RetrogeneDB ID: retro_cjac_1844

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:129980856..129981501(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAN
• Ensembl ID: ENSCJAG00000003927
• Aliases: None
• Description: RAN, member RAS oncogene family [Source:HGNC Symbol;Acc:9846]

Sequence

>retro_cjac_1844
GCCGCGATGGCTGCGCAGGGAGAGCCCCAGGTCCAGTTTAAACTTGTATTGGTTGGTGATGGTGGTACCGGAAAAACTTT
TGTTAAACGTCATTTGACTGGTGAATTTGAGAAGTATGTAGCCACCTTGGGTATTGAGGTTCATCCCCTAGTGTTCCACA
CTAACAGAGGACCTATTAAGTTCAATGTGTGGGACATGGCTGGCCAGGAGAAATTCGACGGACTGAGAGATGGCTATTAT
ATCCAAGCCCAGTGTGCCATCATGTTTGATGTAACATCCAGAGTTACTTACAAAAATGTGCCTAACTGGGATAGAGATCT
GGTGTGAGTGTGTGAGAACATCCCCATCATGTTATGTGGCAACAAAGTGTACATTAAGGACAGGAAAGTGAAGGCAAAAT
CCGTTGTCTTCCACCTAAAGAAGAATCTTCAGTACAATGACATTTCTGCCAAAAGTAACTACAACGTTGAAAAGCCCCTC
CTCTGGCTTGCTAGGAAGCTCATTGGAGACCCTAATTTGGAATTTGCTGCCATGCTTGCTCTTGCCCCACTGGAGGTTGT
CATGGACCCAGCTTTGGCAACGCGGTATGTGCACGACTTAGAGGTTGCTCAAACCACTGCTCTCGCGGATGAGGATGATG
ACCTG

Alignment

ORF - retro_cjac_1844 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.91 %
• Parental protein coverage: 99.54 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AAMAAQGEPQVQFKLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGPIKFNVWDTAG
          AAMAAQGEPQVQFKLVLVGDGGTGKT.FVKRHLTGEFEK.YVATLG.EVHPLVFHTNRGPIKFNVWD.AG
Retrocopy AAMAAQGEPQVQFKLVLVGDGGTGKT-FVKRHLTGEFEK-YVATLGIEVHPLVFHTNRGPIKFNVWDMAG

Parental  QEKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCENIPIVLCGNKVDIKDRKVKAKSIVF
          QEKF.GLRDGYYIQAQCA.IMFDVTSRVTYKNVPNW.RDLV.VCENIPI.LCGNKV.IKDRKVKAKS.VF
Retrocopy QEKFDGLRDGYYIQAQCA-IMFDVTSRVTYKNVPNWDRDLV*VCENIPIMLCGNKVYIKDRKVKAKSVVF

Parental  HRKKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAMPALAPPEVVMDPALAAQYEHDLEVAQTTA
          H.KKNLQY.DISAKSNYN.EKP.LWLARKLIGDPNLEF.AM.ALAP.EVVMDPALA..Y.HDLEVAQTTA
Retrocopy HLKKNLQYNDISAKSNYNVEKPLLWLARKLIGDPNLEFAAMLALAPLEVVMDPALATRYVHDLEVAQTTA

