RetrogeneDB ID: retro_cjac_2129

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:28464583..28465565(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPS5
• Ensembl ID: ENSCJAG00000018942
• Aliases: None
• Description: None

Sequence

>retro_cjac_2129
ACTGTAGATGAGCTGTAGAAAGGTGCTTTAGCAGAGACTGGTGCTGGAGCAAAAAAAGGAAGAGGCAACAGAACTAAAAA
GAAGAGAAGAAAGGATTTGAACAGGGGTCAGATCATCACTGAACGGCATTATGGTTTCTGTGGCCTGGTTTGAGTGTCCC
TCTTATTAAAAATGGAGCAGTACAGATCATTGCCCCAAAGAAACAAGGAAGAGCAGGAGGAGGAGGCCAACATGACCCAG
CAGAGAGAAGAATGGAACCAGACGAGGTAGATGAAGATTGAATGAGAGTGAGGATGGAGTGGAAACTTGTGAGGTGGCAT
CAATCATAGCCCCCCCCACCACCTTGGTTTCAACAGAGAAACATATGGTAATTTTGATACCAGGATACTTGAAGTAGCAA
ATGTTTACAATAGGACAGCAAAAGAGGAAAGAGACTGATAGGTGTTCAGGAGGCTGTGGGGAATGGAGCTTTAAGTTTTG
CTGTTGGGAAAGCCATTAACAGATAGATGCTTTCAGAAAAGCAAAGAACAGAGCAACTCACTATTTACATTTTTAGAATA
ATATGAAGACCAGACAATATTCCATGACATTTCATTCAGATTTAAAAGCAGGCATATCAAGATGAAGAAACAACCCAGAG
GTTATGCTCTCCAGGGCCACAGGGCCATCATCATCATATGCCAGCTCACTGGCATCAAAGACATGTATCCCAAGGTCTCT
GGGTCCATCAATATGCTCCCCTTCACCTGGGGCCTCTCCCATGAGATCTCAGTCAGGAAACCCATCAGCAGCTGGCAGGT
AAGAAGGGTCTCCACGTTGTGGAGTTCCAGGAGGAATGTGGGCCTCTGACTATCATGGCTGCCTTCCCAGAGGGACCTTG
AAAAAGGAGCCAGGTGATGAGGTTCCACGCATCAAACTGGACTTGAAAGAAGTGAATGCTCTACAGGCAATGTAGTGCTC
TACGTGGTCAGGTTTATAGAGA

Alignment

ORF - retro_cjac_2129 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.2 %
• Parental protein coverage: 77.67 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  TAGELWKGALAETGAGTRKGRGKRTKKKKRKDLNRGQIIGEGQCGF-LWPGLNVPLMKNGAVQTIA-QRS
          T..EL.KGALAETGAG..KGRG.RTKKK.RKDLNRGQII.E...GF.LWPGL.VPL.KNGAVQ.IA.QR.
Retrocopy TVDEL*KGALAETGAGAKKGRGNRTKKKRRKDLNRGQIITERHYGF<LWPGLSVPLIKNGAVQIIA>QRN

Parental  KEEQEKVEADMIQQREEWDRRRKMKVKRERGWSGRSWGGVSLGPPDP-GPNGETYEDFDTRILEVRNVFS
          KEEQE..EA.M.QQREEW...R.MK...E.GWSG...GG....PP...G.N.ETY..FDTRILEV.NV..
Retrocopy KEEQEE-EANMTQQREEWNQTR*MKIE*E*GWSGNL*GGINHSPPHHLGFNRETYGNFDTRILEVANVYN

Parental  MTA-KEGRKKSVRVLVAVGNGRGAAGFALGKATDR-LDAFRKAKNRAVHYLHY-IERYEDHTIFHDISLR
          .TA.K.G.K....V..AVGNG..A..FA.GKA..R..DAFRKAKNRA.HYLH...E.YED.TIFHDIS.R
Retrocopy RTA<KRG-KRLIGVQEAVGNG--ALSFAVGKAINR<IDAFRKAKNRATHYLHF<LE*YEDQTIFHDISFR

Parental  YKRTHIKMKKQPKGYGLRCHRAIITICRLIGIKDMYAKVSGSLNMLNLTRGLFHGLS-RQETHQQLADKK
          .K..HIKMKKQP.GY.L..HRAII.IC.L.GIKDMY.KVSGS.NML..T.GL.H..S..QETHQQLA.KK
Retrocopy FKSRHIKMKKQPRGYALQGHRAIIIICQLTGIKDMYPKVSGSINMLPFTWGLSHEIS<SQETHQQLAGKK

Parental  GLHVVEIREECGPLPIVVA-SPRGALSKDPEPDDEVPDIKLDWQDVKTAQGIKGSVWSNLKR
          GLHVVE..EECGPL.I..A..PRG.L.K..EP.DEVP.IKLD...V...Q....S.WS.L.R
Retrocopy GLHVVEFQEECGPLTIMAA<LPRGTLKK--EPGDEVPRIKLDLKEVNALQAM*CSTWSGL*R

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	12.74 RPM
SRP051959_heart	0.00 RPM	20.15 RPM
SRP051959_kidney	0.00 RPM	17.68 RPM
SRP051959_liver	0.00 RPM	19.08 RPM
SRP051959_lung	0.00 RPM	16.79 RPM
SRP051959_lymph_node	0.00 RPM	13.58 RPM
SRP051959_skeletal_muscle	0.00 RPM	14.02 RPM
SRP051959_spleen	0.00 RPM	12.86 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2129 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2129 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2129 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3116
Pan troglodytes	retro_ptro_2107
Gorilla gorilla	retro_ggor_2139
Pongo abelii	retro_pabe_2574

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018942	1 retrocopy	retro_cjac_2129 ,
Homo sapiens	ENSG00000144029	1 retrocopy	retro_hsap_3116,
Gorilla gorilla	ENSGGOG00000001750	1 retrocopy	retro_ggor_2139,
Microcebus murinus	ENSMICG00000007318	1 retrocopy	retro_mmur_565,
Macaca mulatta	ENSMMUG00000016239	2 retrocopies	retro_mmul_2110, retro_mmul_2251,
Mus musculus	ENSMUSG00000027374	1 retrocopy	retro_mmus_2014,
Nomascus leucogenys	ENSNLEG00000000002	1 retrocopy	retro_nleu_1438,
Pongo abelii	ENSPPYG00000012051	1 retrocopy	retro_pabe_2574,
Pan troglodytes	ENSPTRG00000012209	1 retrocopy	retro_ptro_2107,