RetrogeneDB ID: retro_cjac_2139

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:52588739..52589205(+)
• Located in intron of: ENSCJAG00000003060

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL14
• Ensembl ID: ENSCJAG00000017884
• Aliases: None
• Description: ribosomal protein L14 [Source:HGNC Symbol;Acc:10305]

Sequence

>retro_cjac_2139
GATTTCATCCTCAAGTTTCCAAACAGTGCCCCCAGAAGTATGTCCAACAAGCCTGGCAGAAGGTAAACATTAGTACAAAA
TGAGCAGCCACACAGTGGGCCAAGAATATTGAAGCCAGAGAAGGGAAAGCCAAGATGATAGATTTTGATCATTTTAAAGT
TATGAAGGCAAAGAAAATGAGGAACAAAATAATCAAGAATGAAGTTAAGAAGCCTCAAAAGGCAGCTCTCCTGTAAGCTT
CTCCCAAAAAACGTCCTGCCATGAAGGGTGCAGCTGCTGCTGTTAAAGTTCTAGCAAAAAACAAACAAGCCAAACAAAAA
CGACCTCTGCGGGCAAGAAGGCCCCAGCTCAGAAGGTTCCTGTCCAGAAAGCCACAGGCCAGAAGGCAGCACCTCCTCCA
AGAGCTCAGAAGGGTCAAAAATCTCCAGCCCAGAAAGCACCTGCTCCAAAAGCATTTGGCAAGAAA

Alignment

ORF - retro_cjac_2139 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.96 %
• Parental protein coverage: 72.56 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DFILKFPHSAR-QKYVRQAWQKADINTKWAATRWAKKIEAREKKAKMTDFDRFKVMKAKKMRNRIIKNEV
          DFILKFP.SA..QKYV.QAWQK..I.TK.AAT.WAK.IEARE.KAKM.DFD.FKVMKAKKMRN.IIKNEV
Retrocopy DFILKFPNSAP<QKYVQQAWQKVNISTK*AATQWAKNIEAREGKAKMIDFDHFKVMKAKKMRNKIIKNEV

Parental  KKLQKAALLKASPKKAPAAKAAAAAAAQVPAK-KMTAAGKRAPAQK-ATGQKAPAQKATGQKAAPAPKAE
          KK.QKAALL.ASPKK.PA.K..AAAA..V.AK.K.T...K...A.K.A..QK.P.QKATGQKAAP.P.A.
Retrocopy KKPQKAALL*ASPKKRPAMK-GAAAAVKVLAK<KQTSQTKTTSAGKKAPAQKVPVQKATGQKAAPPPRAQ

Parental  KGQKAPAKKAPAPKASGKK
          KGQK.PA.KAPAPKA.GKK
Retrocopy KGQKSPAQKAPAPKAFGKK

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	0.13 RPM	106.63 RPM
SRP051959_heart	0.00 RPM	111.64 RPM
SRP051959_kidney	0.02 RPM	140.06 RPM
SRP051959_liver	0.00 RPM	135.51 RPM
SRP051959_lung	0.00 RPM	168.58 RPM
SRP051959_lymph_node	0.00 RPM	249.78 RPM
SRP051959_skeletal_muscle	0.00 RPM	92.46 RPM
SRP051959_spleen	0.00 RPM	202.94 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2139 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2139 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2139 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3104
Pan troglodytes	retro_ptro_2100

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Parental genes homology:

Parental genes homology involve 26 parental genes, and 87 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001709	4 retrocopies	retro_amel_1876, retro_amel_1933, retro_amel_296, retro_amel_660,
Canis familiaris	ENSCAFG00000005138	1 retrocopy	retro_cfam_31,
Callithrix jacchus	ENSCJAG00000017884	9 retrocopies	retro_cjac_1249, retro_cjac_1393, retro_cjac_1835, retro_cjac_2138, retro_cjac_2139 , retro_cjac_2332, retro_cjac_2797, retro_cjac_3240, retro_cjac_630,
Cavia porcellus	ENSCPOG00000000711	1 retrocopy	retro_cpor_529,
Equus caballus	ENSECAG00000026813	2 retrocopies	retro_ecab_377, retro_ecab_743,
Echinops telfairi	ENSETEG00000012894	6 retrocopies	retro_etel_2117, retro_etel_2155, retro_etel_251, retro_etel_315, retro_etel_356, retro_etel_387,
Felis catus	ENSFCAG00000015655	4 retrocopies	retro_fcat_1000, retro_fcat_1457, retro_fcat_587, retro_fcat_671,
Homo sapiens	ENSG00000188846	6 retrocopies	retro_hsap_1015, retro_hsap_1047, retro_hsap_2796, retro_hsap_3104, retro_hsap_3352, retro_hsap_4777,
Gorilla gorilla	ENSGGOG00000025958	3 retrocopies	retro_ggor_122, retro_ggor_1945, retro_ggor_2272,
Latimeria chalumnae	ENSLACG00000015639	1 retrocopy	retro_lcha_29,
Microcebus murinus	ENSMICG00000009217	4 retrocopies	retro_mmur_1218, retro_mmur_1352, retro_mmur_279, retro_mmur_3,
Myotis lucifugus	ENSMLUG00000014429	4 retrocopies	retro_mluc_1294, retro_mluc_2263, retro_mluc_420, retro_mluc_563,
Monodelphis domestica	ENSMODG00000015262	2 retrocopies	retro_mdom_1499, retro_mdom_1939,
Mustela putorius furo	ENSMPUG00000017961	1 retrocopy	retro_mputfur_90,
Mus musculus	ENSMUSG00000025794	3 retrocopies	retro_mmus_2904, retro_mmus_2929, retro_mmus_3011,
Nomascus leucogenys	ENSNLEG00000005682	2 retrocopies	retro_nleu_763, retro_nleu_918,
Oryctolagus cuniculus	ENSOCUG00000010309	3 retrocopies	retro_ocun_410, retro_ocun_464, retro_ocun_656,
Pan troglodytes	ENSPTRG00000011963	4 retrocopies	retro_ptro_1893, retro_ptro_2100, retro_ptro_2135, retro_ptro_713,
Pteropus vampyrus	ENSPVAG00000013914	7 retrocopies	retro_pvam_1108, retro_pvam_1413, retro_pvam_246, retro_pvam_446, retro_pvam_683, retro_pvam_903, retro_pvam_904,
Rattus norvegicus	ENSRNOG00000019007	4 retrocopies	retro_rnor_2268, retro_rnor_2620, retro_rnor_415, retro_rnor_591,
Sorex araneus	ENSSARG00000003974	2 retrocopies	retro_sara_349, retro_sara_504,
Sarcophilus harrisii	ENSSHAG00000001591	5 retrocopies	retro_shar_397, retro_shar_539, retro_shar_696, retro_shar_737, retro_shar_788,
Sus scrofa	ENSSSCG00000011272	2 retrocopies	retro_sscr_521, retro_sscr_63,
Tarsius syrichta	ENSTSYG00000002161	5 retrocopies	retro_tsyr_1036, retro_tsyr_1404, retro_tsyr_176, retro_tsyr_361, retro_tsyr_956,
Tursiops truncatus	ENSTTRG00000006708	1 retrocopy	retro_ttru_113,
Xenopus tropicalis	ENSXETG00000022018	1 retrocopy	retro_xtro_3,