GgaINT0105270 @ galGal4
Intron Retention
Gene
ENSGALG00000016843 | COL4A2
Description
collagen, type IV, alpha 2 precursor [Source:RefSeq peptide;Acc:NP_001155862]
Coordinates
chr1:138383704-138384487:+
Coord C1 exon
chr1:138383704-138383895
Coord A exon
chr1:138383896-138384200
Coord C2 exon
chr1:138384201-138384487
Length
305 bp
Sequences
Splice sites
5' ss Seq
TAGGTACGT
5' ss Score
8.17
3' ss Seq
TTTTCTTCTTTTTTTAACAGGGC
3' ss Score
11.89
Exon sequences
Seq C1 exon
GCCAGCCAGGTCGTCCTGGTAGCCCTGGGCTGCCAGGCATGCCGGGTCGCAGCGTTAGCATCGGCTACCTGCTGGTGAAGCACAGCCAGTCCGACCAAGAGCCAATGTGCCCGATTGGCATGAACAAACTCTGGAGTGGCTACAGCCTCCTGTACTTTGAGGGACAAGAGAAAGCACACAACCAGGACCTAG
Seq A exon
GTACGTGCAGGTGTTGCTAGCAGCAGCCTCAACTCCATGCCACTGACTGCAGACAAGAAAAAGAAATGGAACTTAGAGAAAGCTTGGATTTCGGTGTGCAAGCTTAGGAAGCACCAAAAAGAGAAGATAAAAACTGTATGTCTCCATAGGGTGTCCCTGAGAGAGATCTTGCAGTTGTAAAGCCAGTGACACATTATGGACTGCGAGGTTTTACTGACACTCACTTAGGAAGGAGCAGGAAACTGAACACATGCATTGTCTTCTGTGTTGCCTTGCCATAATTTCTTTTCTTCTTTTTTTAACAG
Seq C2 exon
GGCTGGCTGGCTCATGCTTGGCTCGTTTCAGTACAATGCCATTCCTCTACTGTAACCCTGGGGATATTTGTTATTATGCAAATCGAAATGACAAATCCTACTGGCTCTCAACTACAGCACCTCTTCCAATGATGCCTGTGGCAGAAGAAGAAATTAGGCCATATATCAGCCGCTGCTCTGTGTGTGAGGCCCCAGCTGTGGCAATTGCTGTCCATAGCCAAGAAGCTTCTATTCCTCGCTGCCCTGAAGGCTGGCGCAGTTTATGGATTGGATATTCCTTCCTTATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000016843:ENSGALT00000027208:45
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.277 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(36.7=33.8),PF0141314=C4=PU(39.8=66.2)
A:
NA
C2:
PF0141314=C4=PD(59.3=66.7),PF0141314=C4=PU(26.3=31.2)
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:
CAGTCCGACCAAGAGCCAATG
R:
TCAGGGCAGCGAGGAATAGAA
Band lengths:
353-658
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]