RetrogeneDB ID: retro_cjac_1673

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 18:15460548..15461082(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000005599
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000016600
• Aliases: None
• Description: None

Sequence

>retro_cjac_1673
ATGAACCAGGAAAAACTCGCCAAACTGCAAGCACAAGTGCACACTGGTGGGAAAGAAACTGCTTGCAGAAAGAAGATGGT
TCATAGAACAGCCACAGCAGATGATAAAATACTTCAGTTCTCCTTAAAGAGGTTGGGGTAAGCAATATCTCTGGTACTGA
AGAGGTGAATATGTTTACAAACCAAGGAACAGTGATCCACTTTAACAACTCTAAAGTGCAAGCATCTCTGGCAGCAAACA
CTTTCACCATTACAGGCCATGCTGAGACAAAGCAGCTGACAGAAGTGCTACCCAGCATCTTAAACCAGCTGGGGGCAGAC
AGTCTGACTAGTTTCAGGAGACTGGTTGAGGCTCTGCCCAAACAATCTGAGGATGGAAAAGCACCACTTGCTACTGGAGA
GGAGGATGATGATGATGAAGTTCCAGATCTTGTGGAGAATTTTGGTGAGGCTTCCAAGATTGAGGCAAACTGAATTGAGT
CAACTTCTGAAGATAAAACTTGAAGAAGTTACTGGGTGCTGCTATTTTATATTA

Alignment

ORF - retro_cjac_1673 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.71 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MNQEKLAKLQAQVRIGGKGTARRKKKVVHRTATADDKKLQFSLKKLG-VNNISGIEEVNMFTNQGTVIHF
          MNQEKLAKLQAQV..GGK.TA.RKK..VHRTATADDK.LQFSLK.LG.V.NISG.EEVNMFTNQGTVIHF
Retrocopy MNQEKLAKLQAQVHTGGKETACRKK-MVHRTATADDKILQFSLKRLG<VSNISGTEEVNMFTNQGTVIHF

Parental  NNPKVQASLAANTFTITGHAETKQLTEMLPSILNQLGADSLTSLRRLAEALPKQSVDGKAPLATGEEDDD
          NN.KVQASLAANTFTITGHAETKQLTE.LPSILNQLGADSLTS.RRL.EALPKQS.DGKAPLATGEE.DD
Retrocopy NNSKVQASLAANTFTITGHAETKQLTEVLPSILNQLGADSLTSFRRLVEALPKQSEDGKAPLATGEE-DD

Parental  E-VPDLILWRILMRLPRMRQTELSQLLKIKLEEVTGSCYFIL
          ......ILWRIL.RLPR.RQTELSQLLKIKLEEVTG.CYFIL
Retrocopy D>MKFQILWRILVRLPRLRQTELSQLLKIKLEEVTGCCYFIL

