GgaINT0011656 @ galGal3
Intron Retention
Gene
ENSGALG00000005797 | COL20A1
Description
NA
Coordinates
chr20:8827015-8827994:+
Coord C1 exon
chr20:8827015-8827187
Coord A exon
chr20:8827188-8827864
Coord C2 exon
chr20:8827865-8827994
Length
677 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAGA
5' ss Score
10.06
3' ss Seq
CATCTTCTTTTGTGTTCCAGGTG
3' ss Score
12.35
Exon sequences
Seq C1 exon
GTAGAGCTGTGAAAGATATCCCTACAAATACAGGTCCAGAGCTGAGCCCGACAGACCTTAAAATATCAGCTGTCACTTCTAAAAGCATGCACTTGGCCTGGAGTCCTCCTCTGAGTCCACCAAAGAAGTACCGGGTTGTGTACTATCCATCAAAGGGCGGCACTCCCAAGGAG
Seq A exon
GTAAGAGGTATTTGTTGGACTGTTGGAAGGCTGCAGTGCCTTCCAGTCAGTGGCTGGGAATTGAGGCAGACGTGGGTAGGCAGAGTGATGAGGGTAGGAGTGCAATGACCATGGGGTATCAGCTAAAGCCAGAAGGAAACTGAACGTTGAGTACAAATGTGACAAGGTGATAGGATGGTGAGGCAGAAGAGAAAACTGGATAGATACTATATTGCTAGAACTACTGCAAGCCATACCCACTCAGTTTTCTCTTGCACAGTGTTATCCCCTTCCTAAGGCACCTCAAGGAACACACACAGGCACACAAAGGTGTTGAAGGATGCTCATCTCTGACAGATAGAATCAGAAAAGCAAATCCAAGCACTTGATGGATTGTCCTTAATTACACACTTCAACTTTTGGTTAGCCCTGAAATGGTAAGACAGTTGTGCTCGGGTATCATGGCAGGTCCCTTCCAACTGAAACTATCAATCATGGAATCGTGTTCTGTTCCATTCACTTCAGTGAGAGCATGATCGGGGTCTTGTGCTATGTGCTTGTACAGATCCAGTCCTTCCAGGACAGGAATGCTGACAGCCTCCTATCTCCATGCTTGCCAGGGAAGACTGCTTCCACTGTTCTTTTGCTGGAGAGTGGCTGGCACCTCCTGGGCTTGACCATCTTCTTTTGTGTTCCAG
Seq C2 exon
GTGCTTCTGGATGGAGCCATCTCCTCTCTGAGGCTTTCCAACCTGACCTCACACACGGAGTACCTGGTGTCAGTGTTTCCTGTTTATGACACAGCCGTTGGGGATGGGCTGAGAGGCGTCACCTCCACAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005797:ENSGALT00000009312:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.276 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0004116=fn3=PU(54.4=74.1)
A:
NA
C2:
PF0004116=fn3=PD(43.0=77.3)
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:
GTAGAGCTGTGAAAGATATCCCT
R:
TGACGCCTCTCAGCCCATC
Band lengths:
294-971
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]