RetrogeneDB ID:

retro_cjac_1237

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:14:99390252..99390591(+)
Located in intron of:ENSCJAG00000006233
Retrocopy
information
Ensembl ID:ENSCJAG00000022953
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCJAG00000012120
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_1237
AGTCCACTATCCCAAACCTCTGAGTTCAACCCCTTTGCTGATGCAAGTAAGGGTGATGACCCGTCGTTTCCTGCTGGCAC
TGAGGATTACATCCATATAAGAATTCAACAGAGAAATGGCAGGAAGACCCTTACTATTGTCCAGGGGATCGCTGATGATG
ATTACGACAAAAAGAAACTGGTGAAGGCGTTGAAGAAGTTTGCCTGCAATGGTACTGTAACTGAGCACCCAGAATGTGGA
GAGGCCATGCAGCTACAGGATGACCAGCGCAGGAACATACGCCAGTTCCTCCTAGGGACTGGACTGGCCAAGGACGACCA
GCTGAAGGTTCATGGGTTC

ORF - retro_cjac_1237 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 78.07 %
Parental protein coverage: 99.12 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalSAIQNLHSFDPFADASKGDD-LLPAGTEDYIHIRIQQRNGRKTLTTVQGIA-DDYDKKKLVKAFKKKFAC
S.......F.PFADASKGDD...PAGTEDYIHIRIQQRNGRKTLT.VQGIA.DDYDKKKLVKA..KKFAC
RetrocopySPLSQTSEFNPFADASKGDDPSFPAGTEDYIHIRIQQRNGRKTLTIVQGIADDDYDKKKLVKAL-KKFAC
ParentalNGTVIEHPEYGEVIQLQGDQRKNICQFLVEIGLAKDDQLKVHGF
NGTV.EHPE.GE..QLQ.DQR.NI.QFL...GLAKDDQLKVHGF
RetrocopyNGTVTEHPECGEAMQLQDDQRRNIRQFLLGTGLAKDDQLKVHGF

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 .42 RPM 23 .78 RPM
SRP051959_heart 0 .19 RPM 45 .74 RPM
SRP051959_kidney 0 .55 RPM 34 .88 RPM
SRP051959_liver 0 .04 RPM 30 .89 RPM
SRP051959_lung 0 .18 RPM 27 .02 RPM
SRP051959_lymph_node 0 .07 RPM 20 .59 RPM
SRP051959_skeletal_muscle 0 .00 RPM 73 .55 RPM
SRP051959_spleen 0 .11 RPM 28 .49 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1237 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1237 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_1237 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 26 parental genes, and 146 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000056209 retrocopies
Bos taurus ENSBTAG000000022821 retrocopy
Canis familiaris ENSCAFG000000295844 retrocopies
Callithrix jacchus ENSCJAG00000012120 6 retrocopies
Cavia porcellus ENSCPOG000000143503 retrocopies
Dasypus novemcinctus ENSDNOG0000000785611 retrocopies
Dipodomys ordii ENSDORG000000138534 retrocopies
Felis catus ENSFCAG000000244552 retrocopies
Homo sapiens ENSG000001738122 retrocopies
Gorilla gorilla ENSGGOG000000272012 retrocopies
Loxodonta africana ENSLAFG000000028522 retrocopies
Macropus eugenii ENSMEUG000000153606 retrocopies
Myotis lucifugus ENSMLUG000000050773 retrocopies
Mustela putorius furoENSMPUG000000108836 retrocopies
Mus musculus ENSMUSG0000003553027 retrocopies
Nomascus leucogenys ENSNLEG000000110133 retrocopies
Otolemur garnettii ENSOGAG000000315776 retrocopies
Pongo abelii ENSPPYG000000296671 retrocopy
Pan troglodytes ENSPTRG000000091753 retrocopies
Pteropus vampyrus ENSPVAG000000106294 retrocopies
Rattus norvegicus ENSRNOG0000003376515 retrocopies
Sorex araneus ENSSARG000000062871 retrocopy
Sarcophilus harrisii ENSSHAG000000057291 retrocopy
Sus scrofa ENSSSCG000000174306 retrocopies
Ictidomys tridecemlineatus ENSSTOG0000000271915 retrocopies
Tursiops truncatus ENSTTRG000000171353 retrocopies



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