GgaINT0105248 @ galGal4
Intron Retention
Gene
ENSGALG00000016843 | COL4A2
Description
collagen, type IV, alpha 2 precursor [Source:RefSeq peptide;Acc:NP_001155862]
Coordinates
chr1:138360155-138362142:+
Coord C1 exon
chr1:138360155-138360261
Coord A exon
chr1:138360262-138361940
Coord C2 exon
chr1:138361941-138362142
Length
1679 bp
Sequences
Splice sites
5' ss Seq
CCGGTAAGT
5' ss Score
10.91
3' ss Seq
TCATTTCCCACTTCCCACAGGGT
3' ss Score
10.36
Exon sequences
Seq C1 exon
GCACCAAAGGAATCCGAGGAGATCCTGGACTTCCTGGTATCAGAGGGGAAGATGGTTTCCCAGGCAGAGATGGATTAGATGGTTTACCAGGACTGCCTGGCCTTCCG
Seq A exon
GTAAGTAGCAAATCTTAAGAAGGGACGAAAGGACGACCCAGGGAACTACCAACCTATCAGCCTCACTTCTGTGCCGGGGAAGATCATGGAACAGATCCTCCTGGAAGCTTTGCTAAGGCACATGGAACACAGGCAGGTGATGCAAGACAACAAGCATGGCTTCACCAAGGGCAGGTCCTGCCTAAACAGCCTAGTGGCCTTCTATGATGGCATGACTCCATCAGTGCACAAGTGAAGAGCCACTGGCATCACGTCTGGACTTCTGTAAGGCCTTTGACACAGTCCCCCACAACATCCAACATCCTTCTGTCCAAGCTGGAAATATAGCTAAACCATTTCCACCACACTCAATTACTAATTCATTTAATTCTGAGGATTAGTGATCATCAGGCTGCCCTTCACACATGGATAGGGATGCACCACTAAACTGGCTTTGCTGATTATTGATATACTAAATATCAATTTTACCTTCAAGATTCTTTAGAACCACCTTACATTTTTATTACAATTTTATTTAAACAAATAAGTAGTAGTGTATAACCCATTTAGGCCAATTTTATATCAGTAGTTTATTTGTGATAATTAGTGGTTTATTATCTAGCCTTGTGTATGGCAAACAGGTATACACATTGTAAGGTAAATAGGTATAGGACCAGAGAGATTATTGCATTTACAAAGGAGTAATGAAATAAAGAGCCTACCCATATTCTGGGCTCACAGAAAGACTCCAAAAGAAGTGAACTCCAAATAAAGATCCTTCCTCCTTGGGAGTCAGCTCTTAAATGGGGTCTAGGAGGGGTGGAGCCAGGCTTCCAGTCACTCAGGTGAAATTGCGTTCACTGGTGCCCCTGTGGTTGACTCAGCACTCGCCTCAGGTGGTCAATCAGAGGTTCAGGCCGTGATTCAACAGTTCCTATAGACCTTGTGTAAGAGATTGTGTGTGGCATTTTGATATGATGGAGTTAACAGTTTACATCCCCAAAACATAGGTCACATCATTATTTATGTGTTTGATAATACCTCATCACCTATCACAAATGTTGTTTTGCACCACTGGGTTGCTCTTGCATCACATATGAGGATGGACCAGAGCTTTGTCATCCGATGTGGACCACAGTGGGTTATACTACCAGTAAAAATGGTACTTTTTATTAAGTCTGTGGATGGGAACGTTTTCTGGTGATGTTCTAAAGATGTTGATTTAATATTGCAGTAACATCACTAGAGTAACAGAGCAAGAAAAAATCTGCCCATTTGGGCACAGTTTTATGTCAGCTTTTGTCAAGGTCTAAGACGTTAATGCCACACCAGAACTAACTTTCACACACCTCTTGTGATGTGTATGCTTTCCCTCATATCCACTCACAGCATTTCAGAAGGGGTAGTAAGGCTGTCCACAGCAGTGATTCATATTTCCCATATGTTCTTCATTTGCCAGCCTTTTTAGGGGAATGCTTCCTCTAAGAGTGCTTCTCTCATGCCTTTTCTGCTATGGGGGTCTAAAATAATGTCTGATTATTCCAAATATATCATATTTGCAATTTTGCTTTAAAAAGCTGGGATGCAGTACATGAGGAATAGCTGCCTATAGGATGTTGTTCATGAGAGTAGTTCAACTCTGTGAGTTTTGTTTCTTTTGCAGCAAAGGCAGAAGTATATTCATTTCCCACTTCCCACAG
Seq C2 exon
GGTGATGGTATCAGAGGTCTCCCCGGGGATCCTGGTTATCCAGGAGAATTAGGCCCAAAGGGCTTTCCAGGAGAAATAGGCCTACCAGGTGAAGGATATCCTGGCCCAAAAGGATACCGTGGTCTTCCAGGTGACCGTGGAACAGATGGACACCCTGGGCCTCCAGGTCTGCCTGGTCCACCAGGAGAGCCTGGCCAATTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000016843:ENSGALT00000027208:23
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(50.0=100)
A:
NA
C2:
PF0139113=Collagen=PD(42.9=44.1),PF0139113=Collagen=WD(100=95.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCACCAAAGGAATCCGAGGAG
R:
CTAATTGGCCAGGCTCTCCT
Band lengths:
309-1988
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]