RetrogeneDB ID: retro_cjac_2194

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:148879677..148881320(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000031141
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_cjac_2194
ATGGTGCTAGCAGAGCTGTACGTCTCTGAATGAGAAGGCGATGATGCCACGGGAGATGGAACCAAGGAGAAGCCATTTAA
AACAGGTCTAAAGGCTTTGATGACAATAGGAAAAGAACCATTTCCTACCATTTACATAGATTCACAAAAAGAAAATGAGA
GGTGGAATGTTATTTCTAAATCACAGATGAAGAACATTAAAAAGATGTGGCATAGGGAACAAATGAAGAGTGACTCCCGG
GATAAGAAAGAGGCAGAAGATAATTTACGAAGAGAAAAGAACCTGGAAGAAGCCAAGAAGGTTACCATTAAAAACGATCC
AAGTCTCCCAGAGCCAAAATGTGTGAAGATTAGTGCGTTAGAAGGATATTGAGGCCAAAGAGTAAAGGTGTTTGGCTGGG
CCCACAGGCTACGTAGGCAAGGAAAGAATTTAATGTTTCTGATGTTGCGAGATGGAACAGGTTTTCTTCAGTGTGTCTTG
TCGGATGAGTTGTGTCTGTGCTACAATGGACTACTCTTGTCCACGGAGAGTAGCGTGGCAGTGTATGGAACGCTAAATCT
TACCCCAAAGGGCAAGCAGGCTCCAGGTGGCCATGAGCTGAGTTGTGACTTCTGGGAACTCATTGGCTTGGCCCCTGCTG
GAGGAGCTGACAACTTGATCAATGAGGAGTCTGATGTTGACGTCCAGCTCAACAACAGACACATGATGATCCGAGGAGAA
AACATGTCCAAAATCTTCAGAGCACGATCCATGATCACCAGGTGCTTTAGAGATCACTTCTTTGATAGGGGGTACTGTGA
AGTTGCTCCTCCAACATTAGTGCAAACACAAGTAGAAGGTGGCTCCACGCTCTTCAAGCTTGACTACTTTGGGGAAGAGG
CATTTTTGACTCAGTCCTCTCAGTTGTACCTGGAGACTTGCCTCCCAGCCCTGGGAGATGTTTTTTGCATCACGCAGTCC
CACCGGGCAGAACAGTCCAGAATACAAAGGCACCTGGCTGAGTATACTCACATGGAAGCCGAGTGTCCTTTCCTGAGCTT
TGAGGACCTCCTGAACCGGCTGGAGGACTTGGTCTGTGATGTGGTAGACCGAGTACTGAAGTCACCTGTAGCCAGCATAG
TGCATGAACTCAACCCGAACTTTAAGCCCCCTCCAAACGGTCTTTCAAATGGATGAACTATTCAGATGCTATTGTGTGGC
TAAAAGAACATGATATAAAGAAAGAAGATGGAACTTTCTATGAATTTGGAGAAGATATCCCAGAAGCTCCTGAGAGACTG
ATGACAGACACCATTAATGAACCAATCTTGCTGTGTCGATTTCCTGTGGAGATCAAGTCCTTCTACATGCAGCAATGTCC
TGAAGATCCCCGTCTTACTGAATCTGTCGTCGTGTTGATGCCCAATGTTGGTGAGATTGTGGGAGGCTCAATACGTATCT
GGGATAATGAAGAAATACTGGCAGGTTATAAAAGGGAAGGGATCGACCCCACTCCCTATTACTGGTATACAGATCCGAGA
AAATACGCCACATGTCCACATGGAGGCTATGGCTTGGGCCTGGAACGATTCTTAACGTGGATTCTGAATAGGTATCACAT
CCGAGACGTGTGCTTATACCCTCAATTTGTCCAGCGCTGCAAG

Alignment

ORF - retro_cjac_2194 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.63 %
• Parental protein coverage: 99.82 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MVLAELYVSEREGDDATGDGTKEKPFKTGLKALMTVGKEPFPTIYVDSQKENERWNVISKSQMKNIKKMW
          MVLAELYVSE.EGDDATGDGTKEKPFKTGLKALMT.GKEPFPTIY.DSQKENERWNVISKSQMKNIKKMW
Retrocopy MVLAELYVSE*EGDDATGDGTKEKPFKTGLKALMTIGKEPFPTIYIDSQKENERWNVISKSQMKNIKKMW

