GgaINT0105269 @ galGal4
Intron Retention
Gene
ENSGALG00000016843 | COL4A2
Description
collagen, type IV, alpha 2 precursor [Source:RefSeq peptide;Acc:NP_001155862]
Coordinates
chr1:138382793-138383895:+
Coord C1 exon
chr1:138382793-138382909
Coord A exon
chr1:138382910-138383703
Coord C2 exon
chr1:138383704-138383895
Length
794 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGA
5' ss Score
10.57
3' ss Seq
TCTTCTCTCTTTCATCTAAGGCC
3' ss Score
7.93
Exon sequences
Seq C1 exon
GTCTCAGAGGCTTACCTGGAGAACCAGGACTCCAGGGCAGAGGTGGCATTCCAGCTCCTCCTGGATCCAGAGGTGAACAAGGAGCAATGGGGTTTCAAGGTCCAGTGGGATTTGAAG
Seq A exon
GTAAGAGTTTCACACAGCATTTCTTCCCTCTTTCCCATTTCACTGCCTTAAATTGTTCTGAAATTATTATCACTGGATGGGGAGGCTGGAGAAAGCTTGTGTCTTCACATATTCTTCACGGGGCACCTCTAACTTCTAAAAGAGGATGCACTGTTTTCAAAATGAGTTTTGATAGGTGTCGATGGCAGTCAACTCATGAGAGTAAGTTTTTGATCTGAGTGTATTTTCATATTGCTTTATTTCAGCACAGTGTTTTGCCAGCACTTAAACAGTGTTTGAGTAGGTGATATTTGGATAGATGATGTTTAAGGGATTGTATTTGTGAAGAGAATACTTGTGTCTTTATCCAGTCAAAGAGCAGCAAGATTGCCATCTTAATAAGCCAAGTACAAAGAGAAAAAGGTATTTGCAGAGCAGAATCATAACCATATGAAGCAAATACAAGCAACCGGAAAACTATTGGTTAATCTTAAGCTAAGAAAATGTTGTGAAGGAAACAGATCCTCATCTGTATTGCACAAATCCTGCTAAAATTCATCAGAACTTTATCTGTGACTTTCCCTGGCTCTGATAGAGAAATACACCATGTTAGGAACCAAGGAGCCTGTTACAGCACCAGTCTGCTTCAAAATCAACTGTTCTAATCCTAGAGCTACTGCTTTTTAAACAGTAACTTACCATAAGAAGAGTTATCTTGCAATTAATCTTTGCTCATGGGCAGTTTAGCTGAAATATCAGCGACCATTTGTGGGAGCACAAACTGAATTGTATTCTTCTTCTCTCTTTCATCTAAG
Seq C2 exon
GCCAGCCAGGTCGTCCTGGTAGCCCTGGGCTGCCAGGCATGCCGGGTCGCAGCGTTAGCATCGGCTACCTGCTGGTGAAGCACAGCCAGTCCGACCAAGAGCCAATGTGCCCGATTGGCATGAACAAACTCTGGAGTGGCTACAGCCTCCTGTACTTTGAGGGACAAGAGAAAGCACACAACCAGGACCTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000016843:ENSGALT00000027208:44
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=0.277
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(40.7=55.0),PF0139113=Collagen=PU(61.7=92.5)
A:
NA
C2:
PF0139113=Collagen=PD(36.7=33.8),PF0141314=C4=PU(39.8=66.2)
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:
GGAGAACCAGGACTCCAGGG
R:
GGTCCTGGTTGTGTGCTTTCT
Band lengths:
289-1083
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]