RetrogeneDB ID:

retro_cjac_2858

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:6:154084395..154084659(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCJAG00000002865
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_2858
ATGGCCCAGGAAAGCATGACTGCTGGAGGTGTCAAGGACCTTAATACTGCTTTACAAGAGGTCCTGAAGGCCCTCCCTCA
TCCACCACAGCTTGGCACGTGGAACTCAAGAAGCTGCCAAACCTTAGACAAGCACTGGGCCCATCCTTGTGTGCTGCCCC
CAACTGTGATGAGCCTGCCTATGTGGCTGGTGAAGGCCCTTGGTGCTGAACACCAGATCACCCTAATTAAGGTTGATGAC
AAGAAACTAGGGGAAGGGGTGGGC

ORF - retro_cjac_2858 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 64.52 %
Parental protein coverage: 68.18 %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMAEEGIAAGGVMDVNTALQEVLKT-ALIHDGLARGIREAAK-ALDKRQAHLCVLASNCDE-PMYVKLVEA
MA.E...AGGV.D.NTALQEVLK...LIH..LARG..EAAK..LDK..AH.CVL.......PM...LV.A
RetrocopyMAQESMTAGGVKDLNTALQEVLKA>SLIHHSLARGTQEAAK<TLDKHWAHPCVLPPTVMSLPMW--LVKA
ParentalLCAEHQINLIKVDDNKKLGEWVG
L.AEHQI.LIKVDD.KKLGE.VG
RetrocopyLGAEHQITLIKVDD-KKLGEGVG

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP051959_colon 0 .00 RPM 160 .57 RPM
SRP051959_heart 0 .00 RPM 148 .13 RPM
SRP051959_kidney 0 .02 RPM 148 .69 RPM
SRP051959_liver 0 .00 RPM 222 .65 RPM
SRP051959_lung 0 .00 RPM 143 .10 RPM
SRP051959_lymph_node 0 .00 RPM 233 .07 RPM
SRP051959_skeletal_muscle 0 .00 RPM 172 .69 RPM
SRP051959_spleen 0 .00 RPM 213 .05 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2858 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2858 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_2858 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 35 parental genes, and 362 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000104791 retrocopy
Ailuropoda melanoleuca ENSAMEG000000080152 retrocopies
Bos taurus ENSBTAG000000013607 retrocopies
Canis familiaris ENSCAFG0000000019015 retrocopies
Callithrix jacchus ENSCJAG00000002865 34 retrocopies
Cavia porcellus ENSCPOG000000004294 retrocopies
Dasypus novemcinctus ENSDNOG0000000621431 retrocopies
Equus caballus ENSECAG000000015998 retrocopies
Echinops telfairi ENSETEG0000000685414 retrocopies
Felis catus ENSFCAG000000284027 retrocopies
Homo sapiens ENSG0000011230626 retrocopies
Gorilla gorilla ENSGGOG0000001223422 retrocopies
Gadus morhua ENSGMOG000000194551 retrocopy
Loxodonta africana ENSLAFG0000000793311 retrocopies
Microcebus murinus ENSMICG000000052525 retrocopies
Myotis lucifugus ENSMLUG000000011375 retrocopies
Macaca mulatta ENSMMUG000000132371 retrocopy
Monodelphis domestica ENSMODG000000175201 retrocopy
Mustela putorius furoENSMPUG000000147711 retrocopy
Mus musculus ENSMUSG000000619831 retrocopy
Nomascus leucogenys ENSNLEG000000146114 retrocopies
Oryctolagus cuniculus ENSOCUG0000000160614 retrocopies
Otolemur garnettii ENSOGAG0000000130920 retrocopies
Pongo abelii ENSPPYG0000001702026 retrocopies
Pelodiscus sinensis ENSPSIG000000034571 retrocopy
Pan troglodytes ENSPTRG0000001861825 retrocopies
Pteropus vampyrus ENSPVAG0000001720112 retrocopies
Rattus norvegicus ENSRNOG000000164115 retrocopies
Sorex araneus ENSSARG000000031702 retrocopies
Sarcophilus harrisii ENSSHAG000000089056 retrocopies
Sus scrofa ENSSSCG000000041778 retrocopies
Tarsius syrichta ENSTSYG0000001009724 retrocopies
Tursiops truncatus ENSTTRG0000000060911 retrocopies
Vicugna pacos ENSVPAG000000100824 retrocopies
Vicugna pacos ENSVPAG000000115043 retrocopies



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