RetrogeneDB ID: retro_cjac_615

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:131908743..131909921(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ME2
• Ensembl ID: ENSCJAG00000001929
• Aliases: None
• Description: Malic enzyme [Source:UniProtKB/TrEMBL;Acc:F7F0S1]

Sequence

>retro_cjac_615
TCTGTTGGTCTTGCCTGCTCCCAGTATGGACACATCTTTAAAAGACCTAAGGAATTATTTATTTCGATCACAGACACAGG
TCATGTTAGATCAATTGTGGATAACTGACCAAAAAAATCATGTTAAAGCTGTCATAGTGATTGATGGAGAGATAATTCTG
GGTCTTGGAGATCTGGGTGTCTATGGTTGGGACTTCCAGTAGGAAACCTTTGTTTGGATACAGTTTATGCAGGAATACGA
CCTGAGAGATGCCTGCCCATGTATAATGATGTGGAAACTGATAATATCACACTCTTAAAAGACTCATTTTACATGGGCTT
GTACCAGAAATGAGATTACACATAACAGTATGATGACCTGATTGATGAGTTTATGAAAGCTATTACTGACAGAAATGGCT
GAAACACACTCATTCAGCTTGAAGACTTTGGAAATCATAATGCATTCAGGTTCTTGAGAAAATACCCAGAAAAATATTAT
ACTTTCAATGATGATATTCAAGGGACAGCTGCATTAGCTCTAGCAGGTCTTACAGCACTAAAAGTTATTAGTAAACCAAT
CTCTGAACACAAAATCTTTTTCCTTGGATTAGGTGAAGCTACTCTTGGAATTGGAAATCTCATAATATATCCATGGTAGA
AAAGGGCCTGTCAGAAGAATGGGCACAAAAAAAAAATATGGATATTTGATCAGTATGGTTAATTAGTTAATGGCAGAAAA
GCAAAAATAGATAGTTATCAGGAACCATTTACTAACCCAGTCCCAGAGAGCATACCTGATGCTTTTGAAGATGTAGTGAA
TATCCTGAAGACTTCAACTACAATAGGATTTGCAGGTGCTAATCATCTTTTTACTCCTGATGTAATCAGAGACATGGCCT
CTATCAATGAAAGGCCTGTAATATTTACATTAAGTAATCCTACAGCATAGGCAAAGTGCACAGCTGAAGAAGCATATACA
CTTACAGAGGGCAGGTGTTTGTTTGCCAGTGGCGGTCCACTTGAGCCAGTGAAACTCACAGGTGGGCAAGTCTTTACACC
AGGTCAAGGAAACAATGTATTTATTTTTCCATGTGCGGCTTTAGCTGTTATCCTCTGTAACACCCACATATTAGGGACAA
TGTTTTCCCAGAAGCTGCAAAAGTACTGACAAGCCAACTGACAGATGAAGAACTAGCC

Alignment

ORF - retro_cjac_615 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.95 %
• Parental protein coverage: 67.47 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  TVGLACSQYGHIFRRPKGLFISISDRGHVRSIVDNWPE-NHVKAVVVTDGERILGLGDLGVYG-MGIPVG
          .VGLACSQYGHIF.RPK.LFISI.D.GHVRSIVDN.P..NHVKAV.V.DGE.ILGLGDLGVYG..G.PVG
Retrocopy SVGLACSQYGHIFKRPKELFISITDTGHVRSIVDN*PK>NHVKAVIVIDGEIILGLGDLGVYG<LGLPVG

Parental  KLCLYTACAGIRPDRCLPVCIDVGTDNIALLKDPFYMGLYQKRDRTQQYDDLIDEFMKAITDRYGRNTLI
          .LCL.T..AGIRP.RCLP...DV.TDNI.LLKD.FYMGLYQK.D.T.QYDDLIDEFMKAITDR.G.NTLI
Retrocopy NLCLDTVYAGIRPERCLPMYNDVETDNITLLKDSFYMGLYQK*DYT*QYDDLIDEFMKAITDRNG*NTLI

Parental  QFEDFGNHNAFRFLRKYREKYCTFNDDIQGTAAVALAGLLAAQKVISKPISEHKILFLGAGEAALGIANL
          Q.EDFGNHNAFRFLRKY.EKY.TFNDDIQGTAA.ALAGL.A..KVISKPISEHKI.FLG.GEA.LGI.NL
Retrocopy QLEDFGNHNAFRFLRKYPEKYYTFNDDIQGTAALALAGLTAL-KVISKPISEHKIFFLGLGEATLGIGNL

Parental  IV-MSMVENGLSEEEAQKK-IWMFDKYGLLVKGRKAKIDTYQEPFTHPGPESIPETFEDAVNILKPSTII
          I...SMVE.GLSEE.AQKK.IW.FD.YG.LV.GRKAKID.YQEPFT.P.PESIP..FED.VNILK.ST.I
Retrocopy II<ISMVEKGLSEEWAQKK>IWIFDQYG*LVNGRKAKIDSYQEPFTNPVPESIPDAFEDVVNILKTSTTI

Parental  GVAGAGRLFTPDVIRAMASINERPVIFALSNPTAQAECTAEEAYTLTEGRCLFASGSPFGPVKLTDGRVF
          G.AGA..LFTPDVIR.MASINERPVIF.LSNPTA.A.CTAEEAYTLTEGRCLFASG.P..PVKLT.G.VF
Retrocopy GFAGANHLFTPDVIRDMASINERPVIFTLSNPTA*AKCTAEEAYTLTEGRCLFASGGPLEPVKLTGGQVF

Parental  TPGQGNNVYIFPGVALAVILCNTR-HISDSVFLEAAKALTSQLTDEELA
          TPGQGNNV.IFP..ALAVILCNT..HI.D.VF.EAAK.LTSQLTDEELA
Retrocopy TPGQGNNVFIFPCAALAVILCNTH<HIRDNVFPEAAKVLTSQLTDEELA

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	57.15 RPM
SRP051959_heart	0.00 RPM	64.36 RPM
SRP051959_kidney	0.00 RPM	22.96 RPM
SRP051959_liver	0.00 RPM	13.75 RPM
SRP051959_lung	0.00 RPM	34.00 RPM
SRP051959_lymph_node	0.00 RPM	49.91 RPM
SRP051959_skeletal_muscle	0.00 RPM	20.99 RPM
SRP051959_spleen	0.06 RPM	48.13 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_615 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_615 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_615 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4237
Gorilla gorilla	retro_ggor_2838
Pongo abelii	retro_pabe_3402

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001929	1 retrocopy	retro_cjac_615 ,
Callithrix jacchus	ENSCJAG00000009064	1 retrocopy	retro_cjac_2740,
Homo sapiens	ENSG00000082212	1 retrocopy	retro_hsap_4237,
Gorilla gorilla	ENSGGOG00000010823	1 retrocopy	retro_ggor_2838,
Nomascus leucogenys	ENSNLEG00000011833	1 retrocopy	retro_nleu_2307,
Pongo abelii	ENSPPYG00000009163	2 retrocopies	retro_pabe_3402, retro_pabe_3510,