Parental  HREQMKSDSRDKKEAEDNLRREKNLEEAKKITIKNDPSLPEPKCVKISALEGYRGQRVKVFGWVHRLRRQ
          HREQMKSDSRDKKEAEDNLRREKNLEEAKK.TIKNDPSLPEPKCVKISALEGY.GQRVKVFGW.HRLRRQ
Retrocopy HREQMKSDSRDKKEAEDNLRREKNLEEAKKVTIKNDPSLPEPKCVKISALEGY*GQRVKVFGWAHRLRRQ

Parental  GKNLMFLVLRDGTGFLQCVLADELCLCYNGLLLSTESSVAVYGTLNLTPKGKQAPGGHELSCDFWELIGL
          GKNLMFL.LRDGTGFLQCVL.DELCLCYNGLLLSTESSVAVYGTLNLTPKGKQAPGGHELSCDFWELIGL
Retrocopy GKNLMFLMLRDGTGFLQCVLSDELCLCYNGLLLSTESSVAVYGTLNLTPKGKQAPGGHELSCDFWELIGL

Parental  APAGGADNLINEESDVDVQLNNRHMMIRGENMSKIFRARSMITRCFRDHFFDRGYCEVTPPTLVQTQVEG
          APAGGADNLINEESDVDVQLNNRHMMIRGENMSKIFRARSMITRCFRDHFFDRGYCEV.PPTLVQTQVEG
Retrocopy APAGGADNLINEESDVDVQLNNRHMMIRGENMSKIFRARSMITRCFRDHFFDRGYCEVAPPTLVQTQVEG

Parental  GSTLFKLDYFGEEAFLTQSSQLYLETCLPALGDVFCIAQSYRAEQSRTRRHLAEYTHVEAECPFLSFEDL
          GSTLFKLDYFGEEAFLTQSSQLYLETCLPALGDVFCI.QS.RAEQSR..RHLAEYTH.EAECPFLSFEDL
Retrocopy GSTLFKLDYFGEEAFLTQSSQLYLETCLPALGDVFCITQSHRAEQSRIQRHLAEYTHMEAECPFLSFEDL

Parental  LNRLEDLVCDVVDRVLKSPVASIVHELNPNFK-PP-KRPFKRMNYSDAIVWLKEHDIKKEDGTFYEFGED
          LNRLEDLVCDVVDRVLKSPVASIVHELNPNFK.PP.KR.FK.MNYSDAIVWLKEHDIKKEDGTFYEFGED
Retrocopy LNRLEDLVCDVVDRVLKSPVASIVHELNPNFKPPP<KRSFKWMNYSDAIVWLKEHDIKKEDGTFYEFGED

Parental  IPEAPERLMTDTINEPILLCRFPVEIKSFYMQRCPEDPRLTESVDVLMPNVGEIVGGSMRIWDNEEILAG
          IPEAPERLMTDTINEPILLCRFPVEIKSFYMQ.CPEDPRLTESV.VLMPNVGEIVGGS.RIWDNEEILAG
Retrocopy IPEAPERLMTDTINEPILLCRFPVEIKSFYMQQCPEDPRLTESVVVLMPNVGEIVGGSIRIWDNEEILAG

Parental  YKREGIDPTPYYWYTDQRKYGTCPHGGYGLGLERFLTWILNRYHIRDVCLYPRFVQRCK
          YKREGIDPTPYYWYTD.RKY.TCPHGGYGLGLERFLTWILNRYHIRDVCLYP.FVQRCK
Retrocopy YKREGIDPTPYYWYTDPRKYATCPHGGYGLGLERFLTWILNRYHIRDVCLYPQFVQRCK

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	0.31 RPM	41.78 RPM
SRP051959_heart	0.19 RPM	33.91 RPM
SRP051959_kidney	0.49 RPM	85.28 RPM
SRP051959_liver	0.28 RPM	53.78 RPM
SRP051959_lung	0.21 RPM	38.15 RPM
SRP051959_lymph_node	0.14 RPM	35.36 RPM
SRP051959_skeletal_muscle	0.22 RPM	38.09 RPM
SRP051959_spleen	0.19 RPM	42.69 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2194 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2194 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2194 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,