GgaINT0125285 @ galGal4
Intron Retention
Gene
ENSGALG00000002546 | COL5A1
Description
collagen alpha-1(V) chain precursor [Source:RefSeq peptide;Acc:NP_990121]
Coordinates
chr17:7527075-7528568:+
Coord C1 exon
chr17:7527075-7527128
Coord A exon
chr17:7527129-7528460
Coord C2 exon
chr17:7528461-7528568
Length
1332 bp
Sequences
Splice sites
5' ss Seq
CGGGTAAGA
5' ss Score
9.84
3' ss Seq
AGCCCTGCTGTTGTTCACAGGGT
3' ss Score
8.4
Exon sequences
Seq C1 exon
GGTGAAGATGGCTTCCCTGGCTTCAAAGGGGATATGGGCATCAAGGGAGACCGG
Seq A exon
GTAAGAACCTGCCCCCATTGAGGTCTCAGAGTGCTCCCACAACAGCTCAGCAAGGCAGGTTTTTGTCATGGTCCTTCTGGAGCATTCATGTTCACCTCAAGCACAGGCATTATAAATCCTTATATTCCCTGGTCCCATTGTGAAGGTAAAATAAAACAGAGTAGTAATAGAGGGGCCCCATCTTGCTGCTTTGATTGCGAAGAATCCTGCACACAATCTTGCTGTATCATATCTATTTCCAGTATCTCTTCTCTCCCATAATATTACATCTGGGGTCTGATAGGCATCGTTATTTGCTGAGCGTTGTGTGCCTTCAATGCCATCAGTGTGAAGTGCAGTTACCAGGAACACAGAGCAGCGGGGGTGCAGGTTTATGTTACTCCTATCTTTAGCTCCAGAAGCTTTTATAAGCAGTGGAATGTGCAGGTCACCAGAAACCCAAAATCATGCTTGGGTGCTGTCTGTCCTCAGCACCTGGGCCCTGGGTGCTGTGTTCCCATCCCATCTCCTTGGGTGATGGCATTGCTTGGTGCTCGGCGCATCGCCCAGCAATCAGGAGCACTCTGTGCTCATCCATCCCCACACTTAAAGGACAAATGAATGCCTTGCATGAAGGCTCATAAAACTGTAAATCAAATCCTCCATCTCTGCTTGGCATTTCAATGGATAATCGATCAGGTTGGTGCTCCACCTGTCACCTTGGAGCTGGTCGTTCCGTGGCGCGAGGACAGAAGGTGGCACGCTGTCCTTGCCGTAAGCTCACAGCTCCGCATCCCACCAGCGCTCTCCCTGTGTTTTATGATGCTATGAAAGGCCAAGGGTACTTGAAAGCCTCGCAGATAAATCTGCAGCCACCCAGCTCCTTGTGAGCCCGCGTTGGTGTGGCAGCATCTCCTGCTGCGCTGCGTGACAATGTTGTTGTGTGTGCTGGAGCCCGCAGTGTCATAACAATTCATGTTAACGGCTCAGTCCTCTCCGTGCTCAGGTTTCCTAATGGTTTGCAGCACAAAAGCTCCAGCCTGATCTTTATTCTCCGGTTGCCCAACTCAGCCCTCAATTAAGCGCTTCCCAGGGCTTGCTTGCACATCAAACTGCAATTTGGGAAGCGGGAAGTGGGTAAAAGGGTGCGTTGCAATCAGAGCTAATGACGGATGTTTCGGTGGAGATGGGATAATTGGGCCACTGGAAAGAGGGTTGCTGCTGGGGATAATGGCACGGCCAAGAATGGGAGCTCTGATAACGCTCTGTGAGTCTCTCGGTGACAGAATGCCTTCACTCCAAGAGTCTTTTGCAGTCTCTGATACTGTCTCTGAGCCCTGCTGTTGTTCACAG
Seq C2 exon
GGTGAAATCGGACCTCCGGGCCCCAGGGGTGAGGATGGCCCTGAAGGTCCCAAAGGTCGCTCGGGTCCCAACGGAGACCCCGGTCCTCTCGGTCCTGCTGGAGAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000002546:ENSGALT00000004020:28
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(26.2=100)
A:
NA
C2:
PF0139113=Collagen=FE(53.8=100),PF0139113=Collagen=PU(23.9=47.2)
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]