RetrogeneDB ID: retro_cjac_2539

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 5:81064614..81064945(+)
• Located in intron of: ENSCJAG00000019846

Retrocopy information

• Ensembl ID: ENSCJAG00000019851
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPLP2
• Ensembl ID: ENSCJAG00000011838
• Aliases: None
• Description: ribosomal protein, large, P2 [Source:HGNC Symbol;Acc:10377]

Sequence

>retro_cjac_2539
ATGTGCTACGTCGTCTCCCACCTGCTTGCTGCCCTCGGAGGCAACCCCTCCCCCAGCGCCAAGGACAAGAGGATCCTGGA
CAGCGTAGGCATTAAGGCGGACGACGACCAGCTCAACAAGGTTATCAGTGAGCTGAATGGAAAAAGCATCGAAGATGTCA
TTGCCCAGGGTATTGGCAAGCTTGCCAGTGTACCTGCCGGTGGGGCTGTGGCTGTCTCTGCTGCCCCAGGCTCTGCAGCT
CCTGCTGCTGGTTCCACCCCCGATGCAGCAGAGGAGAAGATGAGGAGGAGTGTCCAAAGAGTCAGAGGATGACACGGGAT
TTGACCTCTTT

Alignment

ORF - retro_cjac_2539 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80. %
• Parental protein coverage: 99.13 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MRYVASYLLAALGGNPSPSAKDIKKILDSVGIEADDDRLNKVISELNGKNIEDVIAQGIGKLASVPAGGA
          M.YV.S.LLAALGGNPSPSAKD.K.ILDSVGI.ADDD.LNKVISELNGK.IEDVIAQGIGKLASVPAGGA
Retrocopy MCYVVSHLLAALGGNPSPSAKD-KRILDSVGIKADDDQLNKVISELNGKSIEDVIAQGIGKLASVPAGGA

Parental  VAISAAPGSAAPAAGSAPAAAEEKKDEK-KEESEESDDDMGFGLF
          VA.SAAPGSAAPAAGS.P.AAEEK.......ESE...DD.GF.LF
Retrocopy VAVSAAPGSAAPAAGSTPDAAEEKMRRS>SKESE---DDTGFDLF

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	56.29 RPM
SRP051959_heart	0.00 RPM	48.41 RPM
SRP051959_kidney	0.00 RPM	50.56 RPM
SRP051959_liver	0.00 RPM	57.68 RPM
SRP051959_lung	0.02 RPM	68.44 RPM
SRP051959_lymph_node	0.00 RPM	125.31 RPM
SRP051959_skeletal_muscle	0.04 RPM	72.76 RPM
SRP051959_spleen	0.00 RPM	70.78 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2539 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2539 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2539 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1777
Pan troglodytes	retro_ptro_1189
Gorilla gorilla	retro_ggor_2238
Pongo abelii	retro_pabe_1537

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006935	1 retrocopy	retro_amel_197,
Bos taurus	ENSBTAG00000001777	2 retrocopies	retro_btau_117, retro_btau_1399,
Canis familiaris	ENSCAFG00000009523	1 retrocopy	retro_cfam_18,
Ciona intestinalis	ENSCING00000000626	1 retrocopy	retro_cint_34,
Callithrix jacchus	ENSCJAG00000011838	6 retrocopies	retro_cjac_2399, retro_cjac_2497, retro_cjac_2539 , retro_cjac_2745, retro_cjac_3097, retro_cjac_3859,
Echinops telfairi	ENSETEG00000010240	4 retrocopies	retro_etel_1206, retro_etel_1458, retro_etel_1640, retro_etel_455,
Felis catus	ENSFCAG00000008417	1 retrocopy	retro_fcat_860,
Macaca mulatta	ENSMMUG00000020627	2 retrocopies	retro_mmul_221, retro_mmul_311,
Mustela putorius furo	ENSMPUG00000009049	1 retrocopy	retro_mputfur_254,
Nomascus leucogenys	ENSNLEG00000026860	5 retrocopies	retro_nleu_1948, retro_nleu_2144, retro_nleu_2296, retro_nleu_2762, retro_nleu_85,
Otolemur garnettii	ENSOGAG00000016296	2 retrocopies	retro_ogar_156, retro_ogar_275,
Rattus norvegicus	ENSRNOG00000002116	3 retrocopies	retro_rnor_257, retro_rnor_320, retro_rnor_388,
Sarcophilus harrisii	ENSSHAG00000001056	1 retrocopy	retro_shar_321,
Sus scrofa	ENSSSCG00000012842	1 retrocopy	retro_sscr_54,