GgaINT0090134 @ galGal4
Intron Retention
Gene
ENSGALG00000015908 | COL12A1
Description
collagen alpha-1(XII) chain precursor [Source:RefSeq peptide;Acc:NP_990352]
Coordinates
chr3:80309330-80312375:+
Coord C1 exon
chr3:80309330-80309500
Coord A exon
chr3:80309501-80311876
Coord C2 exon
chr3:80311877-80312375
Length
2376 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGT
5' ss Score
10.28
3' ss Seq
GGACAACTATTTTCAACCAGAAC
3' ss Score
3.35
Exon sequences
Seq C1 exon
GTCCACAGGGAGAATCCAGAACAGGTCCACCAGGCTCCACAGGATCACGAGGACCACCCGGGCCTCCAGGTCGTCCTGGAAATGCGGGTATTCGAGGTCCTCCAGGGCCACCAGGATATTGTGATTCATCCCAGTGTGCTAGCATTCCTTACAATGGCCAAGGATTCCCAG
Seq A exon
GTAGGTTATGAACAACAAAATTGCTCTTTGTCAAAAATAGCCTTCACAAATGTGGCTGTTCATATTGAGTTGCTTTACATGAGACAGTCCTGCTGGCCTGGACATACTGAGTAGGGGAAAAAGCTGCAATGAGCAGGCCTGCCTCACTGTAACACGCAGGCGTATGAGCAGCCATGTGTATTTGGATGCAGGTTTAACTGATGTTATGTGTGATTCACTTTAAATAGGAAGTAGAAACAAAGTATTTCAGTTTTTTTTTTCATTAGCATAGAAGGTTAATAGTTGAAAATGTTGCACATAGGATTTAAGTGACCATTTTCTCTTCTTCTTTTTCCCCCCTCTCCCCACCCCTTCCAATCTTCTTCAGAACAAGGTTGAATTCTCCATGTTTCTCTTGAAAAATAAAAAGAATGCTGTGGCTGGCAATTTCCGTGTGTCTCTTTTTGAGCAATGTCAGGATTATTTATACCAAATTTCTACCTGAAATCAAAATTTCCCACAAAGGAAATCCATTTGGTGGTACAGTGCAACTGAAAAATACCACTGTCCTGCAATTTCTGCTGAGTTAAACACCATGGAGTCTCTGACTAACCCTGGGTCATACCAGCCTTCTACTCTGTGTTGAATCTTAAAACAGTAGGCTGCTTCTGGAACCAAATACAGGGTCACCAGTTCTGACTGAAAAGATTCCAGTATGTTTTAATGTGGGGATCCTGCAGGAACACACTATTGTTAACAAATTAATAAGTATGCATTGCAACATCTCAAAATTAGTGTATGTGATACTACTATTGAATATGGTTTGCTGTTAGTATATTGTGCATGTACTCATGGGAAAAAAAAAAAATATATATATATATATATATGTACACACTTGCAGACTCAGTGCTGCTGGCCAAAGAGCCAGATGATTGTGAATATCTCACGAAATTCTTATTTAAAAGAAAAAGGAAGAAATTTTTCCTGTGATTCAGCAATGTTCTTTTTTCTAGTAAGCAGATATGTATACATATATAAATATATGCCTATGAATTAACTATCTGTATTTAGTTGGATGAAAGTATGTTTTTGCACATCAGATGGACTTTTTAAAGGACTAACATCATCTTTGACCTGTTTCAGGTTTCGGCTAACACATTTTCTAAGTCGCCAGTGCTGCTTACAGTTTGAATACATGAAAATCCTGTTTCTGAGATGTTTGCGCACGTGCTTATTAGAAAATGAGTCCGTATGGATATTTCACCACGGATATGGTTTTTGAACCATGTTGGCCTCGTAGAATGGGGAGATTCCTTTTACTAACATGACTTGCGAATGAGATAATGGACAGTGATGTCAATTCATTAAGCCTGTTGCATTTCAGTAATATAAAATAGACAGTCTTTCTTTTTTAAAAAAAGACCCAGAACCATCTAAAGTCTCAGTGGTGAAGGAGGCTTATAAAACTACTAACCAATAAAGGTAATGGCTTTTGAAGAGTCATATTTAACCCGGTAAATGAGAAATGACGTATGTAAATAGTAAACTAATTGTGGCTTGTAAATGATTTGTATGGGACCGTACCCACTAAAATCTGTTAACAACCCTATGTGATGCTTTTGCATAAAAGCCTGCTGCTGCTTGCTGTATGCCAGAATAACATCTTTGACAGCGTAAGAAACCTATCTGTCTGTTGCTTGTTACCAACATGTCAGCATCGGGGCATGTGCCTTTTTTTTTATATGTAATCTTGTTGGATTCTGTAACAACAGTTATAAGTACAAACGTTTTATAATAATTTTTCTTCTGTTTTGCTGTAGTTTTTGGTGTTCCTGAAGCACCAGCTGTAACTCGCTTTGTTTCGAGGAACAGCACAAGAAAATGACATGTACTGTATATTGCCGCTGGTGATAGTTACGTGTACATTTGTTTTCCCAGTCTCAGAGAAAATTAGTACATGCTGAGCCCATCTGTCCATTTTACATACTCCATGTGTTCTATTAATTACGCAATATAAAATAAAGTCCAGTGCTTGGGTTCCCTGAATTAGCTGTAAAATAATAATTTTATTTGCTTTGCTTTGTTTGTTTGTTGTGTGGTGTTTTGTTTTTTTAACAATAATCGGTCCCTTGCATAATTTAAGACTCTTTCTGCAATGTTTTGTGTATTATAAATACAAAGCCTTTCAAAATTAATTTTTAATTTTTTAATATTTTGCTGCCAAAGTTATTCATGAACAAAACTGAAAAGTATCCCCACGAACTATTAATTTATATATTTATTATATGGAAATAAGATTGGACTAACATTGTGTAGACAAACTAACTGTCATTGTATTTGTGGATTCAAAGACATGTGATAACTATAATGTTCAATCGGACAACTATTTTCAACCAG
Seq C2 exon
AACCATACGTTCCTGAAAGCGGACCCTATCAGCCTGAAGGTGAACCCTTCATAGTCCCTATGGAGTCAGAACGGAGAGAGGACGAGTATGAGGACTATGGAGTTGAAATGCATTCACCAGAGTACCCTGAGCACATGCGCTGGAAAAGATCGCTGTCAAGAAAAGCAAAAAGAAAGCCATAAAAGATCTGTCTTGTTTTGTGTTTTTTTCTTGGGGAGGGAGGGGGTTGATTGGTGGTATTGGTTTTGCTATACTTGCATTTGCAGATACACACAGGGAGAGTGCATCATTTGTTTGGCAATCCTATGGCTTTCTGGTCTTCTCATATCAGACGCGCCCTTGTTCTGTATCTTGCTTGTGTGGGGATAGCAATATGTGTAACTAGCAACTTCGTTGTGCTCTGGACATGCTTGTAAAATACTATTGCTTACAGGGGCTGCGTACAGGTTAATATCTGCATTCAGTTATCCCAGGGCTGCCTTTTCCTTAAAGTAATGTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000015908:ENSGALT00000025640:69
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(73.2=70.7)
A:
NA
C2:
NO
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]