAAGGGGTTTCACTCTTGCCAGTGGTGTAGTGATGTAGGCAGTAACCCTTTTCATAGGTATTTTATTATTAGATCACTAATGCTTTTGCATTTCTAAACTTTATGCCTTCTAAGTAGGCTGCATGTGCCTTAAGATCCATTTGTTATATAAAAAACAATGCTGTGCTTAAAGAGTTTGGAAAGCTGTCCACAAAAGTTCCCCACTGTTTGTATGTCATAATCTATTGAGTTATTTCTTGTATTGATTCAG
Seq C2 exon
GACTTCCTGGAGTCAAAGGATTGAGCGGGGATGTAGGTCCTCAAGGCCCTGCTGGTATGAAAGGCTTCCCAGGTCTTGATGGTGCTCCAGGACCTCCTGGGGAAAGAGGATTCTTAGGACCACCTGGACCTTTTGGTCAAGATGGACGTCCAGGTTTCTCTGGGCCAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000008266:ENSGALT00000013447:27
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.994 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(42.9=43.6),PF0139113=Collagen=PU(67.1=92.7)
A:
NA
C2:
PF0139113=Collagen=PD(15.9=19.0),PF0139113=Collagen=PU(87.1=93.1),PF0139113=Collagen=PU(4.8=5.2)
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:
CTGGATGGGAGGCCAGGC
R:
CTTTTGGCCCAGAGAAACCTG
Band lengths:
331-2308
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]