RetrogeneDB ID: retro_cjac_2916

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:90616665..90617564(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GOT2
• Ensembl ID: ENSCJAG00000011234
• Aliases: None
• Description: glutamic-oxaloacetic transaminase 2, mitochondrial [Source:HGNC Symbol;Acc:4433]

Sequence

>retro_cjac_2916
ATGGCCCTGCTGCACTCAGGCTGCTTCCTCTCCTGGATCACCTCTGCCTTCCAACGGGGACTTGCCATGGCAGCCTCCAA
CAGGGCTGGCTCCTGGTGAGCCCATGTGGAGATGGGACTTCCAGATCCTATCTGGGGAGTCACCAAAGCCTGTAAGAGGG
ACACTGATAGCAAAAAGATGAATCTGGAAGTTGGTGCCGATCAGGACAATAACGGACAGCTTTATCTGCTATCTAGCATC
CACAAGGCAGAGGCCCAGACTTCCGCAAAAAATCTGGGCAAAGACTACCTGCCCATTGGGGTACTGTTTGAATTTTGCGA
GACATCTGCAGAATTAGCCCTGGGTGAGAACAGTGAAGTGTTAAAAAGAGACTTTTTGTCACTGTGCAGACTGTTTCTGG
AACTGGGGCCTTAAGGATCAGAGCAGTTTTCTATAAAGAGTTTTAAAGTTCAGCTGAGCTGTCTTTCTGCCCAAACCATC
CTAGGGAAATTACACACCCATCTTCAGGGATGCTGGTGCACAGCCACAAGGTCATCAATACTATGACCTCAAGACTCGTG
ATTTTGACTTCTTAGGCACTATGGAGGACATTTCAAAAACAGTAGCACAAAGTGTTCTCCTGCATGTCTGGGCCCATAAT
CCCATGGGAGTGGACCCTTGTCCAGAGCAGTAGAAGGAAATAGAAATGGGGTGAAGAAAAAGAATCTCTTTGCATTCCTT
GACATAGCCTATCGAGGCTTTGCCAGAGGCAATGGTAACAAGGATGCTGGGGCTGTGTGCCACTTCATCAAACAGGGCAT
TAACATTTGTCCCTGCCAATCATATGCCAAAACATGGGCATATATGGTGAGCATGTGGGAGAATTTACTGTGATCTGCAA
AGCTGTGGATGAAGCCAAA

Alignment

ORF - retro_cjac_2916 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.61 %
• Parental protein coverage: 70.23 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MALLHSRRVLSGIAAAFHPGLAAAASARASSWWTHVEMGPPDPILGVTEAFKRDTNSKKMNLGVGAYRDD
          MALLHS...LS.I..AF..GLA.AAS.RA.SW..HVEMG.PDPI.GVT.A.KRDT.SKKMNL.VGA..D.
Retrocopy MALLHSGCFLSWITSAFQRGLAMAASNRAGSW*AHVEMGLPDPIWGVTKACKRDTDSKKMNLEVGADQDN

Parental  NGKPYVLPSVRKAEAQIAAKSLDKEYLPIGGLAEFCKASAQLALGENSEV-VKSGRFVTVQTISGTGALR
          NG..Y.L.S..KAEAQ..AK.L.K.YLPIG.L.EFC..SA.LALGENSEV.VK...FVTVQT.SGTGALR
Retrocopy NGQLYLLSSIHKAEAQTSAKNLGKDYLPIGVLFEFCETSAELALGENSEV<VKKRLFVTVQTVSGTGALR

Parental  IGA-SFLQRFFKFSRDVFLPKPSWGNHTPIFRDAGMQLQGYRYYDPKTCGFDFTGAMEDISKIPEQSVVL
          I.A.SFL.R..KFS..VFLPKPS.GN.TPIFRDAG.Q.QG..YYD.KT..FDF.G.MEDISK...QS.VL
Retrocopy IRA<SFL*RVLKFS*AVFLPKPS*GNYTPIFRDAGAQPQGHQYYDLKTRDFDFLGTMEDISKTVAQS-VL

Parental  LHACAHNPTGVDPRPEQWKEIAA-VVKKRNLFAFFDMAYQGFASGDGDKDAWAVRHFIEQGINVCLCQSY
          LH..AHNP.GVDP.PEQ.KEI....VKK.NLFAF.D.AY.GFA.G.G.KDA.AV.HFI.QGIN.C.CQSY
Retrocopy LHVWAHNPMGVDPCPEQ*KEIEM<GVKKKNLFAFLDIAYRGFARGNGNKDAGAVCHFIKQGINICPCQSY

Parental  AK-NMGLYGERVGAFTMICKDADEAK
          AK.NMG.YGE.VG.FT.ICK..DEAK
Retrocopy AK<NMGIYGEHVGEFTVICKAVDEAK

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	26.00 RPM
SRP051959_heart	0.00 RPM	105.66 RPM
SRP051959_kidney	0.02 RPM	75.90 RPM
SRP051959_liver	0.00 RPM	104.79 RPM
SRP051959_lung	0.00 RPM	13.86 RPM
SRP051959_lymph_node	0.00 RPM	9.29 RPM
SRP051959_skeletal_muscle	0.00 RPM	128.30 RPM
SRP051959_spleen	0.00 RPM	12.35 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2916 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2916 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2916 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017346	3 retrocopies	retro_amel_1805, retro_amel_815, retro_amel_846,
Canis familiaris	ENSCAFG00000008357	2 retrocopies	retro_cfam_586, retro_cfam_816,
Callithrix jacchus	ENSCJAG00000011234	1 retrocopy	retro_cjac_2916 ,
Equus caballus	ENSECAG00000016504	1 retrocopy	retro_ecab_694,
Felis catus	ENSFCAG00000025552	3 retrocopies	retro_fcat_1068, retro_fcat_1888, retro_fcat_381,
Homo sapiens	ENSG00000125166	4 retrocopies	retro_hsap_4687, retro_hsap_473, retro_hsap_960, retro_hsap_971,
Gorilla gorilla	ENSGGOG00000005767	3 retrocopies	retro_ggor_2912, retro_ggor_449, retro_ggor_774,
Macropus eugenii	ENSMEUG00000012574	1 retrocopy	retro_meug_2109,
Microcebus murinus	ENSMICG00000008954	1 retrocopy	retro_mmur_480,
Macaca mulatta	ENSMMUG00000006000	1 retrocopy	retro_mmul_1337,
Mustela putorius furo	ENSMPUG00000004862	1 retrocopy	retro_mputfur_567,
Mus musculus	ENSMUSG00000031672	1 retrocopy	retro_mmus_2701,
Oryctolagus cuniculus	ENSOCUG00000003871	1 retrocopy	retro_ocun_1516,
Otolemur garnettii	ENSOGAG00000000551	2 retrocopies	retro_ogar_2182, retro_ogar_827,
Pongo abelii	ENSPPYG00000007413	3 retrocopies	retro_pabe_3640, retro_pabe_823, retro_pabe_901,
Pan troglodytes	ENSPTRG00000008185	4 retrocopies	retro_ptro_3115, retro_ptro_354, retro_ptro_665, retro_ptro_670,
Rattus norvegicus	ENSRNOG00000011782	1 retrocopy	retro_rnor_2695,
Tupaia belangeri	ENSTBEG00000001808	1 retrocopy	retro_tbel_3799,