RetrogeneDB ID:

retro_cjac_2697

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:6:20624336..20625718(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCJAG00000013141
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCJAG00000001431
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_2697
CAGCACCACCCGCCCTACCACCAGCAGCACTACCAGGGGCCCCTGCCCGTTGGGCCCTGCGGCCGCAGCGAGGAGAGAAT
CTCGGGCTCAGAGGGGTTTAAAGCCAACTTGTCTCTCTTGAGGAGGCCTGGAGAGAAAACTTACACACAGAGATGTCGGT
TGTTTGTTGGGAATCTACCTGCTGATATCACGGAAGATGAATTCAAAAGACTATTCGCTAAATATGGAGAACCTGGAGAA
GTTTTTAACCACAAAGGCAAAGGATTCGGATTTCTTAAGCTTGAGTCCAGAGCTTTGGCTGAAATTGCCAAAGCTGAGCT
CGATGATACGCCCATGAGAGGTAGACAGCTTCGAGTTCGCTTTGCCACACATGCTGCTGCCCTTTCTGTTCATAATCTTT
CACCTTACGTTTCCAATGAACTGTTGGAAGAAGCCTTCAGCCAGTTTGGTCCTATTGAAAGGGCTGTTGTAATAGTGGAT
GATCATGGAAGATCTACAGGGAAAGGCACTGTTGAATTTGCTTCTAAACCAGCAGCAAGAAAGGCATTTGAACGATGCAG
TGAAGGTGTTTTCTTGCTGACAACAACTCCTCGTCCAGTCATCGTGGAACCACTCGAATAGATGATGAAGATGATCTTCC
TGAAAAACTTGCACAGAAGAATCCAATGTATCAAAAGGAGAGAGAAACTCCTCCTCGTTTTGCCCAGCATGGCGCATTTG
AGTACGAATATTCTCAGCGATGGAAGTCGTTGGATGAAATGGAAAAACAGCAAAGAGAACAAGTTCAAAAAAATATGAAG
GATGCAAAAGACAAATTGGAAAGTGAAATGGAAGATGCCTATCATGAACATCAGGCAAATCTTTTGCGCCAAGATCTGAT
GAGACGACAGGAAGAATTAAGACGCATGGAAGAACTTCATAATCAAGAAATGCAGAAACGTAAAGAAATGCAATTGAGGC
AAGAGGAGGAACGACGTAGAAGAGAGGAAGAGATGATGATTCGTAAGCGTGAGATGGAAGAACAAATGAGGCACCAAAGA
GATGAAAGTTATGGCCGAATGGGCTACACGGATCCAAGAAAAAGAGACATGAGAATGGGTGGCGGAGGAGCAATGAACAT
GGGAGATCCCTATGGTTCAGGAGGCCAGAAATTTCCACCTCTAGGTGGTGGTGGTGGCATAGGTTATGAAGCTAATCCTG
GAGTTTCACCAGCAACCATGAGTGATTCCATGATGGGAAGCGACATGCGTACTGAGCGCTTCGGGCAGGGAGGTGCGGGG
CCTGTGGGTGGACAGGGTCCTAGAGGAATGGGGCCTGGAACTCCAGCAGGATATGGTAGAGGGAGAGAAGAGTACGAAGG
CCCAAACAAAAAACCCCGATTT

