RetrogeneDB ID:

retro_cjac_2066

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:22:20307467..20309848(+)
Located in intron of:ENSCJAG00000032315
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:VPS35
Ensembl ID:ENSCJAG00000010203
Aliases:None
Description:vacuolar protein sorting 35 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:13487]


Retrocopy-Parental alignment summary:






>retro_cjac_2066
ATGCCTACAACACAGCAGTCCCCTCAGGATGAGCAGGAAAAGCTCTTGGATGAAGCCATACAGGCTGTGAAGGTCCAGTC
ATTCCAAATGAAGAGATGCCTGGACAAAAACAAGCTTATGGATGCTCTAAAACATGCGTCTAATATGCTTGGTGAACTCT
GGACTTCTATGTTATCACCAAAGAGCTACTATGAACTTTATATGGCCATTTCTGATGAACTGCACTACTTGGAGGTCTAC
CTGACAGATGAGTTTGCTAAAGGAAGAAAAGTGGCAGATCTCTATGAACTTGTACGGTATGCTGGAAACATTATCCCAAG
GCTTTACCTTTTGATCACAGTTGGAGTTGTATATGTCAAGTCATTTCCTCAGTCAAGGAAGGATATTTTGAAAGATTTGA
TAGAAATGTGCCGTGGTGTGCAGCATCCCTTGAGGGGTCTGTTTCTTCGAAATTACCTTCTTCAGTGTACCAGAAATATC
TTACCTGATGAAGGAGAGCCAACAGACGAAGAAACAACTGGCGATATCAGTGATTCCATGGATTTTGTACTGCTCAACTT
TGCAGAAATGAACAAGCTTTGGGTGCGAATGCAGCATCAGGGACATAGCCGAGATAGAGAAAAAAGAGAAAGAGAAAGAC
AAGAACTGAGAATTTTAGTGGGAACAAATTTGGTGTGTCTCAGTCAGTTGGAAGGTGTAAATGTGGAACGTTACAAACAG
ATTGTTCTGACTGGCATATTGGAGCAAGTTGTAAACTGTAGGGATGCTTTGGCTCAAGAATATCTCATGGAATATATTAT
TCAGGTTTTTCCTGATGAATTTCACCTCCAGACTTTGACTCCTTTTCTTTGGGCCTGTGCTGAGTTACACCAAAATGTAA
ATGTGAAAAACATAATCATTGCTTTAATTGATAGATTAGCTTTATTTGCTCACCGTGAAGATGGACCTGGAATCCCACCA
GATATTAAACTTTTTGCTATATTTTCACAGCAGGTGGCTACAGTGATACAGTCTAGACAAGATATGCCTTCAGAGGATGT
TGTATCTTTCCAACATTAAGTCTCTCTCATTAATCTTGCCATGAAATGTTACCCTGATCGTGTGGACTATGTTGATAAAG
TTCTAGAAACAACAGTGGAGATATTCAATAAGCTCAACCTTGAACATGTTGCTACCAGTAGTGCAGTTTCAAAGGAACTC
ACCAGACTTTGGAAAATACCAGTTGACACTTACAACAATATTTTAACAGTCTTGAAATTAAAACATTTTCACCCGCTCTT
TGAGTACTTTGACTATGAGTCCAGAAAGAGCATGAGTTGTTATGTGCTTAGTAATGTTCTGGATTATAACACAGAAATTG
TCTCTCAAGACCAGGTGGATTCCATAATGAATTTGGTATTCACGTTGATTCAAGATCAGCCAGATCAACCTGTGGAAGAC
CCTGATCCAGAAGACTTTGCTGATGAGCAGAGCCTTGTGGGCCGCTTCATTCATCTGCTGCGTTCTGAGGACCCTGACCA
GCAGTACTCGATTTTGAACACAGCACGAAAACATTTTGGAGCTGGTGGAAATCAGCGGATTCGCTTCACATTGCCACCTT
TGGTATTTTCAGCTTACCAGCTGGCTTTTCGATACAAAGAGAATTCTAAAGTGGATGACAAATGGGAAGAGAAATGCCAG
AAGATTTTTTCATTTGCCCACTAGACTATCAAAGCAGATCTGGCAGAATTGCCCTTAAGACTTTTTCTTCAAGGAGCACT
AGCTGCTGGGGAAATTGGTTTTGAAAATCATGAAACAGTGGCATATGAATTCATGTCCCAGGCATTTTCTCTGTATGAAG
ATGAAATCAGTGATTCTAAAGCACAGCTGGCTGCCATCACCTTGATCATTGGCACTTTTGAAAGGATGAAGTGCTTCTGT
GAAGAGAATCATGAACCCCTGAGGACTCATGTGCCCTTGCTGCATCCAAACTTCTGAAGAAACCTGATCAGGGCCGAGCT
GTGAGCACCTGTGCACATCTCTTCTGGTCTGGGAGAAACACGGACAAAAATGGAGAGGAGCTTCATGGAGGCAAGAGGGT
AATGGAGTGCCTAAAGAAAGCTCTAAAAATAGCAAATCAGTGCATGGACCCCTCTCTACAAGTGCAGCTTTTTATAGAAA
TTCTGAACAGATATATCTATTTTTATGAAAAGGAAAATGTTGCAGTAACAATTCAGGTTTTAAACCAACTTATCCAAAAG
ATTCGAGAAGACCTCCCAAATCTTGAGTCCAGTGAAGAAACAGAGCAGATTAACAAACATTTTCATAACACACTGGAGCA
TTTGCGCTTGCGACAGGAATCACCAGAATCTGAGGGGCCGATTTATGAAGGTCTCATCCTT

