RetrogeneDB ID: retro_cjac_3957

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL286426.1:212922..214818(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: EPRS
• Ensembl ID: ENSCJAG00000003457
• Aliases: EPRS, QARS
• Description: None

Sequence

>retro_cjac_3957
TTCAACATGGGGCTGCTGATGGGAGAAGCTCGGGCTGTGCTTAAGTGGGCAGATGGCAAAATGATCAAGAACGAAGTGGA
CATGCAGGTCCTTCACTTTCTGGGCTGCAAGATGGAGGCTGATCTGGAGAAGCCCAAGGTGGCCAAAGCGCGGCTGGAAG
AAACAGACCGGAGGACAGCAAAAGATGTGATAGAGAATCGTGAGCCTGCCGACCAGACTCTGTCTCTGATGAAGCAGCTC
TGGGAGGAGGCCCTTAAGTTCCACAAGCCTGGTGAGAACTACAAGACTCCAGGCTATGTGATTACTCCACACACCATGAA
TCTATGAAAGCAGCATCTGGAGATTACTGGTGGGCAGATACGTACCCGGTTCCCGCCAGAACCCAATGGAATCCTGCATA
TTGGACATGCCAAAGACATCAGTTTCAACTTTGGCTATGCCAAGGCCAACAATGGCATCTGTTTTCTGTGCTTTGATGAC
AGCAACCCTGAGAAGGAGGAAGCAAAGTTCTTCACTGCCATCTATGACATGGTAGCCTGGCTGGGTTACACACCTTACAG
AGTGACATATGCCTCTGACTATTTTGACCAGCTATATGCCTGGGCTGTGGAGCTCATTCACAGGGGTCTGGCTTATGTGT
GTCACTAGCTAGGGGAGGAGTTCAAAGGCCATAATCCTTTGCCCACACCCTGGAGAGACCATCCCATGGAAAAGTCACTG
CTGCTCTTTGAGGCAATGCACAAGGGCAAGTTTTCAGAGGGTAAGGCCACACTACAGATGAAGCTGGTGATGGAGAATGG
CAAGATGGATTCTGTAGCTTATCGAGTCAAGTATACACCACACCACCACACAGGGGACAAATGGTGCATCTATTCCACCT
ACGACTATACACACTGACTCTGTGACTCCATCGAGCACATCACTCACTTACTCTGCACCAAGAAATTCCAGGCCCGACAC
TCTTCTTACTTCTGGCTTTGCAATGCACTGGACGTCTATTGCCCTGTTCAGTGGGAGTATGGCCACCTCAGCCTGCACTA
CACTCTTGTCTCTAAGAGGAAGATCCTCCAGCGTGTAGAAACTGGTGCTGTATGTGACTGGGATGACCCACAGCTTTTTA
CACTCTTGGCCCTGAGACGATGGGTGTTTCCACTTGAGGGCATCAACAACTTCTGTGCCCGGGTGTTAATGACAGTGGCA
CAAACCACAATGGAACCATATCTTCTAGAAGGCTGTGTGCGTGATGTGCTGCTGAATTACACAGCTTCACAAGCCATGGC
TGTGCTGGAGTCACTACGGGTCACCATTACCAACTTTCCTGCTGCCAAGTCCTTGAACATCCAGGTGCCCAACTTGCCAG
CTGATAAGACCAAAGGCTTCCATCAGGTTCCTTTTGCACCCATTGTGTTCATTGAGAGGACTGGCTTTAAGGAGGAGCCA
GAGCCAGGCTTTAAGCACCCGGCTTGGGGCCAGCCTGTGGGCCTGAGGCATACAGGCTAAGTCATTGAGCTGCAGCATGT
TGTCAAGGGCCCCAGTGGTTGTGTAGAAAGTCTGGAGGTAACCTGCAGAAGGGAAGATTATGGAGAGAAGCCAAAGGCCT
TTATTCACTGGGTTTCACAGCCTTTGACATGTGAGGTTCACCTCTATGAGCGATTATTCCAGCACAAGAACCCTGAAGAT
CCTACTGAGGCGCCTGGTGGATTCTTAAGTGACCTGAACCCAGCATCACTATGCATGGTGGAGGCAGCATTAGTGGACTG
CTCTGTGGCCCTGGCAAAACCCTTCAACAAATTCCAGTTTGAGCATCTTGGGTACTTCTCTGTGGATCCAGACAGTCATC
AGGGAAAGTTTGTTTTTAACCAAACTGTGACACTGAAGGAAGACTCGGAAAAGATG

Alignment

ORF - retro_cjac_3957 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.84 %
• Parental protein coverage: 87.17 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FNMGLLMGEARAVLKWADGKMIKNEVDMQVLHLLGPKMEADLEKKPKVAKARLEETDRRTAKDMIENGET
          FNMGLLMGEARAVLKWADGKMIKNEVDMQVLH.LG.KMEADLEK.PKVAKARLEETDRRTAKD.IEN.E.
Retrocopy FNMGLLMGEARAVLKWADGKMIKNEVDMQVLHFLGCKMEADLEK-PKVAKARLEETDRRTAKDVIENREP

