RetrogeneDB ID: retro_cjac_2495

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 5:1031013..1031305(+)
• Located in intron of: ENSCJAG00000017428

Retrocopy information

• Ensembl ID: ENSCJAG00000017471
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPL37
• Ensembl ID: ENSCJAG00000007388
• Aliases: None
• Description: ribosomal protein L37 [Source:HGNC Symbol;Acc:10347]

Sequence

>retro_cjac_2495
ATGACGAAGGGAACATCATTGTTTGGGAAGCGTCGTAATAAGACACACACGTTGTGCCGCCGTTGTGGCTCTAAGGCCTA
CCACCTTCAGAAGTTGACCTGCGGCAAATGTGGCTACCCTGCCAAGCGCAAGAGAAAGTATAACTGGGGTGCCAAGGCTA
AAAGACGAAATACCACCAGGACTGGTCGAATGAGGTACCTAAAAAATTGCATACCGCAGATTCAGGCACGGATTCCATGA
AGGAACAACACCTAAACCCAAAAAGGCAGCTGTTGCAGCATCTAGTTCATCT

Alignment

ORF - retro_cjac_2495 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.82 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTKGTSSFGKRRNKTHTLCRRCGSKAYHLQKSTCGKCGYPAKRKRKYNWSAKAKRRNTTGTGRMRHL-KI
          MTKGTS.FGKRRNKTHTLCRRCGSKAYHLQK.TCGKCGYPAKRKRKYNW.AKAKRRNTT.TGRMR.L.KI
Retrocopy MTKGTSLFGKRRNKTHTLCRRCGSKAYHLQKLTCGKCGYPAKRKRKYNWGAKAKRRNTTRTGRMRYL>KI

