RetrogeneDB ID: retro_cjac_2230

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:39463638..39464526(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000002016
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MRPL15
• Ensembl ID: ENSCJAG00000016719
• Aliases: None
• Description: mitochondrial ribosomal protein L15 [Source:HGNC Symbol;Acc:14054]

Sequence

>retro_cjac_2230
ATGGCCGGTCCTTTGCAGGGCGTAGGTCCGGGGCCCTGGATCTACTCCGGGACCTGCCACGTGTGAGCCTGACCAACTTA
AAGCCGAATCCCAGCTCCAGGAAACCGGAGAGGCGACCAAGAGGTCGGAGAAGAGGTAGAAAATGTGGCAGAGGCCACAA
AGGAGAAAGGCAAAGAGGAACCCGGCCTCGTCTGGGCTTTGAGGAAGGCCAGAATCCATTTTACATCCAAATCCCAAAAT
ACAGGTTTAAAAGAAGGACATAGCTTCAGATGCCAGTATAAGTCTTTGAGTCTCAATAGACTGCAGTATCTTATTGATTT
GGGTCGTGTTGAACCTACTAAACCTATTGACTTAACCCAGCTTGTCAATGGGAGAGGTGTGACCATCCAGCCACTTAAAA
GAGATTATGGTGTCCAGCTGGTAGAGGAGGGTGCAGACACCTTTACAGCGAAAGTTAATATTGAAGTACAGTTGGCTTCA
GAACTAGCTATTGCTCCAATTGAAAAACATGGTGGTGGTGTTACTACAGCCTTCTATGATCCAAGAAGTCTAGACATTGT
ATGCAAACCATTTCCATTCTTTCTTCGTGGACAACCCATTCCAAAAAGAATGCTTCCACCAGAAGAACTGGTACCGTATT
ACACCGATACAAAGAATCGTGGATATCTGGCAGATCCTGCCAAATTTCCTGAAGCGCGACTTGAACTTGCCAGGAAGTAC
GGTTACATCTTACCCGATATCACTAAAGATGAACTCTTCAAAATGCTCTGTACTAGGAAGGATCCAAGGCAGATTTTCTT
TGGTCTTGCTCCAGGATGGGTGGTGAATATGGCCAATAAGAAAATCCTGAAACCTGTACATGAAAATCTCCTCAAGTATT
ACAGCTCC

Alignment

ORF - retro_cjac_2230 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.28 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAGPLQG-GRSRALDLLRDLPRVSLANLKPNPGSRKPERRPRGRRRGRKCGRGHKGERQRGTRPRLGFEG
          MAGPLQG..RS.ALDLLRDLPRVSL.NLKPNP.SRKPERRPRGRRRGRKCGRGHKGERQRGTRPRLGFE.
Retrocopy MAGPLQG<RRSGALDLLRDLPRVSLTNLKPNPSSRKPERRPRGRRRGRKCGRGHKGERQRGTRPRLGFEE

Parental  GQTPFYIRIPKY-GFNEGHSFRRQYKPLSLNRLQYLIDLGRVDPTQPIDLTQLVNGRGVTIQPLKRDYGV
          GQ.PFYI.IPKY.G..EGHSFR.QYK.LSLNRLQYLIDLGRV.PT.PIDLTQLVNGRGVTIQPLKRDYGV
Retrocopy GQNPFYIQIPKY>GLKEGHSFRCQYKSLSLNRLQYLIDLGRVEPTKPIDLTQLVNGRGVTIQPLKRDYGV

Parental  QLVEEGADTFTAKVNIEVQLASELAIAAIEKNGGVVTTAFYDPRSLDIVCKPVPFFLRGQPIPKRMLPPE
          QLVEEGADTFTAKVNIEVQLASELAIA.IEK.GG.VTTAFYDPRSLDIVCKP.PFFLRGQPIPKRMLPPE
Retrocopy QLVEEGADTFTAKVNIEVQLASELAIAPIEKHGGGVTTAFYDPRSLDIVCKPFPFFLRGQPIPKRMLPPE

Parental  ELVPYYTDAKNRGYLADPAKVPEARLELARKYGYILPDITKDELFKMLCTRKDPRQIFFGLAPGWVVNMA
          ELVPYYTD.KNRGYLADPAK.PEARLELARKYGYILPDITKDELFKMLCTRKDPRQIFFGLAPGWVVNMA
Retrocopy ELVPYYTDTKNRGYLADPAKFPEARLELARKYGYILPDITKDELFKMLCTRKDPRQIFFGLAPGWVVNMA

Parental  DKKILKPVDENLLKYYSS
          .KKILKPV.ENLLKYYSS
Retrocopy NKKILKPVHENLLKYYSS

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	9.85 RPM
SRP051959_heart	0.00 RPM	8.91 RPM
SRP051959_kidney	0.04 RPM	18.44 RPM
SRP051959_liver	0.02 RPM	11.50 RPM
SRP051959_lung	0.00 RPM	3.68 RPM
SRP051959_lymph_node	0.00 RPM	4.57 RPM
SRP051959_skeletal_muscle	0.00 RPM	12.73 RPM
SRP051959_spleen	0.00 RPM	5.13 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2230 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2230 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2230 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001174	1 retrocopy	retro_btau_324,
Canis familiaris	ENSCAFG00000006988	2 retrocopies	retro_cfam_1573, retro_cfam_511,
Choloepus hoffmanni	ENSCHOG00000005299	3 retrocopies	retro_chof_1379, retro_chof_1719, retro_chof_746,
Callithrix jacchus	ENSCJAG00000016719	1 retrocopy	retro_cjac_2230 ,
Dasypus novemcinctus	ENSDNOG00000017664	1 retrocopy	retro_dnov_364,
Erinaceus europaeus	ENSEEUG00000001454	2 retrocopies	retro_eeur_128, retro_eeur_707,
Echinops telfairi	ENSETEG00000001724	1 retrocopy	retro_etel_1304,
Mustela putorius furo	ENSMPUG00000010533	1 retrocopy	retro_mputfur_149,
Mus musculus	ENSMUSG00000033845	2 retrocopies	retro_mmus_1709, retro_mmus_3534,
Ornithorhynchus anatinus	ENSOANG00000007286	1 retrocopy	retro_oana_114,
Otolemur garnettii	ENSOGAG00000003768	1 retrocopy	retro_ogar_534,
Ochotona princeps	ENSOPRG00000000921	2 retrocopies	retro_opri_241, retro_opri_364,
Rattus norvegicus	ENSRNOG00000008566	2 retrocopies	retro_rnor_1344, retro_rnor_2785,
Sus scrofa	ENSSSCG00000030578	1 retrocopy	retro_sscr_617,
Tarsius syrichta	ENSTSYG00000014106	1 retrocopy	retro_tsyr_37,
Tursiops truncatus	ENSTTRG00000011844	2 retrocopies	retro_ttru_1139, retro_ttru_733,