GgaINT0097654 @ galGal4
Intron Retention
Gene
ENSGALG00000009641 | COL1A2
Description
collagen alpha-2(I) chain precursor [Source:RefSeq peptide;Acc:NP_001073182]
Coordinates
chr2:23708287-23710371:+
Coord C1 exon
chr2:23708287-23708343
Coord A exon
chr2:23708344-23710326
Coord C2 exon
chr2:23710327-23710371
Length
1983 bp
Sequences
Splice sites
5' ss Seq
ATGGCAAGT
5' ss Score
3.26
3' ss Seq
TATTTACCTTTCTTCCCTAGGGT
3' ss Score
11.2
Exon sequences
Seq C1 exon
AATTTTGCTGCTCAGTATGATCCATCTAAAGCGGCTGACTTTGGCCCCGGACCTATG
Seq A exon
GCAAGTATATGATTTAACACTTGGTGACTTGCATAAACATGTATTTAAGTGTACTCCAGCTGTGTTAACTCAAAGCATAGGTCTAAAATTAGCATTTTGATCATGTATGTAGAGTCAGGTTATAAACTTATCCCTAGATAGAGCACAACATGAAGTGTCTGATAACAGTCTTAGGGCTGTGTCCTTAACTTGAATATAGCACTACTGGGTCTCATCACACTTTTATGAATCAGTGAATATCATAATCTGGCATCAGATAGTACATCTACTGTGATACAGTGTACTTTACCTGTGCTGAGACAGAGGAAGTCTGCTTTAGGGATTAGATTAATTGTAGAGATACTGACTACAGGAGACGTTTATCTAGAAAGTAACTCAGTATCTCAGATCCAGTTGGTGACCTTTTTTTTTTTTTCTCCCAGAGGCAGGGAGACAGAGACAGGGGAGGTTTAGGTTGGATATTAGGAGGAAGTTATCCAGTCAGAGGGTGGTGATGCATTGGAACAGGTTGCCCAAGGAGGTTGTGGATGCCCTATCCCTGGATGCATTCAAGGCCAGGCTGGATGTGGCTCTGGGCAGCCTGGTCTGGTGGTTGGCAACCCTGCACATAGAATGGGGGGGTTGAAACTAGATGATCTTTGAGGTTCTTTTCAACCCAGGCCAGTCTATGGTTCTGTGATAATTCTATGATTCCGAGCAATTGAAAGCTAGCACTTGCTATCTAGAATCTATGATTCTATGGTTCTGTGATTTGTTACTACAAGGCTATTCTGAGGAGGAATCTTTGCCAATTACTGTATATGATGTTGACATCTAAAGAGTCTACTACCTCCTTACACAAATTTCTAACCCTTGCTGATGTTAGCAAGTATTTTTTTGGTGCATATACATAGCAAAGCTATGGGTTAAGTTCACCTATCTCAATAACATTACAGACAGTGTGTCTGATGGGTGGGTGAATAGCATGACGAAAGCTGTCCAGGATTATTCTGGGTCAAGTACTAGGTCAAGTATTACTATTCCCAAAAATATTATAATTAATTGTTGAAAATATGTTGACGTGCATTTAGATAATAACTATAGGAATACAAGATAATTTTTAATCAGGCTTGGCCTTTGTTGTCTGACAGTAATATAGATCACTATTTATTTGGAGTGTAACAACTCTAAGCTCCAATTTTTTACTCATTGAGGGTTCACCAACAGAAAAAAGCAGTAAATTCTACTTCCTATGAGGAATTTTTAACTCCCTGAAACCAAGTGATAGGAAAGTGTGAGAGACTGGCAAAGCAGAAAAGAAGGGGAAGCAATTATGGAATATAGCTTGTGAACAGATTCGAAGGGCTTGTGCAGCATAGATGATTCAAACTGTGCAGGAAGAAGTTTGAATTAGTTTATTGACTAGAATTAGTGTATACTTCTATAGCTATAGCCTTTTACAGCATTAGCTTTCCAAAATGATGTGTGAGCCTCCCAGTTACTAGGAACACTGACATTTATGCACATTTCTTTTCCTTCTTTTCCTCTACATTTTTAATTATCCTTTTCTTCAATATCTCTTCTTGAAAGTTAGGATGAGATTGACAGGCCCCAAAATACAGCCTTTCGTAGTATGTCATTATGACCTTTTAAGTCTGGAAGTCATTCCCAAGAAAGCAGTGTGTACACAGGAATGAGCCAGCGTGTGAAAGCACTCATTAATGAGCTACAATAGAATGAGATGCCTGATCACAAGGTTCTCGGCCACAATGGCACATTCTTAATAATCTCACAGGGTTCACTGGCATCAGATCTATTTGTATTTGGACTGCCTTTGCAAATTCATTGCAGATCTCTTAACTTCCTCAAATTTGGTTTGAACATTGCACACCAAAAGTTACCATTTTTAACAGAATTTTAGGAACATCAGGAACAGGTATTACAGATGAGTTTATGTAGTAGTGTTAGGGTTTTTTTTTTAAATTATTTACCTTTCTTCCCTAG
Seq C2 exon
GGTTTAATGGGACCTAGAGGCCCACCTGGAGCATCTGGACCTCCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000009641:ENSGALT00000015703:6
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(12.5=36.8),PF0139113=Collagen=PU(4.8=15.8)
A:
NA
C2:
PF0139113=Collagen=FE(22.6=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]