RetrogeneDB ID: retro_cjac_2189

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:140744161..140744700(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000016671
• Aliases: None
• Description: None

Sequence

>retro_cjac_2189
ATGGGGAACATCTTCGACAACCTCTTCAAGGGCCTTTTTGGCAAAAAAGAAATGTGCATCCTCATGGTGGGCCTGGATGC
TGCGGGAAGACCACATCCTGTACAAGCTTAAACTACGCGAGATCGTGACCACCATTCCCACCATAGGCTTAAACGTGGAA
ACCGTGGAATACAAGAACATCGGCTTCACTGTGTGGGACGTGGGTGGCCAGGACCAGATCCCGCCTCTGTGACGCCACTA
TTTCCAAAACACACAAGGCCTGATCTTCGTGGTGGATGACAATGAAAGAGAGTGCATGAGGGAGGCCAGTGAGGCGCTCT
TGAGGATGCTGGCCGAGGACGAGCTCCTTGATGCTGTCCCCTGGTGTCCGCCAAAAAGCAGGACCTCCCCAATGCCATGA
ATGCGGCCGAGATCACAGACAAGCTGAGGCTGCATTCCCTACGCCACAGGAACTGGTACATTCAGGCCACCTGCGCCACC
AGCGGCGACGGGCTCTCTGAAGGACTGGACTAGCTGTCAATCAGCTCCGGAACCAGAAG

Alignment

ORF - retro_cjac_2189 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.41 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MGNIFANLFKGLFGKKEMRILMVGLDAAG-KTT-ILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDV
          MGNIF.NLFKGLFGKKEM.ILMVGLDAAG.KTT.ILYKLKL.EIVTTIPTIG.NVETVEYKNI.FTVWDV
Retrocopy MGNIFDNLFKGLFGKKEMCILMVGLDAAG<KTT<ILYKLKLREIVTTIPTIGLNVETVEYKNIGFTVWDV

Parental  GGQDKIRPLWRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDELRDAV-LLVFANKQDLPNAMNAA
          GGQD.I.PL.RHYFQNTQGLIFVVD.N.RE...EA.E.L.RMLAEDEL.DAV..LV.A.KQDLPNAMNAA
Retrocopy GGQDQIPPL*RHYFQNTQGLIFVVDDNERECMREASEALLRMLAEDELLDAV<PLVSAKKQDLPNAMNAA

Parental  EITDKLGLHSLRHRNWYIQATCATSGDGLYEGLDWLS-NQLRNQK
          EITDKL.LHSLRHRNWYIQATCATSGDGL.EGLD.LS.NQLRNQK
Retrocopy EITDKLRLHSLRHRNWYIQATCATSGDGLSEGLD*LS<NQLRNQK

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	78.14 RPM
SRP051959_heart	0.00 RPM	53.20 RPM
SRP051959_kidney	0.02 RPM	61.57 RPM
SRP051959_liver	0.00 RPM	69.53 RPM
SRP051959_lung	0.00 RPM	68.91 RPM
SRP051959_lymph_node	0.00 RPM	56.92 RPM
SRP051959_skeletal_muscle	0.00 RPM	73.07 RPM
SRP051959_spleen	0.00 RPM	58.74 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2189 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2189 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2189 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 37 parental genes, and 99 retrocopies.