Parental  VYRRFRHGFREGTTPKPKRAAVAASSSS
          .YRRFRHGF.EGTTPKPK.AAVAASSSS
Retrocopy AYRRFRHGFHEGTTPKPKKAAVAASSSS

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	0.29 RPM	80.81 RPM
SRP051959_heart	0.09 RPM	63.02 RPM
SRP051959_kidney	0.29 RPM	67.29 RPM
SRP051959_liver	0.04 RPM	119.20 RPM
SRP051959_lung	0.08 RPM	89.99 RPM
SRP051959_lymph_node	0.00 RPM	146.30 RPM
SRP051959_skeletal_muscle	0.00 RPM	83.77 RPM
SRP051959_spleen	0.02 RPM	117.37 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2495 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2495 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2495 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 205 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015424	14 retrocopies	retro_amel_1101, retro_amel_1370, retro_amel_1461, retro_amel_1603, retro_amel_167, retro_amel_181, retro_amel_1824, retro_amel_207, retro_amel_237, retro_amel_277, retro_amel_701, retro_amel_888, retro_amel_910, retro_amel_916,
Bos taurus	ENSBTAG00000005142	6 retrocopies	retro_btau_1430, retro_btau_1502, retro_btau_1575, retro_btau_1670, retro_btau_181, retro_btau_243,
Callithrix jacchus	ENSCJAG00000007388	10 retrocopies	retro_cjac_107, retro_cjac_1443, retro_cjac_169, retro_cjac_2091, retro_cjac_2443, retro_cjac_247, retro_cjac_2495 , retro_cjac_2654, retro_cjac_2956, retro_cjac_332,
Equus caballus	ENSECAG00000026905	5 retrocopies	retro_ecab_323, retro_ecab_354, retro_ecab_411, retro_ecab_420, retro_ecab_896,
Echinops telfairi	ENSETEG00000003463	23 retrocopies	retro_etel_1003, retro_etel_1030, retro_etel_118, retro_etel_1195, retro_etel_1317, retro_etel_132, retro_etel_1414, retro_etel_1506, retro_etel_1664, retro_etel_1717, retro_etel_1832, retro_etel_1920, retro_etel_201, retro_etel_300, retro_etel_311, retro_etel_360, retro_etel_484, retro_etel_501, retro_etel_572, retro_etel_66, retro_etel_727, retro_etel_732, retro_etel_763,
Gorilla gorilla	ENSGGOG00000003241	19 retrocopies	retro_ggor_1002, retro_ggor_1100, retro_ggor_1452, retro_ggor_1488, retro_ggor_1558, retro_ggor_1643, retro_ggor_1670, retro_ggor_2025, retro_ggor_2169, retro_ggor_2246, retro_ggor_2256, retro_ggor_2436, retro_ggor_2629, retro_ggor_2660, retro_ggor_2909, retro_ggor_362, retro_ggor_490, retro_ggor_718, retro_ggor_769,
Latimeria chalumnae	ENSLACG00000002787	1 retrocopy	retro_lcha_6,
Loxodonta africana	ENSLAFG00000030052	13 retrocopies	retro_lafr_1101, retro_lafr_1123, retro_lafr_1125, retro_lafr_1136, retro_lafr_215, retro_lafr_374, retro_lafr_448, retro_lafr_507, retro_lafr_532, retro_lafr_619, retro_lafr_775, retro_lafr_985, retro_lafr_986,
Macropus eugenii	ENSMEUG00000011938	3 retrocopies	retro_meug_1060, retro_meug_1633, retro_meug_255,
Macaca mulatta	ENSMMUG00000023807	6 retrocopies	retro_mmul_1602, retro_mmul_1672, retro_mmul_206, retro_mmul_329, retro_mmul_976, retro_mmul_997,
Monodelphis domestica	ENSMODG00000020301	3 retrocopies	retro_mdom_130, retro_mdom_1843, retro_mdom_942,
Mus musculus	ENSMUSG00000041841	28 retrocopies	retro_mmus_1333, retro_mmus_1360, retro_mmus_1425, retro_mmus_1560, retro_mmus_1717, retro_mmus_1732, retro_mmus_1804, retro_mmus_1813, retro_mmus_2067, retro_mmus_2379, retro_mmus_2385, retro_mmus_2513, retro_mmus_2559, retro_mmus_2575, retro_mmus_2691, retro_mmus_2811, retro_mmus_2838, retro_mmus_3090, retro_mmus_3222, retro_mmus_3343, retro_mmus_3345, retro_mmus_3364, retro_mmus_3455, retro_mmus_3493, retro_mmus_3503, retro_mmus_3504, retro_mmus_3674, retro_mmus_438,
Oryctolagus cuniculus	ENSOCUG00000029674	11 retrocopies	retro_ocun_1063, retro_ocun_1269, retro_ocun_1476, retro_ocun_1491, retro_ocun_1514, retro_ocun_1870, retro_ocun_295, retro_ocun_683, retro_ocun_771, retro_ocun_879, retro_ocun_956,
Otolemur garnettii	ENSOGAG00000034300	7 retrocopies	retro_ogar_127, retro_ogar_1308, retro_ogar_1662, retro_ogar_1667, retro_ogar_2670, retro_ogar_662, retro_ogar_76,
Procavia capensis	ENSPCAG00000007672	5 retrocopies	retro_pcap_252, retro_pcap_270, retro_pcap_349, retro_pcap_436, retro_pcap_53,
Pteropus vampyrus	ENSPVAG00000000921	8 retrocopies	retro_pvam_1048, retro_pvam_1070, retro_pvam_1478, retro_pvam_315, retro_pvam_49, retro_pvam_738, retro_pvam_803, retro_pvam_844,
Rattus norvegicus	ENSRNOG00000012538	6 retrocopies	retro_rnor_171, retro_rnor_181, retro_rnor_220, retro_rnor_246, retro_rnor_321, retro_rnor_325,
Sarcophilus harrisii	ENSSHAG00000013969	4 retrocopies	retro_shar_295, retro_shar_350, retro_shar_395, retro_shar_715,
Sus scrofa	ENSSSCG00000025883	5 retrocopies	retro_sscr_1004, retro_sscr_1220, retro_sscr_1221, retro_sscr_767, retro_sscr_872,
Tarsius syrichta	ENSTSYG00000006208	21 retrocopies	retro_tsyr_1113, retro_tsyr_1206, retro_tsyr_144, retro_tsyr_1722, retro_tsyr_1893, retro_tsyr_1969, retro_tsyr_201, retro_tsyr_216, retro_tsyr_296, retro_tsyr_307, retro_tsyr_324, retro_tsyr_356, retro_tsyr_426, retro_tsyr_53, retro_tsyr_572, retro_tsyr_682, retro_tsyr_744, retro_tsyr_783, retro_tsyr_829, retro_tsyr_86, retro_tsyr_914,
Tursiops truncatus	ENSTTRG00000010926	7 retrocopies	retro_ttru_1712, retro_ttru_1905, retro_ttru_191, retro_ttru_242, retro_ttru_425, retro_ttru_828, retro_ttru_970,