RetrogeneDB ID: retro_cjac_1068

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 13:1997318..1997917(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000010290
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000004197
• Aliases: None
• Description: 40S ribosomal protein S8 [Source:UniProtKB/TrEMBL;Acc:F6PPW3]

Sequence

>retro_cjac_1068
ATCTTTAGGGGCAACTGGCACAAGTGTGGCAAGCCTGGGGACAAGAGAAAGCCCTACCACAAGAAACAGAAATATAAGTT
GGGGCGCTGGGCTGCCAATACCAAGATTGGCCCCCAGCACATCCACACAGTCCATGTGCAGGGTGGTAACCATGCCCTGA
GACTGGACGTGGGGAATTTCTCCTGGGGCTCAGGGTGTTGTACTCAAACAAGGATCATCAATGTTGTCTATAATGAGTCT
AATAATCAGCTGGTTCGTACCAAAACCCTGGTGAAGAATTGCATCGTGCTCATCAACGGCACACCATACCAACAGTGGTA
CAAGTCCCACTGTGCACTGCCCCTGGGCCTCAAGAAGGGAGCCAAAGCTGACTCCTGAGGAAGAAGAGATTTTAAAAAAA
GATCTAAAAAGATTCAGAAGAAATACGACAAAAGGAAAAAGAATGCCAAAATCAGCAGTCTCCTGGAGCAGTTCCAGCAG
GGCAAGCTTCTCCGTGCGTGGCTTCAAGGAGGGGACAGTGTGGCTGAGCAGATGGCTCTGTGCTAGAGGGCAAAGAGTTG
GAGTTCTATCTTAGGAAAATCAAGGCTCGGATAGGCAAA

Alignment

ORF - retro_cjac_1068 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.95 %
• Parental protein coverage: 99.04 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ISRDNWHKRRKTGGKRKPYHKKRKYELGRPAANTKIGPRRIHTVRVRGGNKKYRALRLDVGNFSWGSECC
          I.R.NWHK..K.G.KRKPYHKK.KY.LGR.AANTKIGP..IHTV.V.GGN....ALRLDVGNFSWGS.CC
Retrocopy IFRGNWHKCGKPGDKRKPYHKKQKYKLGRWAANTKIGPQHIHTVHVQGGN---HALRLDVGNFSWGSGCC

Parental  TRKTRIIDVVYNASNNELVRTKTLVKNCIVLIDSTPYRQWYESHYALPLGRKKGA-KLTPEEEEILNKKR
          T..TRII.VVYN.SNN.LVRTKTLVKNCIVLI..TPY.QWY.SH.ALPLG.KKGA.KLTPEEEEIL.KK.
Retrocopy TQ-TRIINVVYNESNNQLVRTKTLVKNCIVLINGTPYQQWYKSHCALPLGLKKGA>KLTPEEEEIL-KKD

Parental  SKK-IQKKYDERKKNAKISSLLEEQFQQGKLL-ACIASRPGQCGRADGYVLEGKELEFYLRKIKARKGK
          .K..IQKKYD.RKKNAKISSLL.EQFQQGKLL..C.ASR.GQCG.ADG.VLEGKELEFYLRKIKAR.GK
Retrocopy LKR<IQKKYDKRKKNAKISSLL-EQFQQGKLL<PCVASRRGQCG*ADGSVLEGKELEFYLRKIKARIGK

