GgaINT0050806 @ galGal4
Intron Retention
Gene
ENSGALG00000003923 | COL6A3
Description
collagen alpha-3(VI) chain precursor [Source:RefSeq peptide;Acc:NP_990865]
Coordinates
chr7:4771552-4774336:+
Coord C1 exon
chr7:4771552-4772151
Coord A exon
chr7:4772152-4773769
Coord C2 exon
chr7:4773770-4774336
Length
1618 bp
Sequences
Splice sites
5' ss Seq
CAGGTAATA
5' ss Score
8.55
3' ss Seq
CATTTGTGAATTTATTCTAGAAA
3' ss Score
6.25
Exon sequences
Seq C1 exon
TTCAAGTAACCAAAAGGGATATCATCTTTCTTTTGGATGGATCACTCAACGTCGGAAATGCCAACTTCCCCTTTGTGCGGGACTTTGTTGTGACTTTAGTTAACTACCTTGATGTCGGAACCGACAAAATCCGAGTTGGCTTAGTGCAATTTAGCGACACTCCTAAAACCGAGTTCTCCCTATACTCATACCAAACCAAATCAGACATAATTCAACGTTTGGGGCAGCTGAGGCCCAAGGGTGGGTCAGTGCTGAACACCGGCTCTGCACTGAACTTTGTGCTTTCGAATCACTTCACTGAAGCTGGTGGGAGCAGAATAAATGAACAAGTGCCGCAGGTCCTAGTCCTGGTGACGGCAGGGAGGTCGGCCGATCCCTTCCTGCAAGTTTCCAATGACTTAGCTCGGGCCGGAGTGCTGACTTTTGCTGTTGGAGTTAGGAATGCGGATAAGGCAGAGCTTGAACAGATTGCATTTAATCCAAAAATGGTATATTTTATGGATGATTTCAGTGATCTGACAACATTACCTCAGGAGTTAAAAAAGCCTATAACAACATATGTTAGTGGAGGTGTGGAGGAGGTTCCACTCGCCCCAACAG
Seq A exon
GTAATATCTACCTTCCTTCATCTTGACTGCATTAAATTAATCTTGTTTGTCTTGACTGTTTGTTCCCAATGTACACCTTCACACTCGTCCAAGGCCCTCAGTCATCAAAGCATTGAGGACTGTGCCTAACCTTACATGCATTAATTTTGACACAGTCAGCTCTTCATTTTGCTGAAGTCGCACTTTAAAGACAGCACAGTCTGAAGGAGGTAAGAACAGAAGGGTGAACAGAGTGAGTCTATGCCCACTAGTCACCGTTTCAGGCGTTCCCTTTTCACTTCCATAATAATGTCACAACCTGCAAGTTCATTGCTTGTACTATCTCAGGCAATGGGAGCTTGTAGTTTGGCCACAGGGATTATTGTGTGAAGATAGACATAGCATCAGTGATCATGCAGGAGCAAAGGTCTAGCCATGTACATGTAGCTAAATTGTTCCCTACAACCACTCTGTAGAAGTGATATTATCAGACTGTCACAGAGACTGAATTTGTCTTCAGATATTCAAAGTTAGGCTCTGACATTAAGCTTAAAAATTGTTGGTAAGCTTAACCTTTTATAAACAGATGTCTGCTCAGTAATTCCCTTACTGTGGTGTAACTCCGTAACATGATGGAAAACACAGAAATGACAGCAGGGTAGCAGAGTCTCAGGCTGCAGCAAGTGAGGATAAGCTCAAGTGCAGCAGCTGTGGATGCAGAAACAAAGGGAGAAAGGTGCTTGCCTTCAGAAGGTCTCAGGTAGGCAGGGATCTCCAATGATATACCCTCAACTCCACTACCAACCCTTAAATGAGATCTGGGAAGAGGTGGATCCTGGCTCCATCCCTTCCAATCACTCAGGTACATTGCATGCAGCTGAGCTCCCTTGGGTTGGCCCTGCCTTCCACCAGGTACTCAGTCACTGTTTCAGGCCATGACTTAGCATTTCCGCTACTCTATGGCTATGCGTGTACAAAGACACAAGAATATCCAGAATTGTTCAGGCTGGAAAGGAGGCCATTAAGATTAACACAGCAGATGTTAAGATGCACAAATATGAGGTGCTTGGTTTTGCCTTGGATGCTTGATGAAACTAAAAGGGCCACTGATAATGGGTAACAAAAATTTTCCCCTCCCAAAGTCGTAACTCACCTCAGGATATGACTGCCTTGTGATGCAATTGAGAGAATGCTATGTCTGTGTGTATAAATTAGCGTTTATTCATCAACTAATGAGCCTTTAAATACAAAAAAACCCTTCCACTTCTGTTGTACTTCATGCCTCTGTTGTCAGCAGGTTGCTAGAATAGATGTCACTGATCTATTCTGAAATGGCCAATATATGATATGACTGACACAATATGACACAAGTATATGATATGCTATATGATATGACATCCTGGTGCCTGAATTTACTGAGTCTTAAGAGAGGTGTCCCTTGCTTTCCTTTCCTTATCAGATAAACACATGGAAGGTACTGTTTAATCCTGTAGTCTCTGAATACTTTGGTAAATGAGAATCACTTGTTTTGCATATTGAAATCCATCTGACTTAGAGAGAAGTTTCTAGGATGAAATTTAAGAAGAAACGTGCCTTCATATCTTTTATTTCCCTCTTTTCATTTGTGAATTTATTCTAG
Seq C2 exon
AAAGCAAGAAAGACATTTTATTCCTGATTGATGGTTCAGCCAACCTCTTGGGTAGCTTTCCTGCTGTCCGGGACTTTATACACAAAGTCATTTCTGACCTGAACGTGGGTCCCGACGCCACGCGAGTAGCTGTGGCTCAGTTCAGTGACAACATCCAAATTGAATTTGACTTTGCTGAACTCCCATCTAAGCAAGACATGCTTCTGAAAGTGAAAAGGATGAGGTTAAAAACTGGGAAGCAGCTGAATATCGGAGTTGCGCTCGATGAAGTCATGAGGAGGCTGTTCGTGAAGGAAGCTGGAAGCAGGATTGAAGAAGGCATTCCTCAGTTCTTGGTCCTCCTGGCTGCTGGGAGGTCAACCGATGAGGTGGAGCGACCATCGGGAGCTCTGAAGGAAGCTGGAGTTGTGACCTTTGCTATCAAAGCCAAAAATGCTGATTTATCAGAGCTGGAAAGGATAGCTTACGCCCCACAGTTCATTCTGAATGTCGAATCCCTTCCTCGGATTTCGGAGCTCCAGGCAAACATAGTGAACCTACTGAAAACTATCCAGTTTCAGCCAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000003923:ENSGALT00000006250:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0009223=VWA=WD(100=88.1)
A:
NA
C2:
PF0009223=VWA=WD(100=93.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTAGTGGAGGTGTGGAGGAGG
R:
GCTTCCAGCTTCCTTCACGAA
Band lengths:
344-1962
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]