HsaINT0099942 @ hg19
Intron Retention
Gene
ENSG00000019169 | MARCO
Description
macrophage receptor with collagenous structure [Source:HGNC Symbol;Acc:6895]
Coordinates
chr2:119727690-119729110:+
Coord C1 exon
chr2:119727690-119727914
Coord A exon
chr2:119727915-119729074
Coord C2 exon
chr2:119729075-119729110
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-MARCO:NM_006770:3
Average complexity
IR-S
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
Associated events
Other assemblies
Conservation
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
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)