RetrogeneDB ID: retro_cjac_3091

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 8:96693183..96694558(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NARS
• Ensembl ID: ENSCJAG00000003837
• Aliases: None
• Description: None

Sequence

>retro_cjac_3091
GCTTTGATGACAGTAGAAGAACCATTTCCTACCATTTATGTAGATTCACAAAAAGCAAATGAGAGGTGGGATGTTATTTC
TAAATCGCAGATGAACAACATTAAAAAGATGTGGCATAGGAAACAATGAAGAGTGACTCCCGGGATAAGAAAGAGGCAGA
AGATCATTTACAAAGAGAAAAGAACCTGGAGAAGCCAAGAAGATTACCAGTAAAAACGATCCAAGTCTCCCAGAGCCAAA
ATGTGGGAAGATTAATGAGTTAGAAGGATATCAAGGCCAACGAGTAAAGGTGTTTGCCTGGGTCCACAGGCTACGTAGGC
AAGGAAAGGATTTAATGTTTCTGGTGTTGCGAGTGGAACAGGTTTTCTTCAGTGTTGTCTTGGCGGATGAGTTGTGTCTG
TGCTACGGTGGAGTCTCTTGTCCATGGAGAGTAGCGTTGCAGTGTATGGAACGCTAAATCTTACCCCAAAGGGCAAGCAG
GCTCCAGGTGGCCATGAGCTGACTTGTGATTTCTGGGAACTCATTGGCTTGGCCCCTGCTGGAGGAGCTGACGACTTGCT
CAATGAGGAATCTGACGTTGACGTCCAGCTCAACAACAGACACATGATGATCCGAGGAGAAAGCATGTCCAAAACCTTCA
GAGCACGCTCCATGATCACCAAGTGCTTTAGAGATCACTGCTTTGATGGGGGGTACTGTGAAGTTGCTCCTCCAACATTA
GTGCAAACACAAGCAGAAGGTGGCTCCACGCTCTTCAAGCTTAACTACTTTGGGGAAGAGGCATTTTTGACTCAGTCCTC
TCAGTTGTACCTGGAGACTTGCCTCCCAGCCCTGGGAGATGTTTTTTGGATCGTGCAGTCATACCGGGCAGAACAGTCCA
GAACACGAAGGCACCTGGCTGAGTACCCTCACGTGGAAGCGGAGTGTCCTTTCCTGAGCTTTGAGGACCTCCTATACCGG
CTGGAGGACTCGGTCTGTGCTGTGGTAGACCGAGTATTGAAGTCACCTGTAGCCAGCATAGTGTATGAACTCAACCCGAA
CTTTAAGCCCCCCAAACGGCCTTTCAAACAGATGAACTATTCAGATGCTATCATGTGGCTAAAAGAACACGATATAAAAA
AGAAGATGGAACTTTCTAGGAATTTGGAGAAGATATCCCAGAAGCTCCTAGAGACTGATGACAGACACCATTAATGAACC
AATCTTGCTGTGTCGATTTCCTGTGGAGATCAAGTCCTTCTACATGTAGCGATGTCCTGAGGATCCCCGTCTTACTGAAT
CTGTGGATGTGTTGATGCCCAATGTTGGTGAGATTGTGGGAGGCTCAATGAGTATCTGGGATAGTGAAGAAATACTGGCA
GGTTATAAAAGGGAA

Alignment

ORF - retro_cjac_3091 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.1 %
• Parental protein coverage: 84.12 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  ALMTVGKEPFPTIYVDSQKENERWNVISKSQMKNIKKMWHREQ-MKSDSRDKKEAEDNLRREKNLE-EAK
          ALMTV..EPFPTIYVDSQK.NERW.VISKSQM.NIKKMWHR.Q.MKSDSRDKKEAED.L.REKNLE.EAK
Retrocopy ALMTV-EEPFPTIYVDSQKANERWDVISKSQMNNIKKMWHRKQ<MKSDSRDKKEAEDHLQREKNLE<EAK

