RetrogeneDB ID:

retro_cjac_3322

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:9:85334373..85334876(-)
Located in intron of:ENSCJAG00000002761
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCJAG00000007952
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_3322
ATGGCCTCCAATAAAACTACATTGCACAAAATGGGAAAGAAACAGAATGGAAAGGTAAAAAAGCTGAAGAGCTAGAGCCT
GAAGAATTTGTGGTGGAAAATGTACTAGATTGATGTGTAGGGAATGAGAAAATTGAATATTTCCTGAAGTGGAAGGGATT
TACAGATGCTGACAATACTTGGGAACCTGAAGAAAATTTAGATTGTCCAGAGTTAATTGAAGGATTTCTTAGTTCTCAAA
AAGCTGGTAAAGAAAAAGATGGTATAAAAAGAAAATCTTTATCTGACAATGAATCTGATGACAGCAAATCAAAGAAGAAA
AGAGATGCTGCTGACAGATCAAGAGGATTTGCTAGAGGTCTTGATCCTGAAAGAATAATTGGTGCCACAGATGGCAGTGA
AGAATTGACGTTTGTCATCTAATGGGATGATTCAGATGAGGCGGACTTGGTGCTGGCAAAAGAGGCAAATATGAAGTGTC
CTCAAATTATAATTGCTTTTTTT

ORF - retro_cjac_3322 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.62 %
Parental protein coverage: 91.8 %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMASNKTTLQKMGKKQNGK-SKKVEEAEPEEFVVEKVLDRRVVNGKVEYFLKWKGFTDADNTWEPEENLDC
MASNKTTL.KMGKKQNGK..KK.EE.EPEEFVVE.VLD..V.N.K.EYFLKWKGFTDADNTWEPEENLDC
RetrocopyMASNKTTLHKMGKKQNGK<GKKAEELEPEEFVVENVLD*CVGNEKIEYFLKWKGFTDADNTWEPEENLDC
ParentalPELIEAFLNSQKAGKEKDGTKRKSLSDSESDDSKSKKKRDAADKPRGFARGLDPERIIGATDSSGELMFL
PELIE.FL.SQKAGKEKDG.KRKSLSD.ESDDSKSKKKRDAAD..RGFARGLDPERIIGATD.S.EL.F.
RetrocopyPELIEGFLSSQKAGKEKDGIKRKSLSDNESDDSKSKKKRDAADRSRGFARGLDPERIIGATDGSEELTFV
ParentalMKWKDSDEADLVLAKEANMKCPQIVIAFY
..W.DSDEADLVLAKEANMKCPQI.IAF.
RetrocopyI*WDDSDEADLVLAKEANMKCPQIIIAFF

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 .31 RPM 39 .74 RPM
SRP051959_heart 0 .16 RPM 30 .54 RPM
SRP051959_kidney 0 .31 RPM 46 .92 RPM
SRP051959_liver 0 .26 RPM 32 .19 RPM
SRP051959_lung 0 .60 RPM 41 .09 RPM
SRP051959_lymph_node 0 .34 RPM 47 .56 RPM
SRP051959_skeletal_muscle 0 .13 RPM 16 .42 RPM
SRP051959_spleen 0 .23 RPM 40 .99 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_3322 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3322 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_3322 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_1145
Pan troglodytes retro_ptro_780
Pongo abelii retro_pabe_951

Parental genes homology:
Parental genes homology involve 23 parental genes, and 105 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000059691 retrocopy
Canis familiaris ENSCAFG0000000289711 retrocopies
Callithrix jacchus ENSCJAG000000075322 retrocopies
Callithrix jacchus ENSCJAG00000007952 8 retrocopies
Callithrix jacchus ENSCJAG000000188471 retrocopy
Dipodomys ordii ENSDORG0000000548711 retrocopies
Equus caballus ENSECAG000000127801 retrocopy
Gorilla gorilla ENSGGOG000000258536 retrocopies
Loxodonta africana ENSLAFG000000069073 retrocopies
Myotis lucifugus ENSMLUG000000075912 retrocopies
Mus musculus ENSMUSG000000298361 retrocopy
Otolemur garnettii ENSOGAG000000165831 retrocopy
Ochotona princeps ENSOPRG000000117139 retrocopies
Procavia capensis ENSPCAG000000049042 retrocopies
Pongo abelii ENSPPYG0000001771410 retrocopies
Pan troglodytes ENSPTRG0000001900310 retrocopies
Pteropus vampyrus ENSPVAG000000062972 retrocopies
Rattus norvegicus ENSRNOG000000118142 retrocopies
Sarcophilus harrisii ENSSHAG000000179131 retrocopy
Sus scrofa ENSSSCG000000167114 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000062234 retrocopies
Tarsius syrichta ENSTSYG000000081596 retrocopies
Tursiops truncatus ENSTTRG000000007117 retrocopies



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