GgaINT0116576 @ galGal4
Intron Retention
Gene
ENSGALG00000016841 | COL4A1
Description
collagen alpha-1(IV) chain precursor [Source:RefSeq peptide;Acc:NP_001155871]
Coordinates
chr1:138140910-138144531:-
Coord C1 exon
chr1:138144354-138144531
Coord A exon
chr1:138141025-138144353
Coord C2 exon
chr1:138140910-138141024
Length
3329 bp
Sequences
Splice sites
5' ss Seq
CAGGTACAG
5' ss Score
8.68
3' ss Seq
TCACATCTTGGTCTTTCTAGATG
3' ss Score
8.75
Exon sequences
Seq C1 exon
GCACTGCAGGGAGCTGTCTTCGTAAATTTAGTACTATGCCTTTCTTATTTTGCAATATCAACAATGTATGTAACTTTGCATCAAGGAATGACTATTCCTACTGGCTGTCCACTCCTGAACCCATGCCAATGAGTATGGCACCTATCACTGGTGAAAGTATCAGACCATTCATCAGCAG
Seq A exon
GTACAGTTTAAATTCTGTTGTGTTTATAAAATGAAGAAACCCATGAAAGGTGTGCATGGTACTTTATTTCCTTGCAAAAGGCTCATGTTATATACGCTTTTATTTTTTGCCCTTAAATTTAAAATTTGAGTTCTTTTGACGAAGTGCCTCAAAGTGTTAATGTATTCAGTTCACACTTTGATAAAGAATGAATTTATTTTGGAGGAAACCCAAACAAATAAGGTAGTCTGTTTTGAGTCTAGTTGAAACAAAAATATTTACTTTGAAATAATGTTTTGCAAAATCTGTGATGTGCTTTGAAGGAGAGAAAGATTTGAATTTAGTCACAACTCCTGTCCAATTCAACTTTTCTTTGTAGCTAGAAACTTTTCAGGGCTCAGTTTTCTTCTGCCTGCAAATGGCAGCATAGTTTATGTTACAATAGACTTCCAGGCTTCTTTTGGACAGGCTACTTGAATACAGCTATTATCATCTGACTTACAGGAAACTGTTGCAAAATCAATAATCTATGTTTTAGTAGATCCAGAGTCTCAGCTAGCATAAACTGTGGCACTTACATTGGACATAAGTGTTCTGTATCAGTCCAACATCCTAAGATTTTGGTCGATATTAAATCTTCAAAACAAATGTCCTGGCATAACATGCGTAGTGCTGAAGGCAGAGGTGTGAGCAGTAGTGTGGTAAACTCTACTGCTGTCATTAGTCAAGAGTCTGACCAAGGGAAGCTCCAGCCTAAAACTTTAATGATAATCAGTAGATCTAAGCATTACTTAGTTCCCATAATTGGTTCTAACCTTTACTAGTTCTTTTTGATCGCTCTTCCTGCCATATAAGGTGTATAGGAATGGAGATTGTCAGCTCTGCTTTCTCAGACTGGTATACATCATGTAAGAGAAGGGACAGTTAAAATTATTAGAAGTAGTAAGAAGTAGAAGTTGTAGTCTTGATATATTTATATGTTCAAAAAACCTATTTGTTCCTACTGTGAAAGATCTCATATTTACTTTTGCATAGTAGAATCCTTTGTGTTTTGTACTTGTTCTCCATACTTGTGGTATAGTGGCAAAAAAAAAAAAAAAAGTATATTCCTTGAAAATTAGGTGGGCAGATTCTCAAGAGTGACTAGTTTCTGTCGGTCTTGCATCTTTGCTTGTTAACTTAATATGGGTGGAAGGGATCTGACTTGCAGAAAAATTCAAATGACCGATCTTTGAAATTCAAGTTCCTTTTATGCCATCCACGATCAAACACGTGACATTTTGCGCCTTTGACAACCACTTTTGAAAATCTTGCTCAGTGAAGTACAAACAAGCATTTTGCTTTCTTAGGCATATGGAGTAGCTTTCATACCATTGAAATGTGTATGTATACATGCATATGTTGCATATGTAGGTTGCTCTGAAAGTAATGCCTCCTATTTTTTTCCTTAGAAACTGTAACAGATACAAAGAACACAATAACTCTATTTCATAGAGTACATTCCCAGCTACAAAACATTATTTTTCAACATAGTCATCACCATTAGCTATGCATTTTATCCAGCAAAGAGCCTGCATGCTGCACTTGTAAAAAAAAATCTGCATGTCCATTTGGAACTTGGCTTGTCTTTCTTGTCGATGTCACTCTGCTGAAATGTATGACCCACTGCCTCACTGTTTGGTCTCCATAAATGCTTTGCAAGCATAAGTGAATGTCAGTGGGTGCCATTTTTTCTGCATAGAAGAAGTCAGTGACATCCCTTTGCTTCATTCACACTTCCATGTCATACACTGTTGTGTCAGAGTGCCCCTCTGCTCCATCTGTCACAGGGCAACAACATTTAATGGAATACTGGTGGGAAGGTTCAGCCTCTACTGCCATGCAACCAACATCTGCCTCTGACACTGTGGGCCAACATAATAAAATGGGAGGCATTACTTTCAGAGAAGTGTTCACTTATTTAGATACGTGAGTTTTTCTCCTTTTATCCATGCCAAAGAGTGAGATAATTGTAATACACCTTTTTTAAAAGCTGCAGAGGATCTAAGAAGACTACTTTTTCAACTTATTTTATTAGCTGAAGTTGTTAAACCAACAGTTTTCCCTGTTCAAATGTTGAAAAGGTGTCAAAGTGTCACTTGTTGCCTTGGGTCATGGGACTTCTTTTCATGTAAGACCTTCCACTGAAATACCAGAAACCTCTTGAAGCAGTGGGAGCTCCAGGAATGGAGGCAGCTTTTACATTCTTTTAACTTACTCTTTCATTGATATTTCTCTTAAAATGGCTGTTTTGCTTCTGCACTAAAGATGAAGGCCATAGGTGTGAAAGAAGTCTTAACAAGTCAGAAATAGGAAGCTTTCATCCTGAATTCCTTTCCTTTTGTGCATTTTCTAGAATCCAGCTAAAACTGTTTTTTGCACTTGAGTTTTTTTCACAGCTCTAACAATAGAATTCAGACTATTTACTTGTAGGTATCTGCTTTGAATCATTTTCACCATTGTTTACCGCAGTAGCCAACCTAAGTTGGCTCCTGAGAGTTGTACAAGAAGAAAATGGATTATATCTATCAAATTCCTTACTACCAGCTTTCATATTTTAATTGCCAACTGACTTTGTATTTTCTGTAGATCCCCTGTGAAAACAAGATTAGTCTTTGGGGTATTCAGTGACCTAGCAGTTCTGTGAAAAAATGAATTTACTAAAGTAAAAGAACTGGTGCGACTTTTGAAGAATGTCTTTCAAGTACATTGTTCAGTTACTTTGCTAGAAATCTCTTATGGGAAATATAGATCACAAATAGCAATAAAAGCCACTTTCAAGGAAAACGCACAGGGAAGAGTCTGCATCACATTAGGTTGGTGGCGAGTATTTTTGCAAGATCTTTTCCAGAGAGATAACTTTCTCTCTGGAGTTCACTCAGGGCTATGCTCAAGATGATAAATGGCTGCTATTTGTCTCTGATTACAGTAAACCACTTTATAAGTGATACCTGCTGAGTTACAATGTCAGACCATTTGCCTCTGGTGTTCACAACATTGTGTACTTTAAGGGACAGTACAAATGGGACTAGCAAAAGACAAACACATTTAAATATTCAGATAAGAATTTAATTGTTCTGTGCTCTTAGGCACGGTAATATGAGCAAGACTAAAGTGGTTAAGTGGTCCCTAAGTGCATGAGAAATGAAAAAAAGGCAGGTGTTTTTTTTCTAAATGAAATGGTTTGATCTTTGACGTGTTTTTGAAGGCGACAGTATTTTCTAGTTCAGACATTCTGAAGGAAGTCCCTTCAGAAAAGAGAGGTTTAGGCCTCACGTGCACGCTTCTCATTCACATCTTGGTCTTTCTAG
Seq C2 exon
ATGCTCTGTGTGTGAAGCTCCTGCTATGGTAATCGCCGTTCACAGTCAAACAATCCAGATACCACCATGTCCTGAAGGCTGGAGTTCCCTTTGGATTGGTTACTCCTTTGTCATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000016841:ENSGALT00000027197:49
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.017 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0141314=C4=FE(53.6=100)
A:
NA
C2:
PF0141314=C4=PD(6.4=17.9),PF0141314=C4=PU(26.3=76.9)
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]