ORF - retro_cjac_2697 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 91.79 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalQHHPPYHQQHHQGPPPVGPGGRSEEKISDSEGFKANLSLLRRPGEKTYTQRCRLFVGNLPADITEDEFKR
QHHPPYHQQH.QGP.PVGP.GRSEE.IS.SEGFKANLSLLRRPGEKTYTQRCRLFVGNLPADITEDEFKR
RetrocopyQHHPPYHQQHYQGPLPVGPCGRSEERISGSEGFKANLSLLRRPGEKTYTQRCRLFVGNLPADITEDEFKR
ParentalLFAKYGEPGEVFINKGKGFGFIKLESRALAEIAKAELDDTPMRGRQLRVRFATHAAALSVRNLSPYVSNE
LFAKYGEPGEVF..KGKGFGF.KLESRALAEIAKAELDDTPMRGRQLRVRFATHAAALSV.NLSPYVSNE
RetrocopyLFAKYGEPGEVFNHKGKGFGFLKLESRALAEIAKAELDDTPMRGRQLRVRFATHAAALSVHNLSPYVSNE
ParentalLLEEAFSQFGPIERAVVIVDDRGRSTGKGIVEFASKPAARKAFERCSEGVFLLTTTPRPVIV-EPLEQLD
LLEEAFSQFGPIERAVVIVDD.GRSTGKG.VEFASKPAARKAFERCSEGVF.L.TT.............D
RetrocopyLLEEAFSQFGPIERAVVIVDDHGRSTGKGTVEFASKPAARKAFERCSEGVF-LLTTTPRPVI<RGTTRID
ParentalDEDGLPEKLAQKNPMYQKERETPPRFAQHGTFEYEYSQRWKSLDEMEKQQREQVEKNMKDAKDKLESEME
DED.LPEKLAQKNPMYQKERETPPRFAQHG.FEYEYSQRWKSLDEMEKQQREQV.KNMKDAKDKLESEME
RetrocopyDEDDLPEKLAQKNPMYQKERETPPRFAQHGAFEYEYSQRWKSLDEMEKQQREQVQKNMKDAKDKLESEME
ParentalDAYHEHQANLLRQDLMRRQEELRRMEELHNQEMQKRKEMQLRQEEERRRREEEMMIRQREMEEQMRRQRE
DAYHEHQANLLRQDLMRRQEELRRMEELHNQEMQKRKEMQLRQEEERRRREEEMMIR.REMEEQMR.QR.
RetrocopyDAYHEHQANLLRQDLMRRQEELRRMEELHNQEMQKRKEMQLRQEEERRRREEEMMIRKREMEEQMRHQRD
ParentalESYSRMGYMDPRERDMTMGGGGAMNMGDPYGSGGQKFPPLGGGGGIGYEANPGVPPATMSGSMMGSDMRT
ESY.RMGY.DPR.RDM.MGGGGAMNMGDPYGSGGQKFPPLGGGGGIGYEANPGV.PATMS.SMMGSDMRT
RetrocopyESYGRMGYTDPRKRDMRMGGGGAMNMGDPYGSGGQKFPPLGGGGGIGYEANPGVSPATMSDSMMGSDMRT
ParentalERFGQGGAGPVGGQGPRGMGPGTPAGYGRGREEYEGPNKKPRF
ERFGQGGAGPVGGQGPRGMGPGTPAGYGRGREEYEGPNKKPRF
RetrocopyERFGQGGAGPVGGQGPRGMGPGTPAGYGRGREEYEGPNKKPRF

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 .93 RPM 53 .03 RPM
SRP051959_heart 1 .46 RPM 57 .15 RPM
SRP051959_kidney 1 .46 RPM 64 .63 RPM
SRP051959_liver 1 .10 RPM 35 .29 RPM
SRP051959_lung 1 .19 RPM 64 .50 RPM
SRP051959_lymph_node 1 .69 RPM 74 .06 RPM
SRP051959_skeletal_muscle 1 .51 RPM 38 .28 RPM
SRP051959_spleen 1 .64 RPM 63 .68 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_2697 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_2697 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_2697 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 13 parental genes, and 16 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000035951 retrocopy
retro_cfam_198,
Callithrix jacchus ENSCJAG00000001431 4 retrocopies
retro_cjac_1073, retro_cjac_2542, retro_cjac_2697 , retro_cjac_486,
Callithrix jacchus ENSCJAG000000367441 retrocopy
retro_cjac_3990,
Felis catus ENSFCAG000000312871 retrocopy
retro_fcat_1989,
Gasterosteus aculeatus ENSGACG000000020341 retrocopy
retro_gacu_13,
Gadus morhua ENSGMOG000000119501 retrocopy
retro_gmor_20,
Macropus eugenii ENSMEUG000000140821 retrocopy
retro_meug_164,
Oryctolagus cuniculus ENSOCUG000000018771 retrocopy
retro_ocun_1834,
Oreochromis niloticus ENSONIG000000177371 retrocopy
retro_onil_21,
Sarcophilus harrisii ENSSHAG000000161071 retrocopy
retro_shar_36,
Tetraodon nigroviridis ENSTNIG000000113311 retrocopy
retro_tnig_32,
Takifugu rubripes ENSTRUG000000037831 retrocopy
retro_trub_8,
Drosophila melanogaster FBgn00042271 retrocopy
retro_dmel_11,


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