RetrogeneDB ID:

retro_cjac_2473

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:4:126024828..126025521(-)
Located in intron of:ENSCJAG00000003719
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPF2
Ensembl ID:ENSCJAG00000005212
Aliases:None
Description:ribosome production factor 2 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:20870]


Retrocopy-Parental alignment summary:






>retro_cjac_2473
CAGACATCACTGGAATTCTTTTCAAAGAAGTCAGACTGTTCTTTATTTATGTTTGGCTCCCATAATAAGAAGCAGCCAAA
TAATCTAGTCATAGGTCGTATGTATGACTACCATGTGCTAGATATGATTGAATTAGGTATTGAGAATTTTGTCTCTCTAA
AAGACATTAAGAACAGTAAATGCCCTGAGGGAACAAAACCCATGTGAATATTTGCTGGTGATGATTTTGATGTAACAGAA
GATTATAGAAGACTAAAAAGTCTTCTTATTGATTTCTTCAGAGGCCCCACAGTATCAAATATCCACCTGGCTGGATTAGA
GTATGTTCTGCACTTTACTGCACTGAATGGGATGCACTTTCGAAGCTATAAGCTGCTGCTGAAGAAATCTGGTTGCTGAA
CACCATGAACTGAATTAGAAGAAATGGACCCTCACATTGGATCTGGTTCTGAGGAGGGCACACCTGGCATCGGATGACCT
TTATAAATTATCTATGAAATTCCAAAAGCTCTCAAGCCAAAGAAGAAGAAAAATATCTCCCATGATACTTTTGGTACAAC
TTATGGAAGTATTCATATGCAGAAGCAAGACCTAAGCAAACTACAAACCAGGAAAATAATGGGGTTGAAGAAGCGACCTG
CAGAAAGGATAACAGAAGACCAGGAGAAAAAGTAAAAAAGAATTTTAAAAAAT

ORF - retro_cjac_2473 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 91.03 %
Parental protein coverage: 75.82 %
Number of stop codons detected: 4
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalQTSLEFFSKKSDCSLFMFGSHNKKRPNNLVIGRMYDYHVLDMIELGIENFVSLKDIKNSKCPEGTKPMLI
QTSLEFFSKKSDCSLFMFGSHNKK.PNNLVIGRMYDYHVLDMIELGIENFVSLKDIKNSKCPEGTKPM.I
RetrocopyQTSLEFFSKKSDCSLFMFGSHNKKQPNNLVIGRMYDYHVLDMIELGIENFVSLKDIKNSKCPEGTKPM*I
ParentalFAGDDFDVTEDYRRLKSLLIDFFRGPAVSNIRLAGLEYVLHFTALNGKIYFRSYKLLLKKSGCRTPRIEL
FAGDDFDVTEDYRRLKSLLIDFFRGP.VSNI.LAGLEYVLHFTALNG...FRSYKLLLKKSGC.TP..EL
RetrocopyFAGDDFDVTEDYRRLKSLLIDFFRGPTVSNIHLAGLEYVLHFTALNG-MHFRSYKLLLKKSGC*TP*TEL
ParentalEEMGP-SLDLVLRRTHLASDDLYKLSMK-MPKALKPKKKKNISHDTFGTTYGRIHMQKQDLSKLQTRKMK
EEM.P..LDLVLRR.HLASDDLYKLSMK..PKALKPKKKKNISHDTFGTTYG.IHMQKQDLSKLQTRK..
RetrocopyEEMDP>TLDLVLRRAHLASDDLYKLSMK<IPKALKPKKKKNISHDTFGTTYGSIHMQKQDLSKLQTRKIM
ParentalGLKKRPAERITEDQEKKSKRIKKN
GLKKRPAERITEDQEKK.KRI.KN
RetrocopyGLKKRPAERITEDQEKK*KRILKN

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






RNA-Seq - click to see more details

(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 .80 RPM 3 .53 RPM
SRP051959_heart 0 .58 RPM 5 .49 RPM
SRP051959_kidney 2 .48 RPM 6 .90 RPM
SRP051959_liver 0 .37 RPM 4 .96 RPM
SRP051959_lung 0 .80 RPM 4 .38 RPM
SRP051959_lymph_node 1 .35 RPM 5 .37 RPM
SRP051959_skeletal_muscle 0 .04 RPM 7 .34 RPM
SRP051959_spleen 1 .58 RPM 5 .92 RPM

ChIP-Seq - click to see more details

Callithrix jacchus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_cjac_2473 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_2473 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_2473 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 17 parental genes, and 37 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000039182 retrocopies
retro_cfam_1611, retro_cfam_903,
Callithrix jacchus ENSCJAG00000005212 6 retrocopies
retro_cjac_1675, retro_cjac_1768, retro_cjac_2244, retro_cjac_2473 , retro_cjac_606, retro_cjac_933,
Cavia porcellus ENSCPOG000000067972 retrocopies
retro_cpor_332, retro_cpor_582,
Equus caballus ENSECAG000000171211 retrocopy
retro_ecab_782,
Erinaceus europaeus ENSEEUG000000061692 retrocopies
retro_eeur_454, retro_eeur_584,
Felis catus ENSFCAG000000015271 retrocopy
retro_fcat_1584,
Homo sapiens ENSG000001974981 retrocopy
retro_hsap_2425,
Gorilla gorilla ENSGGOG000000014691 retrocopy
retro_ggor_83,
Myotis lucifugus ENSMLUG000000056762 retrocopies
retro_mluc_485, retro_mluc_921,
Macaca mulatta ENSMMUG000000215321 retrocopy
retro_mmul_1903,
Mus musculus ENSMUSG000000385101 retrocopy
retro_mmus_2234,
Nomascus leucogenys ENSNLEG000000128543 retrocopies
retro_nleu_2024, retro_nleu_2434, retro_nleu_2445,
Oryctolagus cuniculus ENSOCUG000000160281 retrocopy
retro_ocun_831,
Pongo abelii ENSPPYG000000169252 retrocopies
retro_pabe_1788, retro_pabe_2464,
Pan troglodytes ENSPTRG000000185031 retrocopy
retro_ptro_1398,
Rattus norvegicus ENSRNOG000000005871 retrocopy
retro_rnor_2336,
Tupaia belangeri ENSTBEG000000171519 retrocopies
retro_tbel_1824, retro_tbel_2243, retro_tbel_2376, retro_tbel_2576, retro_tbel_3547, retro_tbel_3635, retro_tbel_3803, retro_tbel_3876, retro_tbel_4509,


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