RetrogeneDB ID: retro_cjac_2460

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:108159425..108159674(-)
• Located in intron of: ENSCJAG00000005929

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000010529
• Aliases: None
• Description: None

Sequence

>retro_cjac_2460
AAAAAGCTCCAGGAAGGAGTCAAGACTGAGAACAGCAGTCATATTAATCTGAAGGTGGCGGGGCAGGATGGTTCTCTGGT
GCAGTTTAAGATTAAGAGGCATATACCACTTAGCAAACTAATAAAAGCCTATTATGAATGACAGGGATTGTCAATAAGGC
AGATCAGACTCTGATTTGACTGGCAATCAATCAATGAAACAGACACACCTGCACAGTTGGAAATGGAGGATGAAGATACA
ACTGATGTG

Alignment

ORF - retro_cjac_2460 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.93 %
• Parental protein coverage: 79.61 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KKPKEGVKTEND-HINLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTP
          KK..EGVKTEN..HINLKVAGQDGS.VQFKIKRH.PLSKL.KAY.E.QGLS.RQIR..FD.Q.INETDTP
Retrocopy KKLQEGVKTENSSHINLKVAGQDGSLVQFKIKRHIPLSKLIKAYYE*QGLSIRQIRL*FDWQSINETDTP

Parental  AQLEMEDEDTIDV
          AQLEMEDEDT.DV
Retrocopy AQLEMEDEDTTDV

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	1.35 RPM	4.24 RPM
SRP051959_heart	1.67 RPM	4.47 RPM
SRP051959_kidney	0.69 RPM	5.44 RPM
SRP051959_liver	1.71 RPM	3.66 RPM
SRP051959_lung	1.30 RPM	5.60 RPM
SRP051959_lymph_node	0.87 RPM	3.54 RPM
SRP051959_skeletal_muscle	1.20 RPM	5.37 RPM
SRP051959_spleen	1.05 RPM	4.96 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2460 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2460 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2460 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2463

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 110 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002071	3 retrocopies	retro_amel_1388, retro_amel_1586, retro_amel_1863,
Bos taurus	ENSBTAG00000017321	3 retrocopies	retro_btau_1730, retro_btau_580, retro_btau_701,
Bos taurus	ENSBTAG00000030169	8 retrocopies	retro_btau_1047, retro_btau_1484, retro_btau_1804, retro_btau_260, retro_btau_344, retro_btau_489, retro_btau_582, retro_btau_895,
Choloepus hoffmanni	ENSCHOG00000010239	1 retrocopy	retro_chof_2468,
Callithrix jacchus	ENSCJAG00000004961	3 retrocopies	retro_cjac_1686, retro_cjac_1932, retro_cjac_2610,
Callithrix jacchus	ENSCJAG00000010529	20 retrocopies	retro_cjac_1110, retro_cjac_1128, retro_cjac_1525, retro_cjac_1752, retro_cjac_1938, retro_cjac_1957, retro_cjac_1993, retro_cjac_2460 , retro_cjac_2481, retro_cjac_2616, retro_cjac_2651, retro_cjac_2886, retro_cjac_2899, retro_cjac_2985, retro_cjac_3088, retro_cjac_3137, retro_cjac_4123, retro_cjac_711, retro_cjac_771, retro_cjac_774,
Cavia porcellus	ENSCPOG00000025203	3 retrocopies	retro_cpor_328, retro_cpor_645, retro_cpor_963,
Felis catus	ENSFCAG00000026550	4 retrocopies	retro_fcat_1210, retro_fcat_1947, retro_fcat_823, retro_fcat_836,
Homo sapiens	ENSG00000184900	4 retrocopies	retro_hsap_1675, retro_hsap_1841, retro_hsap_3672, retro_hsap_4103,
Microcebus murinus	ENSMICG00000011011	2 retrocopies	retro_mmur_179, retro_mmur_41,
Myotis lucifugus	ENSMLUG00000025342	4 retrocopies	retro_mluc_1502, retro_mluc_272, retro_mluc_340, retro_mluc_625,
Myotis lucifugus	ENSMLUG00000028601	2 retrocopies	retro_mluc_1321, retro_mluc_2494,
Macaca mulatta	ENSMMUG00000006760	3 retrocopies	retro_mmul_2131, retro_mmul_2215, retro_mmul_47,
Mustela putorius furo	ENSMPUG00000010234	1 retrocopy	retro_mputfur_1504,
Mustela putorius furo	ENSMPUG00000013954	9 retrocopies	retro_mputfur_1086, retro_mputfur_1403, retro_mputfur_1535, retro_mputfur_273, retro_mputfur_275, retro_mputfur_385, retro_mputfur_666, retro_mputfur_948, retro_mputfur_995,
Mus musculus	ENSMUSG00000020265	1 retrocopy	retro_mmus_3548,
Nomascus leucogenys	ENSNLEG00000002351	9 retrocopies	retro_nleu_1084, retro_nleu_1253, retro_nleu_1736, retro_nleu_2052, retro_nleu_21, retro_nleu_2128, retro_nleu_3039, retro_nleu_523, retro_nleu_572,
Oryctolagus cuniculus	ENSOCUG00000021739	4 retrocopies	retro_ocun_1024, retro_ocun_1631, retro_ocun_1690, retro_ocun_321,
Otolemur garnettii	ENSOGAG00000004715	10 retrocopies	retro_ogar_1199, retro_ogar_1646, retro_ogar_1945, retro_ogar_2958, retro_ogar_328, retro_ogar_3469, retro_ogar_371, retro_ogar_419, retro_ogar_526, retro_ogar_967,
Rattus norvegicus	ENSRNOG00000038489	1 retrocopy	retro_rnor_2158,
Sus scrofa	ENSSSCG00000024026	2 retrocopies	retro_sscr_1089, retro_sscr_320,
Ictidomys tridecemlineatus	ENSSTOG00000010587	2 retrocopies	retro_itri_116, retro_itri_1259,
Ictidomys tridecemlineatus	ENSSTOG00000024685	10 retrocopies	retro_itri_1017, retro_itri_1123, retro_itri_1355, retro_itri_202, retro_itri_264, retro_itri_272, retro_itri_79, retro_itri_921, retro_itri_981, retro_itri_983,
Takifugu rubripes	ENSTRUG00000014892	1 retrocopy	retro_trub_25,