Parental  KITIKNDPSLPEPKCVKISALEGYRGQRVKVFGWVHRLRRQGKNLMFLVLR-DGTGFLQC-VLADELCLC
          KIT.KNDPSLPEPKC.KI..LEGY.GQRVKVF.WVHRLRRQGK.LMFLVLR..GTGFLQC.VLADELCLC
Retrocopy KITSKNDPSLPEPKCGKINELEGYQGQRVKVFAWVHRLRRQGKDLMFLVLR<SGTGFLQC>VLADELCLC

Parental  YNGL-LLSTESSVAVYGTLNLTPKGKQAPGGHELSCDFWELIGLAPAGGADNLINEESDVDVQLNNRHMM
          Y.G..LLS.ESSVAVYGTLNLTPKGKQAPGGHEL.CDFWELIGLAPAGGAD.L.NEESDVDVQLNNRHMM
Retrocopy YGGV<LLSMESSVAVYGTLNLTPKGKQAPGGHELTCDFWELIGLAPAGGADDLLNEESDVDVQLNNRHMM

Parental  IRGENMSKIFRARSMITRCFRDHFFDRGYCEVTPPTLVQTQVEGGSTLFKLDYFGEEAFLTQSSQLYLET
          IRGE.MSK.FRARSMIT.CFRDH.FD.GYCEV.PPTLVQTQ.EGGSTLFKL.YFGEEAFLTQSSQLYLET
Retrocopy IRGESMSKTFRARSMITKCFRDHCFDGGYCEVAPPTLVQTQAEGGSTLFKLNYFGEEAFLTQSSQLYLET

Parental  CLPALGDVFCIAQSYRAEQSRTRRHLAEYTHVEAECPFLSFEDLLNRLEDLVCDVVDRVLKSPVASIVHE
          CLPALGDVF.I.QSYRAEQSRTRRHLAEY.HVEAECPFLSFEDLL.RLED.VC.VVDRVLKSPVASIV.E
Retrocopy CLPALGDVFWIVQSYRAEQSRTRRHLAEYPHVEAECPFLSFEDLLYRLEDSVCAVVDRVLKSPVASIVYE

Parental  LNPNFKPPKRPFKRMNYSDAIVWLKEHDI-KKEDGTFYEFGEDIPEAPE-RLMTDTINEPILLCRFPVEI
          LNPNFKPPKRPFK.MNYSDAI.WLKEHDI.KKEDGTF.EFGEDIPEAP..RLMTDTINEPILLCRFPVEI
Retrocopy LNPNFKPPKRPFKQMNYSDAIMWLKEHDI<KKEDGTF*EFGEDIPEAPR<RLMTDTINEPILLCRFPVEI

Parental  KSFYMQRCPEDPRLTESVDVLMPNVGEIVGGSMRIWDNEEILAGYKRE
          KSFYM.RCPEDPRLTESVDVLMPNVGEIVGGSM.IWD.EEILAGYKRE
Retrocopy KSFYM*RCPEDPRLTESVDVLMPNVGEIVGGSMSIWDSEEILAGYKRE

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	0.02 RPM	41.78 RPM
SRP051959_heart	0.05 RPM	33.91 RPM
SRP051959_kidney	0.04 RPM	85.28 RPM
SRP051959_liver	0.04 RPM	53.78 RPM
SRP051959_lung	0.02 RPM	38.15 RPM
SRP051959_lymph_node	0.00 RPM	35.36 RPM
SRP051959_skeletal_muscle	0.00 RPM	38.09 RPM
SRP051959_spleen	0.02 RPM	42.69 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3091 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3091 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3091 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003837	2 retrocopies	retro_cjac_2194, retro_cjac_3091 ,
Cavia porcellus	ENSCPOG00000013227	3 retrocopies	retro_cpor_1441, retro_cpor_429, retro_cpor_736,
Loxodonta africana	ENSLAFG00000000559	1 retrocopy	retro_lafr_955,
Macropus eugenii	ENSMEUG00000000774	1 retrocopy	retro_meug_2019,
Otolemur garnettii	ENSOGAG00000016302	1 retrocopy	retro_ogar_1061,
Ictidomys tridecemlineatus	ENSSTOG00000002118	1 retrocopy	retro_itri_591,