Species	Parental gene accession	Retrocopies number
Anas platyrhynchos	ENSAPLG00000004509	1 retrocopy	retro_apla_4,
Bos taurus	ENSBTAG00000007725	2 retrocopies	retro_btau_1257, retro_btau_1390,
Callithrix jacchus	ENSCJAG00000015842	2 retrocopies	retro_cjac_1120, retro_cjac_470,
Callithrix jacchus	ENSCJAG00000016671	10 retrocopies	retro_cjac_1295, retro_cjac_1691, retro_cjac_1719, retro_cjac_2189 , retro_cjac_2896, retro_cjac_300, retro_cjac_3181, retro_cjac_3311, retro_cjac_3335, retro_cjac_390,
Callithrix jacchus	ENSCJAG00000019922	1 retrocopy	retro_cjac_507,
Cavia porcellus	ENSCPOG00000021174	1 retrocopy	retro_cpor_1310,
Ciona savignyi	ENSCSAVG00000007011	1 retrocopy	retro_csav_2,
Dasypus novemcinctus	ENSDNOG00000010454	3 retrocopies	retro_dnov_2375, retro_dnov_2459, retro_dnov_26,
Dipodomys ordii	ENSDORG00000007603	4 retrocopies	retro_dord_31, retro_dord_351, retro_dord_409, retro_dord_573,
Erinaceus europaeus	ENSEEUG00000004638	4 retrocopies	retro_eeur_328, retro_eeur_660, retro_eeur_684, retro_eeur_76,
Ficedula albicollis	ENSFALG00000001088	1 retrocopy	retro_falb_2,
Felis catus	ENSFCAG00000029374	1 retrocopy	retro_fcat_1829,
Homo sapiens	ENSG00000143761	3 retrocopies	retro_hsap_1008, retro_hsap_1160, retro_hsap_3763,
Gallus gallus	ENSGALG00000005393	1 retrocopy	retro_ggal_7,
Gorilla gorilla	ENSGGOG00000011263	5 retrocopies	retro_ggor_161, retro_ggor_2531, retro_ggor_3071, retro_ggor_801, retro_ggor_906,
Latimeria chalumnae	ENSLACG00000019009	1 retrocopy	retro_lcha_10,
Myotis lucifugus	ENSMLUG00000007020	6 retrocopies	retro_mluc_1631, retro_mluc_242, retro_mluc_2605, retro_mluc_428, retro_mluc_511, retro_mluc_876,
Macaca mulatta	ENSMMUG00000002792	3 retrocopies	retro_mmul_237, retro_mmul_541, retro_mmul_810,
Mus musculus	ENSMUSG00000048076	1 retrocopy	retro_mmus_1718,
Nomascus leucogenys	ENSNLEG00000014137	3 retrocopies	retro_nleu_210, retro_nleu_227, retro_nleu_2929,
Oryctolagus cuniculus	ENSOCUG00000023645	2 retrocopies	retro_ocun_1137, retro_ocun_247,
Otolemur garnettii	ENSOGAG00000010974	4 retrocopies	retro_ogar_2431, retro_ogar_295, retro_ogar_3353, retro_ogar_974,
Ochotona princeps	ENSOPRG00000015063	2 retrocopies	retro_opri_317, retro_opri_759,
Procavia capensis	ENSPCAG00000014202	2 retrocopies	retro_pcap_15, retro_pcap_23,
Pongo abelii	ENSPPYG00000000148	3 retrocopies	retro_pabe_3159, retro_pabe_849, retro_pabe_965,
Pelodiscus sinensis	ENSPSIG00000009767	1 retrocopy	retro_psin_12,
Pan troglodytes	ENSPTRG00000002066	2 retrocopies	retro_ptro_112, retro_ptro_5,
Pteropus vampyrus	ENSPVAG00000007383	1 retrocopy	retro_pvam_1324,
Rattus norvegicus	ENSRNOG00000030591	3 retrocopies	retro_rnor_1268, retro_rnor_1348, retro_rnor_1950,
Sarcophilus harrisii	ENSSHAG00000014599	3 retrocopies	retro_shar_106, retro_shar_462, retro_shar_725,
Sus scrofa	ENSSSCG00000013992	2 retrocopies	retro_sscr_429, retro_sscr_82,
Ictidomys tridecemlineatus	ENSSTOG00000009288	3 retrocopies	retro_itri_1754, retro_itri_273, retro_itri_363,
Tupaia belangeri	ENSTBEG00000009218	9 retrocopies	retro_tbel_1943, retro_tbel_2224, retro_tbel_2310, retro_tbel_2358, retro_tbel_2662, retro_tbel_2770, retro_tbel_3103, retro_tbel_4217, retro_tbel_4624,
Taeniopygia guttata	ENSTGUG00000000233	1 retrocopy	retro_tgut_2,
Tetraodon nigroviridis	ENSTNIG00000011685	1 retrocopy	retro_tnig_19,
Tursiops truncatus	ENSTTRG00000014186	2 retrocopies	retro_ttru_1679, retro_ttru_347,
Vicugna pacos	ENSVPAG00000003224	4 retrocopies	retro_vpac_281, retro_vpac_328, retro_vpac_6, retro_vpac_78,