GgaINT0097660 @ galGal4
Intron Retention
Gene
ENSGALG00000009641 | COL1A2
Description
collagen alpha-2(I) chain precursor [Source:RefSeq peptide;Acc:NP_001073182]
Coordinates
chr2:23712064-23713768:+
Coord C1 exon
chr2:23712064-23712117
Coord A exon
chr2:23712118-23713723
Coord C2 exon
chr2:23713724-23713768
Length
1606 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGG
5' ss Score
10.51
3' ss Seq
GTGAATTTTTTCTTTCACAGGGA
3' ss Score
9.97
Exon sequences
Seq C1 exon
GGACACAATGGTCTGGATGGTCAGAAGGGACAACCTGGTACTCCTGGCACCAAG
Seq A exon
GTAAGGATGAAATCTGAAAATGCAGGATTCATTTGTAGCTCTTTCTAGGGAAATACATATGAAGTCTTCTCCAATTGATCTTCCATGTTGTCACTGAATATTGCCCAGCTGCAATATAATCTGGAAGGCAGCAGATCCGTGTAGGACAAATAGATGCAACTCAAGATGAGAAATCATGTTAGGGCCTTTTTCTGTAGTCCTCAGTCAAGTAATAACTGTTAATGAGTAAGAACAGCAGAACTGGCTTCCTAATAATTGCCTTCCTCTGCCTTTCTATGGAATGTAGTTGGAGTTTAGGTATTTTCTCTAAAGCACATTAAAATGAGAATGTAATTTGTCTAGAAAGCTCTGCTGTTGGGGACATACTTTAGTGAAAGGCTTTCTGCTAAAACTTTGGATAAAGAGTTAAGGCTACTCAATCTTCAGACTTCTTCTTTTTCGTCTTCCTCAGCTTAGTGCATATTTTAACACTGCTTAAGAAAGCTTTTCTTAAACGTGGTCTAGAAACATTTAGCAAGCTTTTCCTCTCAATTTCTTCATCACTCCCACTTCAGTGCCTACTGACAATGGTCTTAAAAAACACTACTGCTTTTTTGGGGTGTAGGAAATTTTAATGCTGATGATTCATTCACAGTAGGTCTGCATTCAAAAACTTTTAATGTAACAACGTAAGGGTCAAATTCTAATCCTCATTATTGCTTGTTTACAAGAGCTTAGCACTACTTGCTTGTAGTTACTAACTGTACCACAGTATTTTCCAATGTCACTGCAACTTGTTTAGCTCCAGAAAAAGTTTGGTAATGAAATAGCTACCAAACACTCTGTCCAATTTCTGGTGGCTAAAAGCAGATGAAGTAAATAATCAAATGAAAGAATGCTAATTTGACTGAAAACACAAGTGTGATGTGATTTAATTGTGATTAAGGCAAAAACTTCTACTGTTTGCAGCACTTAAGACTTGGTGCATTCAAATATGCTTAGGATACTAGTGCTCTGGAACAAACTTTGTCACTATAGGCCAGTCTAGACAAACTGTGAGATTACTGAGAGCTCCTAATATTAAGGGAGATAAGTCACATTTTAGTGGTTGTCACTTATATCAATATTATTGGTCATAAGAATTTGGGTCAGATATTTCTGTCTTATTTTTAGTCGTTTGACAGCACAGATGAGGAATTTTGTCACCTTAACTTAAGGCAAAAGAAAGTATTTTCTTTCACTAGCTAAAAAAAAAAAGTTGCAGTTTGATCAGAACTGGTAGTTGACTGTTCTCTAGCCCTATCTCTTAGGTGTGTGCTACAGTGCAAATATAACAGAATGAAGAAAGGGAGTAAAGACAGTTGAGACTGGCAAGTGAACCAATTTGCTCCTAGTCTTCCTCTTTTAGGAGGATTTCAGCTGGCTTTGCTCCAGTATATAATGGGATAGTCACAGCCTCTGCACTGTCAGTGACCCATGTGCTGTTATTCTACACAGTGGTGTGAGTGCTACAGCAGACAAGAACAGTAGGATACAGCAACTGAATACCTCCTCGCTAGCTGGCTTTGTGCTATCAGTCCAAGGAATCCTTTGAGTAACTTAAGCATGTGAATTTTTTCTTTCACAG
Seq C2 exon
GGAGAACCTGGTGCCCCTGGTGAAAATGGTACCCCAGGACAACCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000009641:ENSGALT00000015703:12
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(27.9=100),PF0139113=Collagen=PU(10.3=44.4)
A:
NA
C2:
PF0139113=Collagen=PD(13.2=60.0),PF0139113=Collagen=PU(18.9=93.3)
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]