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	0.27 RPM	23.47 RPM
SRP051959_heart	0.25 RPM	21.87 RPM
SRP051959_kidney	0.24 RPM	20.61 RPM
SRP051959_liver	0.26 RPM	26.34 RPM
SRP051959_lung	0.37 RPM	22.43 RPM
SRP051959_lymph_node	0.18 RPM	24.86 RPM
SRP051959_skeletal_muscle	0.24 RPM	32.74 RPM
SRP051959_spleen	0.21 RPM	28.78 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1673 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1673 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1673 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 32 parental genes, and 227 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011563	14 retrocopies	retro_amel_1257, retro_amel_1279, retro_amel_1324, retro_amel_1334, retro_amel_1433, retro_amel_166, retro_amel_1769, retro_amel_182, retro_amel_1841, retro_amel_480, retro_amel_513, retro_amel_784, retro_amel_908, retro_amel_986,
Bos taurus	ENSBTAG00000010012	5 retrocopies	retro_btau_1161, retro_btau_1344, retro_btau_1361, retro_btau_459, retro_btau_551,
Canis familiaris	ENSCAFG00000008212	3 retrocopies	retro_cfam_1660, retro_cfam_1741, retro_cfam_531,
Choloepus hoffmanni	ENSCHOG00000001861	13 retrocopies	retro_chof_1027, retro_chof_1166, retro_chof_117, retro_chof_1397, retro_chof_1406, retro_chof_1884, retro_chof_1960, retro_chof_2194, retro_chof_2682, retro_chof_2703, retro_chof_344, retro_chof_364, retro_chof_700,
Callithrix jacchus	ENSCJAG00000016600	4 retrocopies	retro_cjac_1454, retro_cjac_1673 , retro_cjac_2640, retro_cjac_281,
Callithrix jacchus	ENSCJAG00000021582	4 retrocopies	retro_cjac_2000, retro_cjac_2929, retro_cjac_4160, retro_cjac_451,
Cavia porcellus	ENSCPOG00000012832	1 retrocopy	retro_cpor_81,
Ciona savignyi	ENSCSAVG00000009653	1 retrocopy	retro_csav_25,
Dasypus novemcinctus	ENSDNOG00000018682	4 retrocopies	retro_dnov_1958, retro_dnov_2107, retro_dnov_497, retro_dnov_817,
Dipodomys ordii	ENSDORG00000014031	5 retrocopies	retro_dord_287, retro_dord_341, retro_dord_422, retro_dord_54, retro_dord_66,
Equus caballus	ENSECAG00000021629	1 retrocopy	retro_ecab_200,
Echinops telfairi	ENSETEG00000017341	5 retrocopies	retro_etel_1216, retro_etel_1394, retro_etel_1997, retro_etel_405, retro_etel_960,
Felis catus	ENSFCAG00000023973	10 retrocopies	retro_fcat_1044, retro_fcat_1378, retro_fcat_1438, retro_fcat_187, retro_fcat_188, retro_fcat_225, retro_fcat_28, retro_fcat_419, retro_fcat_593, retro_fcat_919,
Homo sapiens	ENSG00000145741	11 retrocopies	retro_hsap_1215, retro_hsap_1396, retro_hsap_2259, retro_hsap_2525, retro_hsap_2819, retro_hsap_2964, retro_hsap_3533, retro_hsap_3551, retro_hsap_3972, retro_hsap_4270, retro_hsap_625,
Gorilla gorilla	ENSGGOG00000000166	10 retrocopies	retro_ggor_1082, retro_ggor_1682, retro_ggor_1961, retro_ggor_2054, retro_ggor_2399, retro_ggor_2647, retro_ggor_2667, retro_ggor_548, retro_ggor_81, retro_ggor_946,
Microcebus murinus	ENSMICG00000017182	3 retrocopies	retro_mmur_1219, retro_mmur_1301, retro_mmur_651,
Myotis lucifugus	ENSMLUG00000012912	11 retrocopies	retro_mluc_1024, retro_mluc_1349, retro_mluc_1459, retro_mluc_1748, retro_mluc_1820, retro_mluc_1823, retro_mluc_2560, retro_mluc_2602, retro_mluc_482, retro_mluc_682, retro_mluc_694,
Macaca mulatta	ENSMMUG00000022291	2 retrocopies	retro_mmul_105, retro_mmul_2424,
Monodelphis domestica	ENSMODG00000001762	3 retrocopies	retro_mdom_189, retro_mdom_454, retro_mdom_931,
Mustela putorius furo	ENSMPUG00000005864	28 retrocopies	retro_mputfur_1125, retro_mputfur_1149, retro_mputfur_1267, retro_mputfur_1289, retro_mputfur_1319, retro_mputfur_1321, retro_mputfur_1386, retro_mputfur_1414, retro_mputfur_1472, retro_mputfur_1525, retro_mputfur_1548, retro_mputfur_1576, retro_mputfur_1599, retro_mputfur_246, retro_mputfur_324, retro_mputfur_392, retro_mputfur_403, retro_mputfur_431, retro_mputfur_618, retro_mputfur_661, retro_mputfur_724, retro_mputfur_728, retro_mputfur_753, retro_mputfur_760, retro_mputfur_795, retro_mputfur_901, retro_mputfur_926, retro_mputfur_972,
Mus musculus	ENSMUSG00000021660	11 retrocopies	retro_mmus_1904, retro_mmus_2445, retro_mmus_2769, retro_mmus_3054, retro_mmus_3272, retro_mmus_3344, retro_mmus_3525, retro_mmus_443, retro_mmus_451, retro_mmus_470, retro_mmus_707,
Nomascus leucogenys	ENSNLEG00000004718	9 retrocopies	retro_nleu_1081, retro_nleu_1199, retro_nleu_1284, retro_nleu_1446, retro_nleu_1797, retro_nleu_2526, retro_nleu_451, retro_nleu_496, retro_nleu_734,
Oryctolagus cuniculus	ENSOCUG00000024914	6 retrocopies	retro_ocun_1186, retro_ocun_1299, retro_ocun_1364, retro_ocun_446, retro_ocun_857, retro_ocun_916,
Otolemur garnettii	ENSOGAG00000013918	1 retrocopy	retro_ogar_46,
Pongo abelii	ENSPPYG00000029576	14 retrocopies	retro_pabe_1154, retro_pabe_1477, retro_pabe_180, retro_pabe_1885, retro_pabe_1956, retro_pabe_2207, retro_pabe_2458, retro_pabe_2918, retro_pabe_2919, retro_pabe_2932, retro_pabe_3329, retro_pabe_3484, retro_pabe_558, retro_pabe_649,
Pan troglodytes	ENSPTRG00000016979	12 retrocopies	retro_ptro_1470, retro_ptro_1599, retro_ptro_1675, retro_ptro_1912, retro_ptro_2006, retro_ptro_2413, retro_ptro_2494, retro_ptro_2697, retro_ptro_2896, retro_ptro_455, retro_ptro_832, retro_ptro_959,
Pteropus vampyrus	ENSPVAG00000007160	11 retrocopies	retro_pvam_1011, retro_pvam_241, retro_pvam_301, retro_pvam_440, retro_pvam_456, retro_pvam_515, retro_pvam_602, retro_pvam_647, retro_pvam_70, retro_pvam_882, retro_pvam_919,
Rattus norvegicus	ENSRNOG00000016912	9 retrocopies	retro_rnor_187, retro_rnor_194, retro_rnor_2121, retro_rnor_2520, retro_rnor_2990, retro_rnor_2991, retro_rnor_2999, retro_rnor_836, retro_rnor_953,
Sorex araneus	ENSSARG00000007736	5 retrocopies	retro_sara_195, retro_sara_279, retro_sara_354, retro_sara_427, retro_sara_74,
Tarsius syrichta	ENSTSYG00000001295	7 retrocopies	retro_tsyr_1360, retro_tsyr_1388, retro_tsyr_212, retro_tsyr_707, retro_tsyr_878, retro_tsyr_90, retro_tsyr_954,
Tursiops truncatus	ENSTTRG00000007290	2 retrocopies	retro_ttru_1883, retro_ttru_391,
Vicugna pacos	ENSVPAG00000009607	2 retrocopies	retro_vpac_185, retro_vpac_467,