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	239.34 RPM
SRP051959_heart	0.00 RPM	225.64 RPM
SRP051959_kidney	0.00 RPM	199.52 RPM
SRP051959_liver	0.00 RPM	312.58 RPM
SRP051959_lung	0.00 RPM	272.22 RPM
SRP051959_lymph_node	0.00 RPM	439.66 RPM
SRP051959_skeletal_muscle	0.00 RPM	314.27 RPM
SRP051959_spleen	0.00 RPM	381.72 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1068 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1068 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1068 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 35 parental genes, and 220 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000015697	1 retrocopy	retro_acar_124,
Ailuropoda melanoleuca	ENSAMEG00000014147	3 retrocopies	retro_amel_1883, retro_amel_373, retro_amel_972,
Bos taurus	ENSBTAG00000015285	2 retrocopies	retro_btau_1388, retro_btau_1593,
Canis familiaris	ENSCAFG00000004745	8 retrocopies	retro_cfam_1336, retro_cfam_1662, retro_cfam_1730, retro_cfam_2139, retro_cfam_2177, retro_cfam_261, retro_cfam_589, retro_cfam_791,
Choloepus hoffmanni	ENSCHOG00000008785	10 retrocopies	retro_chof_1197, retro_chof_1258, retro_chof_1466, retro_chof_1638, retro_chof_2066, retro_chof_2617, retro_chof_2633, retro_chof_274, retro_chof_331, retro_chof_951,
Callithrix jacchus	ENSCJAG00000004197	5 retrocopies	retro_cjac_1068 , retro_cjac_181, retro_cjac_3138, retro_cjac_6, retro_cjac_951,
Cavia porcellus	ENSCPOG00000000723	3 retrocopies	retro_cpor_1099, retro_cpor_335, retro_cpor_621,
Dasypus novemcinctus	ENSDNOG00000025236	3 retrocopies	retro_dnov_1717, retro_dnov_802, retro_dnov_908,
Dipodomys ordii	ENSDORG00000009287	1 retrocopy	retro_dord_429,
Echinops telfairi	ENSETEG00000004002	13 retrocopies	retro_etel_1000, retro_etel_1063, retro_etel_1201, retro_etel_147, retro_etel_1495, retro_etel_1733, retro_etel_1864, retro_etel_1941, retro_etel_2050, retro_etel_2060, retro_etel_302, retro_etel_368, retro_etel_395,
Felis catus	ENSFCAG00000022996	4 retrocopies	retro_fcat_1222, retro_fcat_200, retro_fcat_456, retro_fcat_962,
Homo sapiens	ENSG00000142937	8 retrocopies	retro_hsap_1467, retro_hsap_1536, retro_hsap_1942, retro_hsap_2034, retro_hsap_2791, retro_hsap_3158, retro_hsap_3410, retro_hsap_635,
Gorilla gorilla	ENSGGOG00000005645	5 retrocopies	retro_ggor_1127, retro_ggor_1170, retro_ggor_1357, retro_ggor_1465, retro_ggor_556,
Loxodonta africana	ENSLAFG00000027596	3 retrocopies	retro_lafr_531, retro_lafr_647, retro_lafr_904,
Macropus eugenii	ENSMEUG00000001388	1 retrocopy	retro_meug_119,
Microcebus murinus	ENSMICG00000008024	4 retrocopies	retro_mmur_1180, retro_mmur_1434, retro_mmur_1501, retro_mmur_380,
Myotis lucifugus	ENSMLUG00000001559	30 retrocopies	retro_mluc_1114, retro_mluc_1132, retro_mluc_1165, retro_mluc_1277, retro_mluc_1288, retro_mluc_1418, retro_mluc_1467, retro_mluc_1476, retro_mluc_1486, retro_mluc_1634, retro_mluc_1656, retro_mluc_1689, retro_mluc_1808, retro_mluc_1911, retro_mluc_1938, retro_mluc_2043, retro_mluc_2055, retro_mluc_2085, retro_mluc_2111, retro_mluc_2153, retro_mluc_2182, retro_mluc_2209, retro_mluc_2414, retro_mluc_460, retro_mluc_662, retro_mluc_730, retro_mluc_773, retro_mluc_820, retro_mluc_821, retro_mluc_906,
