GgaINT0125293 @ galGal4
Intron Retention
Gene
ENSGALG00000002546 | COL5A1
Description
collagen alpha-1(V) chain precursor [Source:RefSeq peptide;Acc:NP_990121]
Coordinates
chr17:7536373-7539957:+
Coord C1 exon
chr17:7536373-7536426
Coord A exon
chr17:7536427-7539903
Coord C2 exon
chr17:7539904-7539957
Length
3477 bp
Sequences
Splice sites
5' ss Seq
ACCGTAAGT
5' ss Score
10.43
3' ss Seq
CCTCTCCCTTTTCTTAACAGGGT
3' ss Score
11.79
Exon sequences
Seq C1 exon
GGTCCTCCTGGGAAGGATGGATTGCCTGGTCACCCCGGACAGAGAGGAGAAACC
Seq A exon
GTAAGTAGCCAGAACTCTTGGGCAGATCTTTAGCCCTGAGCCTCATCTTGCTGGCTGGTTTCTCTAAACCCTCCTGTGCAGATGGGGAGATGGGGCCACCAGTTTGCTCCCTGCAGAGGTCTGTGTGTCTCCAGCTGCATGGGGTGGTCTACAGGAAGCAACCCTCTTCTGAGCAGGATGGGTTGGGCTAATGATGATTTGCAGGACGGCCACACACCAGCCCCTCTCTCTGTCCCTGTGGTACACGTGGGGGTGATGTGCATTGCACACGGAGTGAATGTGAGTGGGGTGGTAGCGAGGCCAGGGAGTGGCACTGGAGCAGCTGGGGCTCTGTGTGCTGCAGGGGATGGGTGGGAAGATGCTGTAAGTCAGCACGCCAGGACCTGGCCTGTGCTGTGCACCCCACAGGCTCCCTACAGTCCTCCCAGGGGAAGGCTGTGCCTCGGCTCTGCTCTTGTAGCACAGTGGTGAAGCTGGGCTTTCTTCCCCACTCCTCTCTTTGGAAATGCGCAGGTGTAATGTTGCTGTTGTAACTCTAGGTCTGTGGGAACAGAGATGCAAGATGGGCACCCTCCTTCAAAAGCCAGCACTCAGCTTTCTGCACTCACTTGCCTTCACTCAGGGCTGTTTTGCTTTCTCAGGAGCCTGCCATAGGGAGAAATAAATAGCTTTCCCTTCTTTATGCACAGTGCAGCCAGCACCAAGAGCAGTAGCACAGCAGAGAAGTTACAGCCCCATTGCTGCAGTGCTTCTTTGGAGAGGAAAGCAGCTCCTGGCCAGGATCAGTGGTGCCATGGCTTTGCTCTAGCTTTTCTGCCCACACTGGTTATTGCAGCACACGCGTGTATCTGCCCTGCCTTAGCACACCAGCATCTCTGCTGACACCGCCTTTGAGCCAAAGCCACTCACAGGGCTCCCCCAGCACATCTCTCTTGCTGCCCCCCGAGGAGCAGCCCTGCTGCTGGGGCCCTTCTGTGTCGTACACAATGCTGCTTTGTCGATTTTAAAAGGTTTTGTTGCACAGATGTAATCAGTCTTTCTCACCAGAGGAGAGTGATGAGGCATGCGGAAGGTATGATGGCTGTCGTGCGTCTCTGGTGGTCTGTTTCGTGCACCTTTTTGCTTGAAGGATACCCTAAGCAAAAATGACTGTTCTGCCATGTATTCTTCTGCATGCAGTAATTAGTACCTCTCTGTTTGGCATTCTGGGGGATGTTGATTCTTTTTTCCTCAGCTGTTTACAACCCAGTTCATTTGCTGTTGTTGGTACATCACTCTCCCATCACTGCATGCTGCATGTTAGCAGATAGACTCTTTGTTCTGTGTTTATTCTACAGGAAAGAAACCCAACTTCCTCTACCCAGCTTTGCTTTTTTTCTCCACCGCCTTTCCTAGCAAATGAGCATTAAAGAGGCTTTGCACATTATGCATCTTTTCCCCTCAACTTATCACACAACAGTTTAATTAACTTGCCTGGCATTTGCTAAGCGAAGCAGTGCAAATACTGCTCAGTGCAACACCAGATATTTACTCACGCTCCGTGAGACTGACTTCGTGGTGATGGCTGTGGTATTTTGAAGGCACAGCCCTCACTTCAGGATTAACTTCAAGGTGGAGAGAAGAGTTCTCACCTGCCAGAGTCTGACTGTGACATTTACACTTCCTTTATTGAGTTATCTGATATATCCAGGACACTTAAGCTGAGATTAGAAAAAAAGCAGTAAAAATTTGTCTTGCATTGCAGCTCTCAACATTTGAGACTGGAATAAAGCATCACATTCCCAAGTCTGTATAAATGCGAGTGGACAATGGGCTATTTGGGGTCTGAAAGCGTTCCCTGGTAGTTGACCTCTGTCAGTTCAGGGGTAACTGCCCTATCACCATCAAATACATCCAGAAAACCGAGAATCTGTTCATTTTTGTCACAAGCAAACATTTTTGTCACTTTCCCCTGTGCCATCTTGGGTCACACAATCATAGACTGGTTTGAGTTGGAAGGCACCTTTAAGATCATGTCATTCCAACCCCCACGCTATAGGCAGGGGCACCTCCCTCCAGCCCAAATTGCTCACAGCCCCATCCAGCCTGGTCTTGACCCAGGCAGAAGCCCCTTTGTTTGTCCTCTTTCCTTACACAGAGCTGAAAAGGAAGGAGGTGGACATAAAACCAAATTAAATATCATTTCCACACCAGTAACCGTGCCAGCACACTCTGTGCCTTCATGCAAGAAAATCTAGACTTGAAGTCTGCTCGTCAAATAGCTCCCTTTAATTAACTTTTCATTGAGGAGCAACAAATCATGCTGAAGGATGCCAAATATTGGGCCGTATTAGATTTATTAAGACAGGGTCTAGAGAAGATAAGAAAAAAGAGCCCTAAAAGCTCTGTGCTCGTGGTTTAGAAAGGGTAACAGGAAAACCCTTTCTGCAGATAAAAAAGGGAAAGAGGTGGTTGAAATGTTTTTCTAAGATCAGGGTTTGAATGGTGCGTTCTTTTCACAGTGATGGTTTGCCATTTTCCCATTGGTGACATGATATCCTGCCATCTGCAGACAGCTAGAATAGCACAGGGTGGCTTTGTAGCATGACACAGTACCATTGGCTTTGGGACTTATCCCATCATCTTTTGTGGCAGTGAGAAAATAGCCTGGATGCCCTGAATGGCATATCTCAGGCTTGTCAGTGTGCTGTAGTAGGAATGATAATTAATGTGCTTTTTAAGGAGTGGCTTAGGAGAATTAAACAACTGCAGTGGTGATAGCTCGTTATTGTCACTCTTTTTGTGTCATTATAATTAGTTGCTGTGGAGTCTTCGTTGCTCATCGTTTGGCCATCCAGAGAGAAACACAGTTGTGATTTCTTTCAGCAGATGCTGAGGAAGGAAATAAAACTCAGCAGGGGTGGAAAGTGGCTCTGTCTGTGTCGGAGTGCAGGGTGGTCACCCAGGCCCAGAAGTCCTGCAGGGTGAAACCTGGAACAGGAGTCACAGCAGGGCTGGGAGCGGGAGAAGGGAAATGAATGGCTATGAAGAATTGCTCAGCGTTAAGGAAAATGAGCATTTTGACTTTTTAATAGCCATTTCCTCTGTAGGTTTTACGAGTGTAGCAATTTATATCTATATCTATATCCATATATCCGGCCAATCATTCAGCCAAACCACGGTAGCTCCATCACAACAGCAGAAGTGAACTGAAGATCTGATGGCTTTCCACCCAAACACCCATTCCCACCTTGGGGCTCCACTTAGAACCCTCCACTGGAGCTGAAAGGCCCATTTCTACCATTGTCTTTCCCCCTGTCAATGTATGAATACATATTTTGCATCTCCTGTTTGATTTCTTCTCCCTCCTGCCTTTGGGTGTCCATCCATGGTCAGTGGTTCTGCTGGGGGGCAGCAGGCAGGCAGTGCTCTGGGTCCCTCTGGGGAGCACCTCATGGCAGAAATGTCATCTCTTTGTCCTCTCCCTTTTCTTAACAG
Seq C2 exon
GGTTTCCAAGGCAAGACTGGCCCACCTGGCCCCCCTGGTGTTGTAGGCCCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000002546:ENSGALT00000004020:36
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(3.5=16.7),PF0139113=Collagen=FE(20.5=100)
A:
NA
C2:
PF0139113=Collagen=FE(20.5=100),PF0139113=Collagen=PU(17.3=77.8)
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]