RetrogeneDB ID: retro_cjac_1008

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 12:121536838..121537019(+)
• Located in intron of: ENSCJAG00000004917

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000012795
• Aliases: None
• Description: None

Sequence

>retro_cjac_1008
ATGGCCAGCACCGTGGTAGCAGACGACTGGCCACTGCAGCTGCAGGATTTGCAGGCCGTCACGCTTTGCCAGCCATGAAG
CATAAGGAGCCTGAAGTAAAGCAAGTTTTTCAAGTCTGCCAAAATGTGCCTTCAGTGGTGGCTATTACGGAGGTGGGTTT
GAACCCAGTGACAATACTAGG

Alignment

ORF - retro_cjac_1008 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.43 %
• Parental protein coverage: 52.59 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MASTMVAVG-LTIAAAGFAGRYVLQAMKHMEPQVKQVFQ-SLPKSAFSGGYYRGGFEPKMTKR
          MAST.VA...L..AAAGFAGR..L.AMKH.EP.VKQVFQ.SLPK.AFSGGYY.GGFEP....R
Retrocopy MASTVVADD<LATAAAGFAGRHALPAMKHKEPEVKQVFQ<SLPKCAFSGGYYGGGFEPSDNTR

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	0.07 RPM	12.94 RPM
SRP051959_heart	0.05 RPM	19.72 RPM
SRP051959_kidney	0.09 RPM	27.20 RPM
SRP051959_liver	0.19 RPM	42.74 RPM
SRP051959_lung	0.31 RPM	15.88 RPM
SRP051959_lymph_node	0.43 RPM	17.10 RPM
SRP051959_skeletal_muscle	0.02 RPM	42.26 RPM
SRP051959_spleen	0.23 RPM	17.50 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1008 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1008 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1008 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 34 parental genes, and 172 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012255	6 retrocopies	retro_amel_1087, retro_amel_155, retro_amel_252, retro_amel_283, retro_amel_744, retro_amel_994,
Bos taurus	ENSBTAG00000023513	1 retrocopy	retro_btau_127,
Canis familiaris	ENSCAFG00000032714	8 retrocopies	retro_cfam_1256, retro_cfam_1306, retro_cfam_1451, retro_cfam_2015, retro_cfam_346, retro_cfam_389, retro_cfam_741, retro_cfam_819,
Callithrix jacchus	ENSCJAG00000012795	10 retrocopies	retro_cjac_1008 , retro_cjac_1192, retro_cjac_1364, retro_cjac_1430, retro_cjac_1550, retro_cjac_252, retro_cjac_2609, retro_cjac_2890, retro_cjac_3060, retro_cjac_914,
Callithrix jacchus	ENSCJAG00000017589	2 retrocopies	retro_cjac_1663, retro_cjac_634,
Cavia porcellus	ENSCPOG00000021198	1 retrocopy	retro_cpor_126,
Dasypus novemcinctus	ENSDNOG00000019067	1 retrocopy	retro_dnov_49,
Dipodomys ordii	ENSDORG00000005862	7 retrocopies	retro_dord_232, retro_dord_295, retro_dord_320, retro_dord_53, retro_dord_586, retro_dord_684, retro_dord_794,
Erinaceus europaeus	ENSEEUG00000006955	9 retrocopies	retro_eeur_221, retro_eeur_230, retro_eeur_309, retro_eeur_455, retro_eeur_48, retro_eeur_511, retro_eeur_596, retro_eeur_74, retro_eeur_94,
Echinops telfairi	ENSETEG00000006897	7 retrocopies	retro_etel_1071, retro_etel_1222, retro_etel_1559, retro_etel_275, retro_etel_384, retro_etel_81, retro_etel_821,
Ficedula albicollis	ENSFALG00000008296	1 retrocopy	retro_falb_28,
Felis catus	ENSFCAG00000010591	7 retrocopies	retro_fcat_1250, retro_fcat_1481, retro_fcat_1603, retro_fcat_1837, retro_fcat_475, retro_fcat_511, retro_fcat_982,
