GgaINT0039328 @ galGal4
Intron Retention
Gene
ENSGALG00000005180 | COL11A1
Description
collagen, type XI, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2186]
Coordinates
chr8:10238954-10240613:+
Coord C1 exon
chr8:10238954-10239007
Coord A exon
chr8:10239008-10240568
Coord C2 exon
chr8:10240569-10240613
Length
1561 bp
Sequences
Splice sites
5' ss Seq
AGGGTATGA
5' ss Score
6.84
3' ss Seq
CTTCTGTACTTTCTACACAGGGA
3' ss Score
9.16
Exon sequences
Seq C1 exon
GGCTCAACTGGTTTCCCAGGATTTCCAGGTGCCAATGGAGAGAAAGGTGCAAGG
Seq A exon
GTATGATAATTATTGCTTGCATGACAGTTATCTGTTGGTACTCTGCGCTACAGGAATTCACTGAAGCTGTTATCCAAGGAACTCTAAAAACAGGCTTTTCACACTTGAGATGACCAGTTATGTAAAACAGGACATACTGAGTCACTAGTTCTCATTCTTTAAGGTGTTAACCTAAGTATACAGGAACTCAGACACTTTCTCATTGAATATGCTACCAGAATTATATGTTTGAAGAAGAGAGGAAAATACTCCCTTTGCTGAACATCTGATTTGACAGTATAGCCGAGTGATCTGGCAAAGACTATATTTTCCTGTATCCCATTCACTGACTTGCTATGATGCAGTTTACCCTCAAGGAAATTCAACTTCTATTTCATAAGTATTGAGATTTACCACAGGCTTTTTTATAGTCTGAGCTTTGAAAATGTAAAATATACCAAACAAGATAATGAACATATATATATATATAACATATGTATAACATATATACTACAACCAAATAGATACAAAATTACAGATTTTGCTGCTTTGAAGCACATGAGGGAAAATCCATTGTTCACCTTCTTCAAACTTAAAATGACATACAGGCAACTGTATTGCTGTCTCTAAAGCTCATCAGAACATAGCTGAATATGTTTCTAGAAGGCTGACGAAATTTGCAGAAGTGAGAGAATGGATAGAAATTCATAGAGACTATCAACTTAAGTAAAACTAAAATAATGTTTGCTATTGTTCTTAACAGTCTATTTTAATTTGTAGCATGAGAAGCAGAAATTCATGATTTTAAGATGAAATAGAAGAAAACTAATGGCATTTACATTGCTTTTGTATGCTTTAGATTGTTCTTGTATTATTTTATCTCGAGTATGTTGTTATGGACAGAGGAAAGCAGCAAAGCAATGTTCTTTTCATCCCTGTTGAGTTAAATGAGACATGACTGCTAATCAGGATATCAGATCAAAAACAAACAATCAAACAAATAAGTAAAATAGTAACACATCAAAGAGCAGATTTAAAGTATAATTATGTTGATCAATTATCAAGTCTTTGTAAAGCTTTTGATTCAGCTAGGGTACTAATGTCATAATTAACGCCACCAAACTGCATGTATACTTCAGTGTAAGGCTTCTCACCAATAATATAAGAATAACTGCTTTTTTTTTGTGTGTGTGTGTAAAGCAGGCATTATCATTAATCTTGCTTAAAGGTATACACTCATATGTGGTACACTAGTAAGACAGTCATTGTCCCTAAGAAGTCTACAGAGTATACAACATTGTAAGAATAATATATAATTTTATTTTAACATGTGAGATAAGATCAATATAAAAACAAAACAAAACAAAAAAAGTACCGTTCAAGTTCCTTTTTCTACTGGAAGAATACTGTCCAGAATTTTAACCCTCCTTTCATTAGAATACACAGCAATGCTAACCTAACACCAAGCCTAAGGAAAGGAATCTACTGGTTATACATAGGAAATATACTAAAGCAAAAAAATTAAGGGCTAGTATTACTATACTGTATGTTATTCTGTATTGCTTCTGTACTTTCTACACAG
Seq C2 exon
GGATTACATGGCAAACCAGGCCCCAGAGGACAGCGAGGACCAACA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005180:ENSGALT00000008321:32
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=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(17.7=100),PF0139113=Collagen=FE(25.0=100)
A:
NA
C2:
PF0139113=Collagen=PD(10.4=66.7),PF0139113=Collagen=FE(20.6=100)
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]