RetrogeneDB ID:

retro_cjac_567

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:1:82084375..82085494(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCJAG00000011324
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:MAEA
Ensembl ID:ENSCJAG00000001587
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_567
AAGGTGCCCTACGAGACAGTGAACAAACGCTTTTCGCGCCGCTCAGAAGAACACTGACCGGGAGACCAGCCACGTCACTA
TGGTGGTGGCCGAGCTGGAGAAGACGCTGAGTGTCTGCCCCGCCGTGGACTCTGTGGTTAGCCTGCTGGGCGGTGTGGTG
GAGAAGCTCAGCATCCTTAAGAGGAAGGCGGCGGAGTCCATCCAGGCAGAGGTTGAGAGCGCCAAGCTGTGCGAGAGCCG
GATCGAGCACCTCAAAGAGCACAGCAGCTACCAGCCCTCGGTGTCCAGCTTGTGGAAGAGCAAGGACATGGACCGCATGG
TGGGGGAGTACCTGCTACGCTGCGGCTACTACAACACGGCTGTCAAACTGGCACGCCAGAGCGGCATCAAGGACCTCGTG
AATATCGAGATGTTCCTGAGGGCCAAAGAGGTAGAGGAGTCCCTGGAGCGATGTGAGACGGCCACCTGCCTGGCCTGGTG
CCATGACAAGTCCTGGCTCCGGAAGATGAAGAGCTGCCTGGAGTTCAGCCTCAGAATCCAGGAGTTCTTTGAACTCATCC
GGCAGAATAAGAGACTGGACGCCATTAGACATGCGAGAAAGCACTTCACCCAAGCGGAAGGGAGCCAGCTGGACGAGGTG
CGCCAGGCCATGGGCATGCTGGCCTTCCTCCCTGACACGCACGTCTCCCCGTACAAGGACCTCCGGGACCCCGCACGGTG
GCGGATGCTGATCCAGCAGTTCCGGTACGACAATACCGACTACACCAGCTGGGAAACAACTCCGTGTTCACCCTCACCCT
GCAGGCTGGCCTCTCCGCGATCAAGACACCACAGTGCTACAAGGAGGACGGCAGCTCCAAGAGCCCCGACTGTCCTGTGT
GCAGCCGCTCTCTCAACAAGCTGGCGCAGCCCCTGCCCATGGCCCACTGCGCCAACTCCCGCCTGGACTGCAAGATCTCC
GGTGATGTGATGAACGACAACAACCTGCCCATGATGCTGCCCAACGGCTACGTCTACGGCTACAATTCTCTGCTTTCTAT
CCGTCAAGAAGATAAAGTCCTTTGCCCGAGAACCAAAGAAGTCTTTCACTTCTCATAAGCCGAGAAGGTGTACATCATG

ORF - retro_cjac_567 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 79.84 %
Parental protein coverage: 99.73 %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalQVPYETLNKRF-RAAQKNIDRETSHVTMVVAELEKTLSGCPAVDSVVSLLDGVVEKLSVLKRKAVESIQA
.VPYET.NKRF.RAAQKN.DRETSHVTMVVAELEKTLS.CPAVDSVVSLL.GVVEKLS.LKRKA.ESIQA
RetrocopyKVPYETVNKRF>RAAQKNTDRETSHVTMVVAELEKTLSVCPAVDSVVSLLGGVVEKLSILKRKAAESIQA
ParentalEDESAKLCKRRIEHLKEHSSDQPAAASVWKRKRMDRMMVEHLLRCGYYNTAVKLARQSGIEDLVNIEMFL
E.ESAKLC..RIEHLKEHSS.QP...S.WK.K.MDRM..E.LLRCGYYNTAVKLARQSGI.DLVNIEMFL
RetrocopyEVESAKLCESRIEHLKEHSSYQPSVSSLWKSKDMDRMVGEYLLRCGYYNTAVKLARQSGIKDLVNIEMFL
ParentalTAKEVEESLERRETATCLAWCHDNKSRLRKMKSCLEFSLRIQEFIELIRQNKRLDAVRHARKHFSQAEGS
.AKEVEESLER.ETATCLAWCHD.KS.LRKMKSCLEFSLRIQEF.ELIRQNKRLDA.RHARKHF.QAEGS
RetrocopyRAKEVEESLERCETATCLAWCHD-KSWLRKMKSCLEFSLRIQEFFELIRQNKRLDAIRHARKHFTQAEGS
ParentalQLDEVRQAMGMLAFPPDTHISPYKPCLSQVKSALTLQR-VEIRAFTLQRVDIRVKSALTLQRVDIRVKSA
QLDEVRQAMGMLAF.PDTH.SPYK............Q..V..R...L..........LTLQ......K..
RetrocopyQLDEVRQAMGMLAFLPDTHVSPYKDLRDPARWRMLIQQ<VPVRQYRLHQLGNNSVFTLTLQAGLSAIKTP
ParentalLQCYKEDGSSKSPDCPVCSRSLNKLAQPLPMAHCANSRLVCKISGDVMNENNPPRMLPNGYVYGYNSLLS
.QCYKEDGSSKSPDCPVCSRSLNKLAQPLPMAHCANSRL.CKISGDVMN.NN.P.MLPNGYVYGYNSLLS
Retrocopy-QCYKEDGSSKSPDCPVCSRSLNKLAQPLPMAHCANSRLDCKISGDVMNDNNLPMMLPNGYVYGYNSLLS
ParentalIRQDDKVVCPRTKEVFHFSQAEKVYIM
IRQ.DKV.CPRTKEVFHFS.AEKVYIM
RetrocopyIRQEDKVLCPRTKEVFHFS*AEKVYIM

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 4 .90 RPM
SRP051959_heart 0 .23 RPM 6 .12 RPM
SRP051959_kidney 0 .29 RPM 5 .57 RPM
SRP051959_liver 0 .15 RPM 3 .36 RPM
SRP051959_lung 0 .41 RPM 7 .24 RPM
SRP051959_lymph_node 0 .46 RPM 6 .35 RPM
SRP051959_skeletal_muscle 0 .44 RPM 4 .06 RPM
SRP051959_spleen 0 .46 RPM 5 .80 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_567 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_567 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_567 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 1 parental gene, and 2 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG00000001587 2 retrocopies
retro_cjac_3821, retro_cjac_567 ,


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