Homo sapiens	ENSG00000205981	8 retrocopies	retro_hsap_1330, retro_hsap_2061, retro_hsap_2062, retro_hsap_2349, retro_hsap_3497, retro_hsap_387, retro_hsap_538, retro_hsap_583,
Gallus gallus	ENSGALG00000008852	1 retrocopy	retro_ggal_17,
Gorilla gorilla	ENSGGOG00000009120	7 retrocopies	retro_ggor_1037, retro_ggor_1483, retro_ggor_1484, retro_ggor_1783, retro_ggor_2365, retro_ggor_491, retro_ggor_517,
Loxodonta africana	ENSLAFG00000001910	5 retrocopies	retro_lafr_48, retro_lafr_515, retro_lafr_611, retro_lafr_881, retro_lafr_929,
Microcebus murinus	ENSMICG00000010381	4 retrocopies	retro_mmur_1160, retro_mmur_225, retro_mmur_320, retro_mmur_728,
Myotis lucifugus	ENSMLUG00000006865	1 retrocopy	retro_mluc_84,
Macaca mulatta	ENSMMUG00000012104	3 retrocopies	retro_mmul_2142, retro_mmul_2454, retro_mmul_946,
Mustela putorius furo	ENSMPUG00000002336	7 retrocopies	retro_mputfur_1099, retro_mputfur_1652, retro_mputfur_287, retro_mputfur_662, retro_mputfur_841, retro_mputfur_848, retro_mputfur_984,
Mus musculus	ENSMUSG00000027679	3 retrocopies	retro_mmus_1446, retro_mmus_3071, retro_mmus_3554,
Oryctolagus cuniculus	ENSOCUG00000014043	5 retrocopies	retro_ocun_1100, retro_ocun_1650, retro_ocun_1869, retro_ocun_334, retro_ocun_398,
Otolemur garnettii	ENSOGAG00000008754	11 retrocopies	retro_ogar_1214, retro_ogar_1334, retro_ogar_138, retro_ogar_1625, retro_ogar_1811, retro_ogar_2012, retro_ogar_2048, retro_ogar_2881, retro_ogar_301, retro_ogar_442, retro_ogar_718,
Ochotona princeps	ENSOPRG00000009256	5 retrocopies	retro_opri_1127, retro_opri_122, retro_opri_440, retro_opri_529, retro_opri_844,
Procavia capensis	ENSPCAG00000014950	2 retrocopies	retro_pcap_195, retro_pcap_25,
Pongo abelii	ENSPPYG00000014328	2 retrocopies	retro_pabe_2126, retro_pabe_44,
Pan troglodytes	ENSPTRG00000030046	7 retrocopies	retro_ptro_1374, retro_ptro_1719, retro_ptro_2370, retro_ptro_2927, retro_ptro_404, retro_ptro_429, retro_ptro_907,
Rattus norvegicus	ENSRNOG00000049819	1 retrocopy	retro_rnor_2913,
Sus scrofa	ENSSSCG00000011770	2 retrocopies	retro_sscr_651, retro_sscr_891,
Ictidomys tridecemlineatus	ENSSTOG00000011508	1 retrocopy	retro_itri_552,
Tupaia belangeri	ENSTBEG00000015089	27 retrocopies	retro_tbel_1126, retro_tbel_1166, retro_tbel_1167, retro_tbel_1296, retro_tbel_1301, retro_tbel_1491, retro_tbel_1693, retro_tbel_1780, retro_tbel_2117, retro_tbel_2136, retro_tbel_2267, retro_tbel_2459, retro_tbel_266, retro_tbel_2830, retro_tbel_3233, retro_tbel_3303, retro_tbel_3556, retro_tbel_3716, retro_tbel_3814, retro_tbel_384, retro_tbel_3849, retro_tbel_3963, retro_tbel_4043, retro_tbel_42, retro_tbel_633, retro_tbel_833, retro_tbel_889,
Tarsius syrichta	ENSTSYG00000001611	3 retrocopies	retro_tsyr_112, retro_tsyr_174, retro_tsyr_312,
Tursiops truncatus	ENSTTRG00000014700	6 retrocopies	retro_ttru_1023, retro_ttru_1630, retro_ttru_1830, retro_ttru_662, retro_ttru_704, retro_ttru_962,
Vicugna pacos	ENSVPAG00000003387	1 retrocopy	retro_vpac_533,