GgaINT0079924 @ galGal4
Intron Retention
Gene
ENSGALG00000016292 | COL21A1
Description
collagen, type XXI, alpha 1 [Source:HGNC Symbol;Acc:HGNC:17025]
Coordinates
chr3:86650807-86653232:+
Coord C1 exon
chr3:86650807-86650890
Coord A exon
chr3:86650891-86653169
Coord C2 exon
chr3:86653170-86653232
Length
2279 bp
Sequences
Splice sites
5' ss Seq
AAAGTAAGT
5' ss Score
9.72
3' ss Seq
TACCTACTACTTCTCTACAGGGA
3' ss Score
8.18
Exon sequences
Seq C1 exon
TGCATGAATGGCCCAAGCGATGTAGGCTCCACACCTGCCCCCTGCATATGCCCTCCAGGGAAACAAGGACCTCCAGGCCCCAAA
Seq A exon
GTAAGTTTCTATTGTTTCTTCTTGAATATACACTACATGTTTTTTTTCCTTCTATTCTCATGCTGACCACTCATAGTCATGCAGATTATATAAGTAGGGTCCTAGTTCTGCTAGTTCTGGTTTCCAGTGAATGAATATAGTGATTAGAAGCAACCAATCTTTTTTTACCAGTCTTCAGCAAATGATCTTGCACTGCTAATTATTTCAGAATGAAGTGGATTGCTAATCAAGTAGTCTTTAAGGGAGAGTTTTCTTCTTAATTTAAGACAAAATGCTTGCTGCAGAGCTCCACCTTCGCTGTTCTGATTTTTGTGACCTCCCATGAGTGCTGACAAAGGGTAAGAAGGATGAAGGTGTGAAGTAGGCTCGGGTCTCTGATGCCTAATGTGTCAGACTCACATCACAAGTGTTTTGCTGCCCTATCTTCCCCAGTTGCTGTGCTATGCAGCACTGTCCCCAGTTACTGTTTTTCCACATGTGGATAGACAAGAAGATCCCAAACTGCTTATCTTTCATTAAGCAAATGATTTAAAGAAAATGCTTTCATAATTTAAGTGGTAACAGTCTGCTGCAGCTAACTCGTATTAGAGGGCTGTTTGCTATTGTGATAATGGTTTCTAATCAGGGAATTGAAAACCACATGTTGGAGACCATTGTTATTTCATCTAATAGAGTGTGGTGTTTTTTTGTTTTGTTTTGTTTTTGTTTTTTCCTTATTTCTCCTTTAGCATATTAGAGAAAAAAGAGAAGAAAATATTTATAACAAAAAATTTTGAAAGCTACATCCTGTAAAGCATGAAAGAGTAAGAAATATCTGAACTAAGGTGATCTATACAATTTTAATTAAGTATCTGTTTCACATGCACTGTGAAAGAATGCATTCTTCCAATTGCACTGCAGTATAATATTTGAGATAATAATACAGATAACAAAATGGTGCCCAACCCAAAAGACTGCAGGAAGAATGAAAAGGAAGCCAATTTAAGATCTATAGGTATCTCAGTTACAGTACTTCTTAACTCTTGAATACTGGACTTTGCAAGCTTATAGATTTTATCTTAATTTGTGTGCTTGTGATATTAATGAAGTGTAATAAAATTAATTCATTTATAAACTTTGAAATACAAATAAATGATATTTCAACTTTTTCAAGACAAAAACATAGCATTTTATAGTTCAGGTAGTGTAACTGAAAGGAAATTTATTTTCTCTTGGATCTTGATCCTGGACTCTTTAATTTGGTCAATAATAATTCTAGAGAATCTACTGTTAGTTTAGAAAATTGTAACTGTTACACTCAGTGGCTTTTTAAAGGGACGTTATTCAATATCCTTTTCCATTTAGCTCAGCATTACATTTCTCATGCTTATATGTTAAAATATGTGTATTTTACAATGAAAGCTATTTCTCTTCTGATGTCCTCCCTATTCATAACAATTCTGCAAAGTAGCTGGCCTGAATGTCTGTTGATGGATCAAACTATACTTGCTTAATGCTTGTGCAAGAGTGAAATGTTTTATTGACTGAGGCTTTAATGGATTTTTCAAGTCCAGATCAAGTCTGTTAGTAAAATAAACAGAGAACTTAATGTATTTAAGAGGATATATTGAGTAGGAAGGTATGTTCTTGCTCTCTGACAACAAACACAATGCTTGAGAGATTGAGTTTTCTTTTCCCTTACTGTGGTCTTAACAGAGGTTATCAAAATAATTGCAAAGGCCTTATAAGAAGAAATCTAAAAAAAAAAAAAAAAAAAACCAACTTTTTTTTCAGACAGCAATGTCTGGAGAGTTTATTTAACAGGTTTTGATCTTAGCTCTTGTCTTTTCAGTGCTTTTCTTTAAAAACTAGACTCAGCCAACTCTTTGCTAAATGGGTGAGAGTTTTCTTCAGAGTAGAACTGGTAGAATAACAAGTTTTATTAAAGATTTGATTACATTTAATTGATGAAAACTATTTATTTTTAATTTTATTTATTTATTTTTTTGTTGCTGATGATGTTGAGAAGCTTGAAGGCATACGTGATGATAGGTCAAACCTGCACTGTGACACTAAGCATGGGCTTGCTTCTCCATGTCCTGCATCTGAAGTTAGGGATAATTTTCCCAGGGTAGGGTTGCAAAATCAGTTCCCTTTTTCTGTATGAATTACTCCTCAATTGCAGGTATCCGGGACTGCAGCCACAGTTTTATGGGATGTATTAGGGTTAAGGCTAATCTGTGCTAATTTTAAAATGCTCTTTCATGTCTTATGTGTGTTTACCTACTACTTCTCTACAG
Seq C2 exon
GGAGATCCTGGGCAGCCTGGGAATCATGGTTATCCTGGTCAGCCTGGTCCAGATGGTAAGCCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000016292:ENSGALT00000026273:9
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=PU(19.0=39.3)
A:
NA
C2:
PF0139113=Collagen=FE(34.5=100),PF0139113=Collagen=PU(0.1=0.0)
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]