RetrogeneDB ID:

retro_cjac_618

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:1:135008715..135010271(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCJAG00000007938
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:GSPT1
Ensembl ID:ENSCJAG00000018191
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_618
GCACCTGTGGAATCCTCTCAAGAGGAGCAGTCATTGTGTGAAGGTTCAAATTCAGCAGTTAGCATGGAACTTTCAGAACC
CATTGTAGAAAATGGAGAGACAGAAATGTCCCCAGAAGAATCATGGGAGCACAAAGAAGAAATAAGTGAAGCAGAGCCGG
GGAGTGGTTCCTTGGGAGATGGAAGGCCGCCAGAGGAAAGTACCCATGAAATGATGGAGGAGGAAGAGGAAATCCCAAAA
CCGAAATCTGTGGTTGCACTGCCTGGTGCTCCTAAGAAAGAGCATGTAAATGTAGTATTCATTGGGCATGTAGATGCTGG
CAAGTCAACTATTGGAGGACAAATAATGTATTTGACTGGAATGGTTGACGAAAGGACACTTGAAAAGTATGAAAGAGAAG
CTAAAGAGAAAAACAGAGAAACTTGGTACTTGTCTTGGGCCTTAGACACAAATCAGGAAGAACGAGACAAGGGTAAAACA
GTAGAAGTGGGTCATGCCTATTTTGAAACCGAAAAGAAACATTTCACAATTCTAGATGCCCCTGGCCACAAGAGTTTTGT
CCCAAATATGATTGGTGTTGCCTCTCAAGCTGATTTGGCTGTGCTGGTAATCTCAGCCAGGAAAGGAGAGTTTGAAACTG
GATTTGAAAAAGGAGGACAGACAAGAGAACATGCAATGTTGGCAAAGACAGCAGGTATAAAACACTTAATTGTGCTAATA
AGATGGATGATCCAACGGTAAATTGGAGCAATGAGAGATATGAAGAATGTAAAGAGAAACTAGTGCCATTTTTGAAAAAA
GTTGGCTTCAATCCCAAAAAGGACATTCACTTCATGCCCTGCTCAGGACTTACCGGAGCAAATCTCAAAGAGCAGTCAGA
TTTCTGTCCTTGGTACATTGGATTACCATTTATTCCGTATCTGGATAATTTGCCAAACTTCAGTAGATCAGTTGATGGAC
CAATCAGGCTGCCAATTGTGGATAAGTACAAGGATATGGGCACTGTGGTCCTGGGAAAGCTGGAATCAGGATCTATTTGT
AAAGGTCAGCAGCTTGTGATGATGCCAAACAAGCACAATGTGGAAGTTCTTGGAATACTTTCTGATGATGTAGAAACTGA
TACTGTAGCCCCAGGTGAAAACCTCAAAATCAGACTGAAAGGAATTGAAGAAGAGGAGATTCTTCCAGGATTTATACTTT
GTGATCCTAATAATCTTTGTCATTCTGGACGCACATTCGATGCCCAGATAGTAATTATAGAGCACAAATCCATCATCTGC
CCAGGCTATAATGCGGTGCTGCATATTCATACCTGTATTGAGGAAGTCGAAATAACAGCCTTAATCTGCTTGGTAGACAA
AAAATCAGGAGAAAAAAGTAAGACCCGACCCCGTTTTGTGAAACAAGATCAAGTATGCATTGCTCGCTTGAGGACAGCAG
GAACCATCTGCCTTGAGACCTTTAAAGACTTCCCTCAGATGGGTCGTTTTACCTTAAGAGATGAGGGTAAGACATTTGCA
ATTGGAAAAGTTCTGAAACTGGTTCCAGAGAAAGAC