Parental  ADQTLSLMEQLRGEALKFHKPGENYKTPGYVMTPHTMNLLKQHLEITGGQVRTRFPPEPNGILHIGHAKA
          ADQTLSLM.QL..EALKFHKPGENYKTPGYV.TPHTMNL.KQHLEITGGQ.RTRFPPEPNGILHIGHAK.
Retrocopy ADQTLSLMKQLWEEALKFHKPGENYKTPGYVITPHTMNL*KQHLEITGGQIRTRFPPEPNGILHIGHAKD

Parental  ISFNFGYAKANNGICFLRFDDTNPEKEEAKFFTAIYDMVAWLGYTPYRVTYASDYFDQLYAWAVELIRRG
          ISFNFGYAKANNGICFL.FDD.NPEKEEAKFFTAIYDMVAWLGYTPYRVTYASDYFDQLYAWAVELI.RG
Retrocopy ISFNFGYAKANNGICFLCFDDSNPEKEEAKFFTAIYDMVAWLGYTPYRVTYASDYFDQLYAWAVELIHRG

Parental  LAYVCHQRGEDLKGHNPLPSPWRDRPMEESLLLFEAMRKGKFSEGEATLRMKLLMEDGKMDPVAYRVKYT
          LAYVCH..GE..KGHNPLP.PWRD.PME.SLLLFEAM.KGKFSEG.ATL.MKL.ME.GKMD.VAYRVKYT
Retrocopy LAYVCH*LGEEFKGHNPLPTPWRDHPMEKSLLLFEAMHKGKFSEGKATLQMKLVMENGKMDSVAYRVKYT

Parental  PHHRTGDKWCIYPTYDYTHCLCDSIEHITHSLCTKEFQARRSSYFWLCNALDVYCPVQWEYGRLNLHYAV
          PHH.TGDKWCIY.TYDYTH.LCDSIEHITH.LCTK.FQAR.SSYFWLCNALDVYCPVQWEYG.L.LHY..
Retrocopy PHHHTGDKWCIYSTYDYTH*LCDSIEHITHLLCTKKFQARHSSYFWLCNALDVYCPVQWEYGHLSLHYTL

Parental  VSKRKILQLVATGAVRDWDDPRLFTLTALRRRGFPPEGINNFCARVGVTVAQTTMEPHLLEACVRDV-LN
          VSKRKILQ.V.TGAV.DWDDP.LFTL.ALRR..FP.EGINNFCARV..TVAQTTMEP.LLE.CVRDV.LN
Retrocopy VSKRKILQRVETGAVCDWDDPQLFTLLALRRWVFPLEGINNFCARVLMTVAQTTMEPYLLEGCVRDVLLN

Parental  DTAPRAMAVLESLRVIITNFPAAKSLDIQVPNFPADETKGFHQVPFAPIVFIERTDFKEEPEPGFKRLAW
          .TA..AMAVLESLRV.ITNFPAAKSL.IQVPN.PAD.TKGFHQVPFAPIVFIERT.FKEEPEPGFK..AW
Retrocopy YTASQAMAVLESLRVTITNFPAAKSLNIQVPNLPADKTKGFHQVPFAPIVFIERTGFKEEPEPGFKHPAW

Parental  GQPVGLRHTGYVIELQRVIKGPSGCVESLEVTCRRADAGEKPKAFIHWVSQPLTCEVRLYERLFQHKNPE
          GQPVGLRHTG.VIELQ.V.KGPSGCVESLEVTCRR.D.GEKPKAFIHWVSQPLTCEV.LYERLFQHKNPE
Retrocopy GQPVGLRHTG*VIELQHVVKGPSGCVESLEVTCRREDYGEKPKAFIHWVSQPLTCEVHLYERLFQHKNPE

Parental  DPTEVPGGFLSDLNPASLRVVEAALVDCSVALAKPFNKFQFERLGYFSVDPDSHQGKLVFNRTVTLKEDP
          DPTE.PGGFLSDLNPASL..VEAALVDCSVALAKPFNKFQFE.LGYFSVDPDSHQGK.VFN.TVTLKED.
Retrocopy DPTEAPGGFLSDLNPASLCMVEAALVDCSVALAKPFNKFQFEHLGYFSVDPDSHQGKFVFNQTVTLKEDS

Parental  GKV
          .K.
Retrocopy EKM

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP051959_colon	0.00 RPM	33.68 RPM
SRP051959_heart	0.00 RPM	23.15 RPM
SRP051959_kidney	0.04 RPM	37.16 RPM
SRP051959_liver	0.00 RPM	34.42 RPM
SRP051959_lung	0.00 RPM	28.52 RPM
SRP051959_lymph_node	0.00 RPM	31.55 RPM
SRP051959_skeletal_muscle	0.00 RPM	29.35 RPM
SRP051959_spleen	0.00 RPM	30.82 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3957 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3957 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3957 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003457	2 retrocopies	retro_cjac_3957 , retro_cjac_996,
Rattus norvegicus	ENSRNOG00000043447	1 retrocopy	retro_rnor_203,