GgaINT0090626 @ galGal4
Intron Retention
Gene
ENSGALG00000016195 | COL22A1
Description
collagen, type XXII, alpha 1 precursor [Source:RefSeq peptide;Acc:NP_001132911]
Coordinates
chr2:144147659-144149028:-
Coord C1 exon
chr2:144148962-144149028
Coord A exon
chr2:144147842-144148961
Coord C2 exon
chr2:144147659-144147841
Length
1120 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAGT
5' ss Score
11.01
3' ss Seq
CCATTCCCCTCTCTTCACAGCAA
3' ss Score
10.14
Exon sequences
Seq C1 exon
GGGGAACCTCCGTCTCTAGAGACTCTGAGAAGACTCATCCAAGAGGAGTTAGCTAAGCAGCTAGATG
Seq A exon
GTAAGTAATCAGCTCTGAGTAGCCAGCAGATAGATCTGAGAGCATGAAAGATAACTTTCCATAGTTGTGGTGTTGTAGCTGACATCTGAAACTCTCCTGCTTGTGGAAGGCATTGTTGCAACAAGTCTACCTGGAAGACACATTTGTGTAAAATGACATTTAATGCCCACCAGTATAAGGAGAGGGTGGAGAGTGGATGTAGGTTGCTGTTTTTCTCAAAGTATTTGAATTGCAGGCCAGTATTGACTTACATCTACAGTGATCTGCAGAGCTGTAGTGCTTCTCTACGCACAGCTCTTGGAGCAGCTGAAACATATCCATGCACATTTTCCTCCATTCTAGAGATCGTGGTGAAATTAGGTGATTTGTTTGAAGGAGTTTATTTACATGTTCTCAGAATTTCATTTCCACCCCAATCTAATAGCAGTCAAGAGTTTGCATCACTGAAGAGAACATAGAAAACCCTTTTCCCTTCATTCTGTAGGATGTTTTTGTGATGTTAAGTGTATCTAAAGAGCCCTCAAGGCTGCTCAGAGTTTGAATCTGAGAGTTATGAGCAATGTGGCTGCATGGAATTCAGATGATATGTTGACACAGGGAGCTGCCTTAGTTGCAATTTCTGATTTCCCAGGCAGAGATGGGTACATTGGCTGATAGGTACTTTGGCTTTCAGTCCATTTATGTAACAGTCCAGAACAAGAAAAGAAAGCTTTCTCCCTAAAGAGCAGCCACATAGCATCCCACTGTATAGCAGAAGCAATGGAAACATTCTTCTTTTCAGATCAGCTATGATCTGAGTTCTACAGAAATCCACCAGCTGTACTGTTAAAGAGAAGGACATTCAGATCTTCCTTGAACAAGGAACAGAGATAAGTGTTTAGGATTATGCATGATATTCAAGAGAAGTATGAAACTATGGAGAAATAAGGCTAAAATCATTTACAAAGGGTAAGGTACTATCATGGCATTTGAGAAAGGGTTATGTGGCAACAACAAGTGAATGGTCCTGAAAATTTCATCAGTTCCTTATTTGGACTTTACTGGACCAATGTTTCCAGCTCTCCATCAGTTGGAGCACTGATCTTCTTGTCTAACAAACCCCATTCCCCTCTCTTCACAG
Seq C2 exon
CAAAGTTAGCCTATCTCTTGGCTCAGATACCGCCTGCACATGTGAAAGCATCCCATGGCAGACCAGGACCTCCTGGTCCCCCTGGGAAAGAAGGACTACCAGGAAGAACTGGCCCTCCAGGAGAGCCTGGCCGCCCTGGACAGACTGGATCTGAAGGACCACCCGGACCCATTGGTCCCAAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000016195:ENSGALT00000026109:62
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=PD(6.5=17.4)
A:
NA
C2:
PF0139113=Collagen=PU(76.3=72.6)
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:
GGAACCTCCGTCTCTAGAGA
R:
AATGGGTCCGGGTGGTCC
Band lengths:
238-1358
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]