ORF - retro_cjac_618 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 97.5 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalAPVESSQEEQSLCEGSNSAVSMELSEPVVENGETEMSPEESWEHKEEISEAEPGSGSLGDGRPPEESTHE
APVESSQEEQSLCEGSNSAVSMELSEP.VENGETEMSPEESWEHKEEISEAEPGSGSLGDGRPPEESTHE
RetrocopyAPVESSQEEQSLCEGSNSAVSMELSEPIVENGETEMSPEESWEHKEEISEAEPGSGSLGDGRPPEESTHE
ParentalMMEEEEEIPKPKSVVAPPGAPKKEHVNVVFIGHVDAGKSTIGGQIMYLTGMVDKRTLEKYEREAKEKNRE
MMEEEEEIPKPKSVVA.PGAPKKEHVNVVFIGHVDAGKSTIGGQIMYLTGMVD.RTLEKYEREAKEKNRE
RetrocopyMMEEEEEIPKPKSVVALPGAPKKEHVNVVFIGHVDAGKSTIGGQIMYLTGMVDERTLEKYEREAKEKNRE
ParentalTWYLSWALDTNQEERDKGKTVEVGRAYFETEKKHFTILDAPGHKSFVPNMIGGASQADLAVLVISARKGE
TWYLSWALDTNQEERDKGKTVEVG.AYFETEKKHFTILDAPGHKSFVPNMIG.ASQADLAVLVISARKGE
RetrocopyTWYLSWALDTNQEERDKGKTVEVGHAYFETEKKHFTILDAPGHKSFVPNMIGVASQADLAVLVISARKGE
ParentalFETGFEKGGQTREHAMLAKTAGVKHLIVLI-NKMDDPTVNWSNERYEECKEKLVPFLKKVGFNPKKDIHF
FETGFEKGGQTREHAMLAKTAG.KH......NKMDDPTVNWSNERYEECKEKLVPFLKKVGFNPKKDIHF
RetrocopyFETGFEKGGQTREHAMLAKTAGIKH-LIVL<NKMDDPTVNWSNERYEECKEKLVPFLKKVGFNPKKDIHF
ParentalMPCSGLTGANLKEQSDFCPWYIGLPFIPYLDNLPNFSRSVDGPIRLPIVDKYKDMGTVVLGKLESGSICK
MPCSGLTGANLKEQSDFCPWYIGLPFIPYLDNLPNFSRSVDGPIRLPIVDKYKDMGTVVLGKLESGSICK
RetrocopyMPCSGLTGANLKEQSDFCPWYIGLPFIPYLDNLPNFSRSVDGPIRLPIVDKYKDMGTVVLGKLESGSICK
ParentalGQQLVMMPNKHNVEVLGILSDDVETDTVAPGENLKIRLKGIEEEEILPGFILCDPNNLCHSGRTFDAQIV
GQQLVMMPNKHNVEVLGILSDDVETDTVAPGENLKIRLKGIEEEEILPGFILCDPNNLCHSGRTFDAQIV
RetrocopyGQQLVMMPNKHNVEVLGILSDDVETDTVAPGENLKIRLKGIEEEEILPGFILCDPNNLCHSGRTFDAQIV
ParentalIIEHKSIICPGYNAVLHIHTCIEEVEITALICLVDKKSGEKSKTRPRFVKQDQVCIARLRTAGTICLETF
IIEHKSIICPGYNAVLHIHTCIEEVEITALICLVDKKSGEKSKTRPRFVKQDQVCIARLRTAGTICLETF
RetrocopyIIEHKSIICPGYNAVLHIHTCIEEVEITALICLVDKKSGEKSKTRPRFVKQDQVCIARLRTAGTICLETF
ParentalKDFPQMGRFTLRDEGKTIAIGKVLKLVPEKD
KDFPQMGRFTLRDEGKT.AIGKVLKLVPEKD
RetrocopyKDFPQMGRFTLRDEGKTFAIGKVLKLVPEKD

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 .35 RPM 26 .91 RPM
SRP051959_heart 0 .72 RPM 26 .50 RPM
SRP051959_kidney 0 .64 RPM 28 .80 RPM
SRP051959_liver 0 .39 RPM 34 .33 RPM
SRP051959_lung 0 .62 RPM 28 .58 RPM
SRP051959_lymph_node 0 .41 RPM 27 .56 RPM
SRP051959_skeletal_muscle 0 .55 RPM 34 .70 RPM
SRP051959_spleen 0 .61 RPM 24 .60 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_618 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_618 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_618 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 25 parental genes, and 28 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000095891 retrocopy
retro_amel_4,
Bos taurus ENSBTAG000000035772 retrocopies
retro_btau_1793, retro_btau_1840,
Canis familiaris ENSCAFG000000188561 retrocopy
retro_cfam_2072,
Callithrix jacchus ENSCJAG00000018191 1 retrocopy
retro_cjac_618 ,
Cavia porcellus ENSCPOG000000093811 retrocopy
retro_cpor_73,
Equus caballus ENSECAG000000211951 retrocopy
retro_ecab_739,
Echinops telfairi ENSETEG000000182491 retrocopy
retro_etel_1626,
Felis catus ENSFCAG000000222811 retrocopy
retro_fcat_1913,
Gorilla gorilla ENSGGOG000000040711 retrocopy
retro_ggor_2906,
Microcebus murinus ENSMICG000000141371 retrocopy
retro_mmur_28,
Myotis lucifugus ENSMLUG000000007921 retrocopy
retro_mluc_98,
Macaca mulatta ENSMMUG000000231781 retrocopy
retro_mmul_118,
Monodelphis domestica ENSMODG000000047281 retrocopy
retro_mdom_1420,
Mustela putorius furoENSMPUG000000145041 retrocopy
retro_mputfur_147,
Mus musculus ENSMUSG000000622031 retrocopy
retro_mmus_238,
Nomascus leucogenys ENSNLEG000000101991 retrocopy
retro_nleu_2705,
Oryctolagus cuniculus ENSOCUG000000047591 retrocopy
retro_ocun_1664,
Otolemur garnettii ENSOGAG000000070831 retrocopy
retro_ogar_100,
Pteropus vampyrus ENSPVAG000000050091 retrocopy
retro_pvam_1426,
Rattus norvegicus ENSRNOG000000023351 retrocopy
retro_rnor_2931,
Sarcophilus harrisii ENSSHAG000000059081 retrocopy
retro_shar_14,
Ictidomys tridecemlineatus ENSSTOG000000154061 retrocopy
retro_itri_109,
Tupaia belangeri ENSTBEG000000088732 retrocopies
retro_tbel_3810, retro_tbel_4659,
Tarsius syrichta ENSTSYG000000138122 retrocopies
retro_tsyr_1169, retro_tsyr_148,
Tursiops truncatus ENSTTRG000000116301 retrocopy
retro_ttru_12,


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