GgaINT0125306 @ galGal4
Intron Retention
Gene
ENSGALG00000002546 | COL5A1
Description
collagen alpha-1(V) chain precursor [Source:RefSeq peptide;Acc:NP_990121]
Coordinates
chr17:7546475-7547721:+
Coord C1 exon
chr17:7546475-7546582
Coord A exon
chr17:7546583-7547667
Coord C2 exon
chr17:7547668-7547721
Length
1085 bp
Sequences
Splice sites
5' ss Seq
CCTGTAAGT
5' ss Score
7.52
3' ss Seq
TCTCTCTTCTCTCTTTGCAGGGT
3' ss Score
13.36
Exon sequences
Seq C1 exon
GGTCCAAAAGGTGAAAGAGGTGAAAAGGGTGAAGCAGGTCCCTCTGGTGCCGCTGGTCCACCTGGCCCTAAAGGTCCACCAGGTGATGATGGTCCCAAAGGCAGCCCT
Seq A exon
GTAAGTACCCCCTCCTGTCAAAATAGTGCTTCCTTGCCTTGCCTTGTGGAGATTTTCACATGGGAAGATATTTTCCAGAGAATTTTGTGAAGTCTGACGTCATTTACCAGCCAGATAATTGCCCGTCTAATATTATGCAATGATAATCCCATTCCTTTAGAGTGCTAATGAGGAAAAGACCCAGTTGTACCTTGTCTTCCAGCAATACTTGAGTTGTTAGTCTCTTTTTGCAGGCTATCAGGAAACACATCCCTATGTAGAAGGCGGTACCTCTACTTTGCACTCGAGTTTATGCACTGCCAGTGTCCTTTGCACCAAAGCAAAGCTTCCAAAATAGCCTAGAGCAGATTTATGTGAATTTGGGAGCTGTATCTCCAGGGTCAGATCCCCGCTAATGCAAGTTGTTGTAGCTCTATTGAAGCCAGCAGGGCTGTACTGATTTATACCAGATGACAATGGTACGATATTTGTCTTGCCTGGTCCTTTGATGCTTGTTGGCTGAAGAAATTCATCATGCGATAAGTAAAGATGGTACGAAGCAGCAGAGGAGGCAGGGGAGTTTGTCATCTCCCTTAACAGATGGTTTTTGGGATGCCGCATTATTGGTTGAAACCTATTGTCTGAGCACTGCTCTAAGGATCATTTGAAGTGCACAATAGGATTGTAGGGAGAACTGTGGTGAAGTTATTTTAGTCATCAAATGATCTGAGAGTCTCTTCAGGTGAAAAATGTTACGCATTAAATGGAAAGGAAAAGCAAAACCTTCTAATCTTCACATTCCCCAGAGCTGAGGGGATTCTGCTGTCACTTGTCTAATATATTTATGAAAAGCTCAATGAAATCCCATGTTGATACTGGAGCTTTGTGTAAACTGGCTGCAGAGCTGAACTGGTAACCGTGACGGGTTGAAATTACCGAGCACGCAAAGCTGGGATGTGAACTGGGCTTAGGTTTGAGGGTAGGGAATTGGGTTTTTGCTCCCCAGGGTGGATGCACACGTTGCTCCCAGGGTGAGGGGTACGAGTGCTCTGCAGGTCTGCAGGTGCAGTCTCTGACCTGGGGATGTCTCTCTTCTCTCTTTGCAG
Seq C2 exon
GGTCCAGTTGGTTTCCCTGGTGACCCCGGTCCTCCTGGAGAGCCTGGTCCAGCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000002546:ENSGALT00000004020:49
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(16.0=41.7),PF0139113=Collagen=FE(38.0=100)
A:
NA
C2:
PF0139113=Collagen=FE(18.5=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]