ORF - retro_cjac_2066 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 96.5 %
Parental protein coverage: 100. %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMPTTQQSPQDEQEKLLDEAIQAVKVQSFQMKRCLDKNKLMDALKHASNMLGELRTSMLSPKSYYELYMAI
MPTTQQSPQDEQEKLLDEAIQAVKVQSFQMKRCLDKNKLMDALKHASNMLGEL.TSMLSPKSYYELYMAI
RetrocopyMPTTQQSPQDEQEKLLDEAIQAVKVQSFQMKRCLDKNKLMDALKHASNMLGELWTSMLSPKSYYELYMAI
ParentalSDELHYLEVYLTDEFAKGRKVADLYELVQYAGNIIPRLYLLITVGVVYVKSFPQSRKDILKDLVEMCRGV
SDELHYLEVYLTDEFAKGRKVADLYELV.YAGNIIPRLYLLITVGVVYVKSFPQSRKDILKDL.EMCRGV
RetrocopySDELHYLEVYLTDEFAKGRKVADLYELVRYAGNIIPRLYLLITVGVVYVKSFPQSRKDILKDLIEMCRGV
ParentalQHPLRGLFLRNYLLQCTRNILPDEGEPTDEETTGDISDSMDFVLLNFAEMNKLWVRMQHQGHSRDREKRE
QHPLRGLFLRNYLLQCTRNILPDEGEPTDEETTGDISDSMDFVLLNFAEMNKLWVRMQHQGHSRDREKRE
RetrocopyQHPLRGLFLRNYLLQCTRNILPDEGEPTDEETTGDISDSMDFVLLNFAEMNKLWVRMQHQGHSRDREKRE
ParentalRERQELRILVGTNLVRLSQLEGVNVERYKQIVLTGILEQVVNCRDALAQEYLMECIIQVFPDEFHLQTLN
RERQELRILVGTNLV.LSQLEGVNVERYKQIVLTGILEQVVNCRDALAQEYLME.IIQVFPDEFHLQTL.
RetrocopyRERQELRILVGTNLVCLSQLEGVNVERYKQIVLTGILEQVVNCRDALAQEYLMEYIIQVFPDEFHLQTLT
ParentalPFLRACAELHQNVNVKNIIIALIDRLALFAHREDGPGIPPDIKLFDIFSQQVATVIQSRQDMPSEDVVSL
PFL.ACAELHQNVNVKNIIIALIDRLALFAHREDGPGIPPDIKLF.IFSQQVATVIQSRQDMPSEDVVS.
RetrocopyPFLWACAELHQNVNVKNIIIALIDRLALFAHREDGPGIPPDIKLFAIFSQQVATVIQSRQDMPSEDVVSF
ParentalQ--VSLINLAMKCYPDRVDYVDKVLETTVEIFNKLNLEHIATSSAVSKELTRLLKIPVDTYNNILTVLKL
Q..VSLINLAMKCYPDRVDYVDKVLETTVEIFNKLNLEH.ATSSAVSKELTRL.KIPVDTYNNILTVLKL
RetrocopyQH*VSLINLAMKCYPDRVDYVDKVLETTVEIFNKLNLEHVATSSAVSKELTRLWKIPVDTYNNILTVLKL
ParentalKHFHPLFEYFDYESRKSMSCYVLSNVLDYNTEIVSQDQVDSIMNLVSTLIQDQPDQPVEDPDPEDFADEQ
KHFHPLFEYFDYESRKSMSCYVLSNVLDYNTEIVSQDQVDSIMNLV.TLIQDQPDQPVEDPDPEDFADEQ
RetrocopyKHFHPLFEYFDYESRKSMSCYVLSNVLDYNTEIVSQDQVDSIMNLVFTLIQDQPDQPVEDPDPEDFADEQ
