GgaINT0105256 @ galGal4
Intron Retention
Gene
ENSGALG00000016843 | COL4A2
Description
collagen, type IV, alpha 2 precursor [Source:RefSeq peptide;Acc:NP_001155862]
Coordinates
chr1:138371110-138372224:+
Coord C1 exon
chr1:138371110-138371253
Coord A exon
chr1:138371254-138372098
Coord C2 exon
chr1:138372099-138372224
Length
845 bp
Sequences
Splice sites
5' ss Seq
AAGGTATTT
5' ss Score
7.64
3' ss Seq
GGTGTTTCTGTACCCTTTAGGTG
3' ss Score
8.72
Exon sequences
Seq C1 exon
GCTCAAGAGGTTCACCTGGCATTGATGGTTTCAAAGGCATGCCAGGCCTGAAAGGAAGACCAGGAATCAAAGGAATCAAAGGAGAATTTGGCTTACTTGGGACTCGGGGTGATAAAGGCGCACAGGGTGCACGAGGCTTTAAAG
Seq A exon
GTATTTGCTTATGAGTGGGTACAGCGTTTGCTTTTCACATACAGAGAACTATTTTGCAAGGGTGCACTGACAAAGATGACACATTTTAGACATAGTTTAGCTCAGACTTTCCTTCACCTATTTCACACATGGGCCTCTGGCTGAGAGGCTTGGATTTGAGGCTCAAGGGAAGGCTGTTTCTTTGTGAATCTTGAGCATGGTCAGGATGGAGGTGGACACTCCACTGAGTTTGAATGCACCTCCAGGCATATGCAGAACTCAACAGAGTTTTTCCCTGGGAGGTGTAAGACGCTCTGGGGAAAAGATTCAGATTTTGCCTCAAGATAAAGGCAACAAAATATTCAGAAAACTGTGCAGTTAAGTCAGAAACGTATCAGTTGATATCACTGTCAGCGAAAGGAACACTGTAATTTAGTCCTCCAAAGGGAAGTTGGAACAAAATAGCTGGTAACGAATCCAGACGCTTTCTTTCACCCAGGCCTTTTTAAGTCCCGTTTGACTGAGGGCTTCCCTTTCACTGGAACCTACCCACTTGTCTCTGCTATCTGTGATTTTGGTAACTGATCTACTGAGAGGTAAACTCCTCTAATCACAGAGGAGCCCAAGTCAAGCTCCCCAGAATAGCGTATGGAAGTCTAGCTCAGTTTTCATATTCTCTTACGCTTAACTGTTCTGCAGGTATGTTGTTTTGATATGGGCAGTTTTCCATGCAGACAGGTTTTCCATGGCTTGTGCAAGGTTTTCCATTAATCCATTTTCACTAATTTCACTATTCTGTTGTCTCTTTTTTCAGCACAGTGCAGCTGACCAGCTTTTTTAAATATGGGTGTTTCTGTACCCTTTAG
Seq C2 exon
GTGACCGTGGAGAGCAAGGTCCCCCAGGAGAGCCCCCGAAGCTGAAGCCTAGCATGATGATGGAAGTTAAAGGTGAAAAAGGAGATGCTGGAGAAACTGGCACCAAGGGATTCTTTGGCATAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000016843:ENSGALT00000027208:31
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=PD(30.0=42.9),PF0139113=Collagen=PU(77.4=98.0)
A:
NA
C2:
PF0139113=Collagen=PD(21.0=30.2),PF0139113=Collagen=PU(34.5=46.5)
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:
GGTTCACCTGGCATTGATGGT
R:
CTTTTATGCCAAAGAATCCCTTGGT
Band lengths:
262-1107
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]