Macaca mulatta	ENSMMUG00000015270	2 retrocopies	retro_mmul_275, retro_mmul_70,
Monodelphis domestica	ENSMODG00000028389	1 retrocopy	retro_mdom_998,
Mustela putorius furo	ENSMPUG00000013485	6 retrocopies	retro_mputfur_334, retro_mputfur_337, retro_mputfur_493, retro_mputfur_780, retro_mputfur_908, retro_mputfur_986,
Mus musculus	ENSMUSG00000047675	33 retrocopies	retro_mmus_1003, retro_mmus_1067, retro_mmus_1184, retro_mmus_1694, retro_mmus_1755, retro_mmus_1796, retro_mmus_2001, retro_mmus_2002, retro_mmus_2003, retro_mmus_2031, retro_mmus_2132, retro_mmus_2173, retro_mmus_2264, retro_mmus_2732, retro_mmus_2772, retro_mmus_2847, retro_mmus_2861, retro_mmus_293, retro_mmus_2956, retro_mmus_2998, retro_mmus_3018, retro_mmus_3052, retro_mmus_3057, retro_mmus_3279, retro_mmus_3307, retro_mmus_3521, retro_mmus_364, retro_mmus_392, retro_mmus_548, retro_mmus_559, retro_mmus_596, retro_mmus_646, retro_mmus_876,
Nomascus leucogenys	ENSNLEG00000014147	1 retrocopy	retro_nleu_34,
Oryctolagus cuniculus	ENSOCUG00000012476	1 retrocopy	retro_ocun_168,
Otolemur garnettii	ENSOGAG00000006922	16 retrocopies	retro_ogar_1156, retro_ogar_1746, retro_ogar_1895, retro_ogar_2501, retro_ogar_2529, retro_ogar_2556, retro_ogar_2699, retro_ogar_2723, retro_ogar_2947, retro_ogar_308, retro_ogar_3291, retro_ogar_3436, retro_ogar_394, retro_ogar_521, retro_ogar_730, retro_ogar_805,
Pongo abelii	ENSPPYG00000001426	1 retrocopy	retro_pabe_147,
Pan troglodytes	ENSPTRG00000000659	1 retrocopy	retro_ptro_30,
Pteropus vampyrus	ENSPVAG00000009859	10 retrocopies	retro_pvam_1285, retro_pvam_1315, retro_pvam_1345, retro_pvam_403, retro_pvam_419, retro_pvam_463, retro_pvam_514, retro_pvam_578, retro_pvam_685, retro_pvam_991,
Rattus norvegicus	ENSRNOG00000018768	2 retrocopies	retro_rnor_222, retro_rnor_235,
Sorex araneus	ENSSARG00000000899	1 retrocopy	retro_sara_462,
Sarcophilus harrisii	ENSSHAG00000000111	5 retrocopies	retro_shar_408, retro_shar_472, retro_shar_480, retro_shar_636, retro_shar_667,
Sus scrofa	ENSSSCG00000003930	4 retrocopies	retro_sscr_353, retro_sscr_550, retro_sscr_607, retro_sscr_919,
Ictidomys tridecemlineatus	ENSSTOG00000006322	3 retrocopies	retro_itri_1337, retro_itri_1380, retro_itri_750,
Tupaia belangeri	ENSTBEG00000000418	20 retrocopies	retro_tbel_1066, retro_tbel_1537, retro_tbel_1538, retro_tbel_163, retro_tbel_1699, retro_tbel_2356, retro_tbel_244, retro_tbel_2580, retro_tbel_3058, retro_tbel_3230, retro_tbel_3478, retro_tbel_3905, retro_tbel_3950, retro_tbel_4241, retro_tbel_4250, retro_tbel_4530, retro_tbel_552, retro_tbel_803, retro_tbel_827, retro_tbel_934,
Tarsius syrichta	ENSTSYG00000005525	5 retrocopies	retro_tsyr_1412, retro_tsyr_1507, retro_tsyr_2176, retro_tsyr_552, retro_tsyr_734,
Tursiops truncatus	ENSTTRG00000003388	4 retrocopies	retro_ttru_1839, retro_ttru_282, retro_ttru_300, retro_ttru_344,