GgaINT0125265 @ galGal4
Intron Retention
Gene
ENSGALG00000002546 | COL5A1
Description
collagen alpha-1(V) chain precursor [Source:RefSeq peptide;Acc:NP_990121]
Coordinates
chr17:7496566-7499881:+
Coord C1 exon
chr17:7496566-7496622
Coord A exon
chr17:7496623-7499854
Coord C2 exon
chr17:7499855-7499881
Length
3232 bp
Sequences
Splice sites
5' ss Seq
CCGGTAAGG
5' ss Score
10.19
3' ss Seq
CAGCACGCAGCTGGTCCCAGGCT
3' ss Score
-4.87
Exon sequences
Seq C1 exon
ATTGGAGGCCCACGGGGTGAGAAGGGGCAGAAGGGCGAGCCTGCCATTATTGAGCCG
Seq A exon
GTAAGGACAACCTCTCTGCATTCTGTATGGTGTGGTGCTCTTGGTAGTACAGCCGAGAAGAAAATTTCCCATTACTTGGGCCATTTTAGTGTAAAATACTGCAATTATTTCTTTTTAAGACACTTCACAAAGCAGCTTAAATTAGGAAGGAAGTGCTCAATTTCCCATGACATCTCATTTGCTGTAGCGTAACCCCAGACCTTCCGCAATAGAAGTGCCTGGCAGAGGCCATTCCCCACCTCTGCAGGGATTTTGGAGGCCCCACAACGCTACTCCTGCAGCCTGGGGCCAGACCACACTCTGACCCAAACCCTCAGCTTGGGGATGGCTTTAATGGTGCAGCCAATAGGTTTGGCTCTGTGCAAATAAAGGGTTCTCGGCGCACAGCTTGCTCCATTGCCTGCTCCCAGGTCCCAGCAGCTCCCAGAGAAGCCCTGTGTAGTCCCAGGGGGAACATCACTGCTTTCCTTCTTTACAGTTCCACTCTGACCCATTCCTGGGGTTGTTTTGCTTTCTAAGGAATGGTTATAAACTGTGCAGTCTGCACAAAAGGTCAGCGCCCAGCGGAGCATCCCATAGGTGCAGATGGGTCTCCCCAGTGCTGCTCATGTGCCCTCAGCAGGACAAGGGGCTGTTGGCACATGTGTCTGTGCGCCCATGTCTGTGTCCCTCTTGAGGTGCTGGGGTGCTCCTGGGCTGGGAGTAGGGCTTGGCATCACTGCGCCCACCCCACCGGCCGCATCTGCAAAGGGCAAAGCTGCACACCAGCAGCTCAATTAACCCAGTTTCTCTTGGCAGAGAGCCCAAGCGATGCCCAGCAAAGCAGTAGTACTTCCCATTGCCCACAGTCCATTCTTTTTCTTCCAATTCTTCCTCCATTTCCTTCTCAAGGAGACTTTGTCGATGCTGGCAGAGCAAGGGAGGAGCTGGGGGCAGCAGTGGGGCTTCACGGGCCTCCACCACTGCCTTATGAAAGCATTTCCGAGCCTTCCTTCCCTCTTTCCTTCCTGGGTCCTGCTATCCCCCTGCAAACAAAGGCAAGGAGCGAATGCTTTGCTGAACCATGCAGCAACACAGAGAAGGCAGCTTCAGCAGCCCACCCTGGGCCGGAACCAATCTGCAATGTTACAGAGCGAACAAAATAATGGTTAAGTTTAATCATCCAGAAAGAATTTGGCTGCCTTCGCTATTTCAAAACACTGGAGCACGTATAGCTTTTGCCAGAGAGTAAACAAGACCAAATGCTGCCGTGTTCCCCTCCGTTCGGTTCCTCTTTAGCAGAGAGAAATTCGCATTTGCTGCGCTCTTTATCTGGTTTTTGATCGGAGCTGCAGCAGAGGTGGAGGGGGGGGGGGAGAAAAACCGAAGGCGGGTTCTGCTGAATTCTCTTATCTTGGCCTTCAGGCTGCCTGTCCTTCAATCCTTGCTCTGTGCTGACGCTCGCTGGAAGCAGCAGGGCAGCACAGGCTGCTCGGGGACGTGGCGGGGATGCTGGGACCCCTGTGTCCCCATGGCCCAGCTGTGGGGGTGACAGGCTGCCTTTCCCTGCTCTGGGGCAGACTCAGGTGCTCACAGCTGCCTTCAGAGAGGGTTTGCTCAGCCTTTGCACAGCTCCCCCATACACTGCAGCCAGTTTTTGTTCTTTCTCTGCAGCGTTAGCCTCACCTTTGGGTAGCAACTGGGTTTTGAGGGGACTGACATCCCTTTTTTTTTTCCCCTGGATGGCCCCAAACATGTGCTTTGCTTACTGCCCCCAAGGCAACCCCCTTTGGTCCTTTGGTGGCATGCCCCCAGCTGGTCCCACAGCCTCCCGTATCCCCACCCCTGTGCTGATGAGAGGTCGTGTAAACAGCAGCGATCTCTTGCCGGGGAGAATCTCCAGATGTCCCTAAAGCTGGAGCTCAACATAAACCAACTGATAAATATGGGAAGATGCCAAGGATGTTTGCATCATGAATGGGCTAATTAGCCCAGGCTGTGCATAGGAGCATCCTGCAGCCGGCTGTGGGAAGCAGAGCTCAGCCCTGTGCGTGCTCAGCCTGCAGTAACCCTGGGGGCACCCCTAGAAAGTTCTGGGAGGGACAGATGTGGGCTTGGGCTCTCTGCATCAGACTGGAGACACTGTTAGCACAGAGAAGGGGAAGGGTTGGTGTTGGGTTCTGTATCGGAGGCTGCCACACACCAATGTGCCATCGTTTGTCTCAGTGGGGATGGACTCTGTGGTCCCTATATGGGAGGATGTTTGCTGAGAGCTCTGGGATTGTCCATGGAAAAGGATGTAGGGCCTTGTGGATGTCATTCCTGGGGGTGCAGGGTCACCTGCCCCATCCTGCTAGCCCTCGACAGCAAGGAGTTCGTATTTAGTGTGGGTTGAAGGAGTGTTGTGTAGGGATTACTTCTAATTCCCAGCCAGAAGAGAGCGATGCCTCCATGGCTGGCAGTGAAATTACTTCCAGAAAGCATTTGCCTGGCTGAATGGGAGGTTTTTTTCCTGCCTCTTACATAGCCATGAGGGGGGAGAACAACCGAGTAAATAAATGAACAGAAACAGCTCAATTCCACTGAGTATGTGCTAGACCTGATTTAAAGTTAGGACAAAATATCTGGATGAAAAGGAATGGAATAACATAATTCTGCTGTTTTGCCTGCGCAGTGATTTCCTGGGTACACAGAGTAAATCATGGTGTGCAGCTGCTAGGAAAGTAATTTCAAAAAAACCCCAAACCTTTGCAGTTTGCTTATTAACTTTCTATTGTTCTCTCTCCAAGCTGCTGGGTCTTAGGGGCTGCTGCTTCCCAAAAAGGAGCTCTTCTCCCCATCACCATAACCGAGGTTTGCCCTTTAGTGAGGGGAGGAGGGCAGTGGGCAGGAAGGCAGCCCAGTGCTGCGGTGAAGGGCTGTTTCTCCATGCCCTGCATGATCCAAATAAATGCTATTTGGTTTTGGTGATGTCACCGAGGGAGTATGGAAGCGAGCAGAGAGGTCTGAGCTATTTAAGGATGGAGAAAGCATTGGGTTTCCAGCCCTGAAGTTGGGGTGGCTTTGAGGATGTGCCTTGCTAATCCCTGTTATTCCTTCCTCTTGTTTAGGGTATGCTTGTGGAAGGTCCCCCTGGTCCCGAAGGCCCCGCAGTAAGTGGTGTTGGGGTTACACCTTTAGGCTGGGTGGAGATGGATGCATGCATTGCGGGGGGCTGATGCCCGCACGGGGCTCAGCACGCAGCTGGTCCCAG
Seq C2 exon
GCTCTATTGCTTCCATATGCCACGTGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000002546:ENSGALT00000004020:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.930 A=NA C2=0.481
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0139113=Collagen=PU(2.2=11.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
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]