GgaINT0050808 @ galGal4
Intron Retention
Gene
ENSGALG00000003923 | COL6A3
Description
collagen alpha-3(VI) chain precursor [Source:RefSeq peptide;Acc:NP_990865]
Coordinates
chr7:4777392-4779653:+
Coord C1 exon
chr7:4777392-4778012
Coord A exon
chr7:4778013-4779053
Coord C2 exon
chr7:4779054-4779653
Length
1041 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGA
5' ss Score
9.22
3' ss Seq
TCCTTCCTTCTTTTCCACAGTGG
3' ss Score
10.01
Exon sequences
Seq C1 exon
TAGTTGAGAGAGGTGAGAAGAAGGATGTGGTGTTTCTAATCGATGGCTCGGATGGTGTCAGAAGAGGTTTCCCTCTCCTGAAAACCTTTGTGGAAAGAGTTGTTGAAAGCCTTGATATTGGCCGTGACAAGGTCCGTGTTGCCATTGTGCAGTACAGCAACGCCATACAACCTGAGTTCTTGCTGGATGCCTACGAAGACAAAGCCGATTTAGTCAGTGCCATCCAGGCGCTGACAATTATGGGAGGATCTCCTCTGAACACCGGAGCAGCCCTCGACTATCTCATCAAGAACGTGTTCACCGTGTCGAGTGGCAGCAGGATAGCTGAGGGCGTCCCGCAGTTCCTGATCCTGCTCACTGCCGACCGATCCCAGGATGATGTGAGGAGGCCCTCAGTGGTCCTCAAGACGAGTGGCACAGTGCCCTTCGGCATCGGGATTGGAAATGCCGACCTCACAGAGCTTCAGACGATCTCCTTCCTCCCGGATTTTGCTATCTCTGTACCCGACTTCAGCCAGCTGGATTCAGTGCAACAGGCCGTGTCCAACAGAGTCATCCGGCTGACCAAGAAAGAAATAGAGTCTCTTGCCCCTGATCTGGTTTTTACATCACCCAGCCCAG
Seq A exon
GTGAGAAGAAGTTTGTGTCTGCACCAAGAGCCAGCGGCAAAATATGATGTTTAGTAACATCATGGTTGCAACACAAACAGAAAAGCGGAGACGGTCACGGCTCTACATCCACCTTGGTCTCACTGTCAATGTATTTTCTGATGTACTTAGGGTTAGTAGGAGCTGTGACATTAAGCTGACCCACCATTAATCACAGTCCTACAAAGTGGTCCATGTTACATCAACATGGAAGACACACAGAGTGGATGCCAGGACTTTAATCTCATTTTAATTCAGTGAACTGTTATTTCAGTCCGTACTATTCCTCTCAAAAAGGAAATGGCATCGTTTAGATGATGCAGGGATTCCTTCACAAAACTACATATCAACGTCACCTTTCTGCTAAATGTAAGACCTTCTTCTGATGTGTCTAACATTTGCTACGCTCATTCACAGGGGGAAAGGAAAATGGAAAAGAATCAGAACTTCCATTTCTGGTCTCACTTTGAATGAAATCCAGCCAGCATTCACCCGTCCTGAGGGGATGAAGGGTACCCAATCCAAATCAGTCCCTTTGAAGTCCACCAGTCTACTCTATCTGTTTCTTCCCTTCAAAGTCAGACTGCTTTCCCCCAGCCCCACTTGTCAATGTAATATTCAGTGATAATTCAGGCTCTGACCTGAATTACTGAGAGAATCATGGGATAAAATCTATCTTAGAGGAGAAAGACAAGGAAAGAGGAATGGCTTGTGTGGCAGCCCGCCTTGAGTAAGGAGCATCACCATGCTACATTTCCTTATGTGTAGATCCCACCAGGTATTAATATTCCAAGATTCCCTTGCTCTCTCTTGCTTCCTTTTCTCTGGAAACTGCTGTTCTTGCACTGCCTTGGGATGTGCCCAGTAGACTGGCCCAGTCTCTGGGGCTCCCAGGAGAAATCATAAGGAAAGAAACAACAAGCATCTTCCCAAAGCATGGGCCAGTGATGTAGATGATGACGTTAGCTGCCTTCCATAGGCAATGCTTGATACATCCTCTGACTCCTTCCTTCTTTTCCACAG
Seq C2 exon
TGGGTGTGAAGAGGGATGTTGTGTTCCTGGTCGATGGCTCCCGCTACGCCGCCCAGGAATTCTACCTCATCCGTGATCTCATTGAGAGGATAGTGAACAACCTGGATGTGGGCTTTGACACCACTCGGATTTCGGTGGTCCAGTTCAGCGAGCATCCCCATGTAGAGTTTCTTCTCAATGCCCACTCCACCAAGGATGAGGTGCAAGGTGCAGTGAGGCGGCTGCGGCCACGGGGTGGCCAGCAGGTGAACGTGGGGGAAGCCCTTGAATTTGTGGCAAAAACCATCTTTACCCGTCCGTCTGGGAGCCGCATAGAAGAGGGCGTCCCTCAGTTTTTGGTTATCCTCTCCTCCCGCAAGTCCGACGATGACTTAGAATTCCCATCGGTACAAGTCAAACAAGTAGGAGTGGCACCTATGGTCATAGCAAAGAACATGGATCCTGAGGAGATGGTGCAGATTTCCCTTAGCCCTGACTATGTGTTCCAAGTCTCCAGCTTCCAGGAACTGCCCAGCCTTGAACAGAAGCTGCTGGCTCCTATTGAAACCCTGACTGCAGACCAAATCAGACAACTCCTGGGAGATGTGACAACAATTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000003923:ENSGALT00000006250:8
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=0.025
Domain overlap (PFAM):
C1:
PF0009223=VWA=WD(100=84.1)
A:
NA
C2:
PF0009223=VWA=WD(100=85.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTTCGGCATCGGGATTGGAAA
R:
GCTGAACTGGACCACCGAAAT
Band lengths:
346-1387
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]