ParentalSLVGRFIHLLRSEDPDQQYLILNTARKHFGAGGNQRIRFTLPPLVFAAYQLAFRYKENSKVDDKWEKKCQ
SLVGRFIHLLRSEDPDQQY.ILNTARKHFGAGGNQRIRFTLPPLVF.AYQLAFRYKENSKVDDKWE.KCQ
RetrocopySLVGRFIHLLRSEDPDQQYSILNTARKHFGAGGNQRIRFTLPPLVFSAYQLAFRYKENSKVDDKWEEKCQ
ParentalKIFSFAHQTISALIKAELAELPLRLFLQGALAAGEIGFENHETVAYEFMSQAFSLYEDEISDSKAQLAAI
KIFSFAH.TI....KA.LAELPLRLFLQGALAAGEIGFENHETVAYEFMSQAFSLYEDEISDSKAQLAAI
RetrocopyKIFSFAH*TI----KADLAELPLRLFLQGALAAGEIGFENHETVAYEFMSQAFSLYEDEISDSKAQLAAI
ParentalTLIIGTFERMKCFSEENHEPLRT-QCALAASKLLKKPDQGRAVSTCAHLFWSGRNTDKNGEELHGGKRVM
TLIIGTFERMKCF.EENHEPLRT..CALAASKLLKKPDQGRAVSTCAHLFWSGRNTDKNGEELHGGKRVM
RetrocopyTLIIGTFERMKCFCEENHEPLRT<SCALAASKLLKKPDQGRAVSTCAHLFWSGRNTDKNGEELHGGKRVM
ParentalECLKKALKIANQCMDPSLQVQLFIEILNRYIYFYEKENDAVTIQVLNQLIQKIREDLPNLESSEETEQIN
ECLKKALKIANQCMDPSLQVQLFIEILNRYIYFYEKEN.AVTIQVLNQLIQKIREDLPNLESSEETEQIN
RetrocopyECLKKALKIANQCMDPSLQVQLFIEILNRYIYFYEKENVAVTIQVLNQLIQKIREDLPNLESSEETEQIN
ParentalKHFHNTLEHLRLRRESPESEGPIYEGLIL
KHFHNTLEHLRLR.ESPESEGPIYEGLIL
RetrocopyKHFHNTLEHLRLRQESPESEGPIYEGLIL

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 2 .68 RPM 60 .28 RPM
SRP051959_heart 1 .42 RPM 49 .18 RPM
SRP051959_kidney 1 .86 RPM 57 .20 RPM
SRP051959_liver 1 .08 RPM 36 .78 RPM
SRP051959_lung 3 .43 RPM 59 .95 RPM
SRP051959_lymph_node 5 .11 RPM 69 .86 RPM
SRP051959_skeletal_muscle 0 .72 RPM 29 .94 RPM
SRP051959_spleen 3 .70 RPM 76 .37 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_2066 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_2066 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_2066 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000024931 retrocopy
retro_btau_1810,
Callithrix jacchus ENSCJAG00000010203 1 retrocopy
retro_cjac_2066 ,
Cavia porcellus ENSCPOG000000037731 retrocopy
retro_cpor_880,


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