Parental  LPDEDDDL
          L.DEDDDL
Retrocopy LADEDDDL

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	36.54 RPM
SRP051959_heart	0.00 RPM	22.59 RPM
SRP051959_kidney	0.04 RPM	28.46 RPM
SRP051959_liver	0.04 RPM	30.19 RPM
SRP051959_lung	0.02 RPM	25.74 RPM
SRP051959_lymph_node	0.00 RPM	33.06 RPM
SRP051959_skeletal_muscle	0.00 RPM	29.68 RPM
SRP051959_spleen	0.00 RPM	28.53 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1844 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1844 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1844 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 29 parental genes, and 152 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004222	4 retrocopies	retro_amel_1119, retro_amel_1625, retro_amel_1631, retro_amel_700,
Canis familiaris	ENSCAFG00000006670	6 retrocopies	retro_cfam_1406, retro_cfam_1584, retro_cfam_1604, retro_cfam_2058, retro_cfam_426, retro_cfam_899,
Callithrix jacchus	ENSCJAG00000003927	8 retrocopies	retro_cjac_1558, retro_cjac_1844 , retro_cjac_2509, retro_cjac_2952, retro_cjac_3071, retro_cjac_3107, retro_cjac_4222, retro_cjac_492,
Dasypus novemcinctus	ENSDNOG00000009230	12 retrocopies	retro_dnov_1154, retro_dnov_1269, retro_dnov_1485, retro_dnov_1543, retro_dnov_1585, retro_dnov_1795, retro_dnov_1924, retro_dnov_1945, retro_dnov_2142, retro_dnov_2189, retro_dnov_2613, retro_dnov_991,
Equus caballus	ENSECAG00000020532	3 retrocopies	retro_ecab_195, retro_ecab_591, retro_ecab_680,
Echinops telfairi	ENSETEG00000011875	18 retrocopies	retro_etel_1051, retro_etel_1161, retro_etel_1351, retro_etel_1365, retro_etel_1584, retro_etel_1673, retro_etel_1878, retro_etel_1896, retro_etel_1915, retro_etel_2141, retro_etel_2150, retro_etel_2189, retro_etel_294, retro_etel_383, retro_etel_409, retro_etel_412, retro_etel_514, retro_etel_813,
Felis catus	ENSFCAG00000027375	6 retrocopies	retro_fcat_1097, retro_fcat_1230, retro_fcat_1297, retro_fcat_1586, retro_fcat_1904, retro_fcat_269,
Homo sapiens	ENSG00000132341	3 retrocopies	retro_hsap_3126, retro_hsap_3446, retro_hsap_4908,
Gorilla gorilla	ENSGGOG00000015340	4 retrocopies	retro_ggor_2142, retro_ggor_2328, retro_ggor_2556, retro_ggor_3066,
Loxodonta africana	ENSLAFG00000017673	1 retrocopy	retro_lafr_1253,
Microcebus murinus	ENSMICG00000000653	4 retrocopies	retro_mmur_1270, retro_mmur_669, retro_mmur_791, retro_mmur_866,
Macaca mulatta	ENSMMUG00000020927	2 retrocopies	retro_mmul_1990, retro_mmul_2641,
Monodelphis domestica	ENSMODG00000015601	8 retrocopies	retro_mdom_100, retro_mdom_1718, retro_mdom_1990, retro_mdom_543, retro_mdom_580, retro_mdom_806, retro_mdom_814, retro_mdom_969,
Mustela putorius furo	ENSMPUG00000004044	6 retrocopies	retro_mputfur_1190, retro_mputfur_1523, retro_mputfur_228, retro_mputfur_755, retro_mputfur_784, retro_mputfur_899,
Mus musculus	ENSMUSG00000029430	4 retrocopies	retro_mmus_1653, retro_mmus_182, retro_mmus_2029, retro_mmus_265,
Nomascus leucogenys	ENSNLEG00000008282	4 retrocopies	retro_nleu_1565, retro_nleu_2303, retro_nleu_2353, retro_nleu_775,
Ornithorhynchus anatinus	ENSOANG00000006447	1 retrocopy	retro_oana_62,
Oryctolagus cuniculus	ENSOCUG00000026506	2 retrocopies	retro_ocun_1139, retro_ocun_958,
Otolemur garnettii	ENSOGAG00000025046	8 retrocopies	retro_ogar_1482, retro_ogar_1611, retro_ogar_2058, retro_ogar_2560, retro_ogar_2692, retro_ogar_2810, retro_ogar_377, retro_ogar_497,
Ochotona princeps	ENSOPRG00000002629	7 retrocopies	retro_opri_1062, retro_opri_1227, retro_opri_514, retro_opri_622, retro_opri_647, retro_opri_74, retro_opri_97,
Pongo abelii	ENSPPYG00000005124	3 retrocopies	retro_pabe_2582, retro_pabe_2853, retro_pabe_3815,
Pan troglodytes	ENSPTRG00000005636	4 retrocopies	retro_ptro_1762, retro_ptro_2115, retro_ptro_2338, retro_ptro_3273,
Pteropus vampyrus	ENSPVAG00000014742	15 retrocopies	retro_pvam_1023, retro_pvam_1049, retro_pvam_1328, retro_pvam_365, retro_pvam_485, retro_pvam_597, retro_pvam_61, retro_pvam_746, retro_pvam_770, retro_pvam_863, retro_pvam_933, retro_pvam_934, retro_pvam_935, retro_pvam_948, retro_pvam_968,
Rattus norvegicus	ENSRNOG00000000938	3 retrocopies	retro_rnor_138, retro_rnor_410, retro_rnor_917,
Sarcophilus harrisii	ENSSHAG00000018018	1 retrocopy	retro_shar_538,
Sus scrofa	ENSSSCG00000009746	3 retrocopies	retro_sscr_1136, retro_sscr_194, retro_sscr_771,
Ictidomys tridecemlineatus	ENSSTOG00000003992	3 retrocopies	retro_itri_1009, retro_itri_1442, retro_itri_723,
Tursiops truncatus	ENSTTRG00000012732	6 retrocopies	retro_ttru_1481, retro_ttru_204, retro_ttru_387, retro_ttru_439, retro_ttru_792, retro_ttru_892,
Vicugna pacos	ENSVPAG00000008880	3 retrocopies	retro_vpac_436, retro_vpac_589, retro_vpac_85,