HsaINT0099942 @ hg38
Intron Retention
Gene
ENSG00000019169 | MARCO
Description
macrophage receptor with collagenous structure [Source:HGNC Symbol;Acc:HGNC:6895]
Coordinates
chr2:118970114-118971534:+
Coord C1 exon
chr2:118970114-118970338
Coord A exon
chr2:118970339-118971498
Coord C2 exon
chr2:118971499-118971534
Length
1160 bp
Sequences
Splice sites
5' ss Seq
CAGGTTTGG
5' ss Score
5.63
3' ss Seq
TCACTCTCCTTCCCTTGCAGGGA
3' ss Score
12.72
Exon sequences
Seq C1 exon
TTCTGAATCTGCAGGCGCGGCTCCGGGTCCTGGAGATGTATTTCCTCAATGACACTCTGGCGGCTGAGGACAGCCCGTCCTTCTCCTTGCTGCAGTCAGCACACCCTGGAGAACACCTGGCTCAGGGTGCATCGAGGCTGCAAGTCCTGCAGGCCCAACTCACCTGGGTCCGCGTCAGCCATGAGCACTTGCTGCAGCGGGTAGACAACTTCACTCAGAACCCAG
Seq A exon
GTTTGGCCTCCTCCCCTCTGGGTCAGGACTTCTCAACAGAGGTCTGGGAGACAGCGGGATCAGGAACCAGGAAATTAAGGACCCTGTCCAAGCAAAGTGTGACCTCCAAGAGCCAGGGACTTAGAGCAACCAGCTCAATGCCAAGTCTGAACCCAGAGTCCCCACATGGATCCAGAATGTCTGGGAGGGAGGGTAAAACACAGAGCCTGGGGCGGTTCCCTGGACCACTCCCCCACAGCTGACTTACACTGACATGAGGTTGGGGAGAGAGCAACTGAAGGCACCAAACTAGTTCAGACAATGTGGGGACTTTGTGGGGAGGAGGACACCCGGACCTGCTGGGGGAAAGGTGGTGACTTGGGTGGTAGGGCTGCAGGCTGGGGAAAATTGAGCCAAGGGTTAAAACCCCAAGGGTGCCCCTTCCCTCGGTGCTCTCAGGGCCTTGCAGCTGCACCCTCTCCTCTCTCAGCCTGCCCCAAAATGGGAAGAGCCTCGCCCTCAGACAGTTTCAGCAAAACCAGCTGCTAGGTGTGGCTCAACTGTTGTAGGGTTTACCCCGTGACACAGAGCTCCAGCCCCAGCAGGGTTCCTTGCTCTGGGCCCTGTGTGAGCTGAGGCTTAGGAGGGTGATCCCATGGCTAGGTCCTGTGACCAAGGGGTACGCCCAGCACGGGACCCAGGAGGCCAATCCCTCCAGAGGCTGTGGCCTCCCCAGGGAGAAAAGACGAAGGCTGAGTGGGGGTGTGAGGAGGGGCGATAGCTGTGGGCAGATGGAAGGAGTCCACGTTCAGACACAGACACCATGGGAGTGTCTCTTCCTTCCTTGAAATGTGAAGGAGCTCATTTTGACCAATACGAAGGGGTTCTACCTCCTCAGGCTGGTTTGAAGCAACCTCCTTTCCCCACCTCCAAGACTCCCAGGGATCTACAGGTCTCGGGGTGCAGTCCGCTAGTTGCAGCTGAGCATCTGGCTCTTTCCAAGGACTCTTTCCCAAAAAACAGCCAGGTGCTTGGCTCCTGTTGTCCAAACCCCCACAGTCTGATGGGAGCCCCACACAGGAGGGCTTACCCTCCCACTGCAGAACCTGGGCACTCTCAGTTGGGGCTTGGGCCAAGGGTACCCCACAGCTCAGCTGCAGCTCACTCTCCTTCCCTTGCAG
Seq C2 exon
GGATGTTCAGAATCAAAGGTGAACAAGGCGCCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000019169:ENST00000327097:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.224 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PU(3.1=2.6)
A:
NO
C2:
PF0139113=Collagen=FE(18.5=100)
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Cow
(bosTau6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTCTGAATCTGCAGGCGCG
R:
GGCGCCTTGTTCACCTTTGAT
Band lengths:
257-1417
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- Autistic and control brains
- Pre-implantation embryo development