GgaINT0079937 @ galGal3
Intron Retention
Gene
ENSGALG00000016292 | COL21A1
Description
NA
Coordinates
chr3:90085627-90090421:+
Coord C1 exon
chr3:90085627-90085698
Coord A exon
chr3:90085699-90090385
Coord C2 exon
chr3:90090386-90090421
Length
4687 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGC
5' ss Score
10.22
3' ss Seq
CTTTTTGAATATTTTTACAGGGG
3' ss Score
7.25
Exon sequences
Seq C1 exon
GGAGAACCAGGAGGACCGGGTGCCCCAGGTGAACCAGGCTATCCAGGCATTCCCGGTACCCAAGGTATAAAG
Seq A exon
GTAAGCAGCTTTTTTCTAGTTTTATGTTAATTACATCTTTTATTGGAAGTGCTTTTCCAAGAAGTGGCCGGTATCAGGGAAAAACTTTTTTTTTTAATACCTTGTTTTTATTAGAGATAATTTGGTATATTTTGGAAAATATATTGAATATGCAGTATGTTAGCTAGAAAATCACTCACATTTCACAGGGAGGAGAGAATGATGAAAAGGGAGAAACTGTTGACATCAAATGCTGTGACATAGGCATTGATAAAAATTTCCTTTATGAATTATAGTACATCAGGGCATGAGCTGTGGTTCAATATTTACTTAATATTTTATCTTATAGCAAGCAGTATATTGACAGATTCTATAGCACAGAGTCTTCTGGGGATCTCTGCAATGAACTGGAGCAATTATACCTACGTAGTTGGAACAGATTCAATTCAGTTACCCCCTTTGCTGTTTAGAGTCATCTGATCTAACCAGCTTGCCTAGGCTCTCTCCATATTTAGCTGAGGGAGTGTGAGCTCCTTGGGGAGTCATTCACTCATATCTTTGTTTAGGGATGAATGAATCTGGAAGTACTTATCTATTTCCATTGACTGTAACTGAAGCCTAGATAATTAGCTAAAGTAAATGTTGAAAATTTTTATGGCAAAAGCTAGAGGGATCCTACTTATACTATCCTGGTTGAAAATTATTTCTTCTGTTCAGTCAAGAACCTGTTGTTCTAACTCTTGCATTCTGAGTTTTCGGAGATAACGTGCTTTCAGGATCTCACCATCTCTTAGTGTGGCCTTGTGTCAGTCAAACACTGTTACTGACATGGATACGTAGACATTCTTCATTGCTAAAGAACTGTTTTGTGAACATGTAAAATTTAGTATTGTCTCAAAGGGCTGCCCAGGGAGGTGGTGGAGTCACCATTTGGAGGTGTTCAAGAAACATTAGATGTTGTACTGAGGGACGTGGTTTAATCGGGAAATACTGGTGATAGGTGAACAATTGGACTGGATGATCTTAGAGGTCTTTTCCATCTTCGGTCATTCTGTGATTCTATGAATTTCTGAATAGTCACCTATTTTTAAACTGTAGGTATGTCGGATTTTCTGACAATCACCTGAGGAGTGATTTTTAAGGAGTCCCAGGTTGAGAAGATTATAGGCAATATGGTTGTTTGGTACGTTCTGAAATTGAAACCTACATTGCTTTTCATTCTATTTTTTGTAGTTAACATCACATTAAATAAGTCCTTTTCTTGAGACTTCCTTGTACACATTGATGCCATTCTGAAAATCTCATATGTATTTAAAACTTCTCATTTTCATCTCAGCCAATAAGGCAAAACTTTTTGACTGGAAGCTGGAAAGCTCCTAGAAAATTTCCAGTTTTAAAATACTGACGGAGTTGTTTCATGCTGTAACACACAGAACTTACTGGAGTGTGAAATGAATCTCTTGAGGAAAAATCAGCTTTGCATTGTTTATGAAATGGATTTTATGCCTGTAATTTAGAAGTAATAGAAAATCTTTACTTTTCATGCCCTATGGGTAACTACAAAAAACTTAACAAAATTGTGTTTCCTAGATAATGTTTTTTCAGGATGGCGCCTTTTGTCTGTGTAACTCAACCAAGAAAAAGAAATATCAAGAATTTACACTTCATCTATGCTATTAGGCAAATTGCTATGAAAGAAATGGATTGGATTGAAGTTGTTGACTTCACTGTTACAAATCAATTATTTTGAATTGTAAATGGAGCTTTTATGTATATCCATTACATGTATAGTATAATTTTTATTTGGAATTTCTTTACTCTAGACACTTTCAAAGCAAAAATATCAGTGTCCTGAAAAATAAATGTTTAATTGCTTTGCAAGATAATAAGTACTGCTGTTGCTTTCAGTATCTTGTATTTTTTGTGAGGTTGGTCAAACAAAACATTTTTAATCACTTAATCACAGTTGTCATATACAACTATAAGGCTTCTTTTAATGTTATGCTGTTTCTTTGGAGCAACATCAGAGATCTGATGTCATATAATGAAATTGTTTCTTCAAGATATGGTTTATTATAAATACCAAGCTTTACATGAAACCCTTCAGATATTTATTCAAGTAAGAAGGTTTTGAGGTTAAAAATGTTCCTGCATTTTCTGTCAGTCAATATAAAATTTAAAATGTTAAGGTTAAATTTTAAATAATTAATAAGGGTACCTAAGTTAATTAATAAATCGGCTTAAAATGATANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGTTAAATTTTAAATAAATTAAGTTGGTTACCTAAGTTAATTAATAAATCGGCTTAAAATGATATTTGAACTGGTTTAATAATGGCTGTATATTAAAATACATAGAGTTTTAAAATATAAAAATAAATTACATATGCTTAGGTAGTGTATCTAGTGTATCTGACTTTTCTTTTGGAAGCCTAATAATATTCCTTGAGAAGTACTCACATCTCAACTAGGTTAAAGATTTCTCCATTGCATATTTGAATTACAGGTTTCTGAATAAACAGGAAGACTTGTAAAAGCAAAGGAAAGTAGAAAGGTAGAAAGAACTAAGCAGTTATTCAAACCTAAAGCTGATAACATGCCTGTGTAGTAGTAGAGGACAACCTTTTGAAGGATGAAGACCTTCATAGAAAGGTATTACAGAAATAGAGGTACTTCATTATGGAAAGAATGTCTGGAAGGTAAAGAAGCATAAGTTAGAGGTATGGTGTTACATTTGAAGTTTTACGGAAAATCACATGCAGAGGTATTCCACTAGACTTTAGCTTCTGCTCCATAGGTTTCCTATATGTCCTGTATCATATATGACAGCATACATGTATGCAATAAAATATGAGTGTCTTAGATGTGCTAGGGTATTTTAGATGTCAATAAGCACGTATGGGGATGCCTTAGGTTGCCTAGAATACTTTCAATAGCACTGTATGTGTGTGCTTAGACAACTGAAACAAGTCCCTGCTCAGTGTAGTAAAGGAGTCTAGAAAATGATCCAAATTTAGGTGCAGTTATCTCAACTGTTCTGTTTTCTAAGACAACGTGTAGAAGTAGTCTTCTGACAAGTTTTGAGATAGTGATTTCCAGAGCATGTAAGGATGAAGACTTCCTGGCTTACGTCTCAAAATCCACTGAAGCCCAACAGTGACCAGAGTTGAGCTAGCATCGCCAGAATAGTTTAATTAAATTCATTTCCACCATACACTCAGTCCCAATATCTAAGGGTAATTGATCAAGACAGAAATATTGATTTTAAGGAGGGAGAATTTGTTAAAGTTTATGGAAGGTCTTTAGATTTTAAATCGCGGAAGATAAATCTTGCAAAATTCATTATCCATTCCATATGAAGATGCAAGTCAGAATATGTATTTCTGGTTAACTGAAGTTGAAAGTATGACAAAGTCTTGAATTATTCAGGAAAAATGTTGCAGTAAATGTGAAGCCCTTCAGCTATGGCTTATTTTAAAACTTGAAACCAAACCAAATATTTTACTTTCAAGTACAATACACAGCTGGCATTGGTACCTTCTTATCTTGTGGGATTTTTTATTCGGAAAATATTTGCCATGGTCAGAATCTTCTCCATGCTACTGTTTAGTGTTTAAATAAATATTTTCTCCAAAAAAAAAAAAAATACAACTAAATACACGCATGGTTGGTTTTTACCAGGAAACTGGCAAAACAAACACACAAGTTCCATCCCACTTCTTTCCATTATTAAATGCAATTTTACACCACCACCACCAGTTCTGTCTTTTGTTTCATGTATTGCTGTGCTCTCAGCCCAACGTTTTGTTTCAAGGCAATTTGAATAGTCACACCAATTTAAGAGATCTCTCATAACTTGTAAGTTTCCTTTTCTGTCAACGAAGATAGACAGACACATTTTAGGATTACATTGTTATTGTAATTATTGTTTTCCTTTCCTTGTCTTTTTTCCTCCCATACACTCAATAGATGAACTCCTCCTAGATTTGCCATTTAATTTGATATCTGAGTATCCACTTTTCTTTCTGACAACACTTTCTATGCCAGATTCTCTTATTATAACTTTCTGTATTAATTTCAGTTTTTGTGTACAAGGATAAAATTTTCTGTTTTCTTTCAGTATAAATAGAGGCTATTAGATGCTTCCCTTGTATTTACTGTGTTAAATTAAATCTGGGTACAAGTCTTTAAGATGAATCATGTTATGATGGAGACTTTTTGAATATTTTTACAG
Seq C2 exon
GGGGACAAAGGAAGCCAGGGTGAAAGTGGTATCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000016292:ENSGALT00000026273:21
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(29.9=100),PF0139113=Collagen=PU(32.4=95.8)
A:
NA
C2:
PF0139113=Collagen=PD(1.3=8.3),PF0139113=Collagen=FE(15.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Mouse
(mm10)
No conservation detected
Mouse
(mm9)
No conservation detected
Rat
(rn6)
No conservation detected
Zebrafish
(danRer10)
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]