RetrogeneDB ID: retro_cjac_2176

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:116592761..116593203(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000020883
• Aliases: None
• Description: None

Sequence

>retro_cjac_2176
ATCAAGAATGGGGCCAACAACAGCAGGCCCAACGATTTATGGCGTGAATTTGGTCGTTATGATCCTCTAGTTGGTGTGTA
TGTTCCACTTGATTTCTACACTCACTGACCAAGAGGAGTTGCTTATGTTCAATTTGAGGATGTTAGCGATGCTGAAGATG
CTTTACATAATTTGGACAGAAAGTGGATTTGTGGATGTCAAACTGAAATAGTTTGCACATGGGGATTGGAAGACACCAAA
TCAGATGAAAGCAAAGGAAGGGAGGAATGTGTACAGTTTTTCACGCTATGATTATGACAGATACAGATATTCTAGAAGCC
AAATTTATGAAAGAAGATCAAGAAGTCAGTATTTTGCTTACACCTATAAAAGACCTTGTAGTCCTAGAAATAGTGGATGG
ACTGAAAGGCCACAGTGTAGCAGAAGCCATTCCAACAATGAC

Alignment

ORF - retro_cjac_2176 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.47 %
• Parental protein coverage: 81.97 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VRNVADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALHNLDRKWICGRQIEI
          ..N.A...R..DL.REFGRY.P.V.VYVPLDFYT..PRG.AYVQFEDV.DAEDALHNLDRKWICG.Q.EI
Retrocopy IKNGANNSRPNDLWREFGRYDPLVGVYVPLDFYTH*PRGVAYVQFEDVSDAEDALHNLDRKWICGCQTEI

Parental  QFAQGDRKTPNQM-KAKEG-RNVYSSSRYDDYDRYRRSRSRSYERRRSRSRSFDYNYRRSYSPRSSRPTG
          ....G...T.....K...G.RNVYS.SRY.DYDRYR.SRS..YE.RRSRS..F.Y.Y.R..SPR.S..T.
Retrocopy VCTWGLEDTKSDE<KQRKG<RNVYSFSRY-DYDRYRYSRSQIYE-RRSRSQYFAYTYKRPCSPRNSGWTE

Parental  RPRRSRSHSDND
          RP..SRSHS.ND
Retrocopy RPQCSRSHSNND

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	0.04 RPM	20.70 RPM
SRP051959_heart	0.05 RPM	18.47 RPM
SRP051959_kidney	0.02 RPM	25.16 RPM
SRP051959_liver	0.00 RPM	18.06 RPM
SRP051959_lung	0.08 RPM	28.01 RPM
SRP051959_lymph_node	0.11 RPM	36.78 RPM
SRP051959_skeletal_muscle	0.02 RPM	12.95 RPM
SRP051959_spleen	0.08 RPM	32.00 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2176 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2176 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2176 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3054
Pongo abelii	retro_pabe_2529

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Parental genes homology:

Parental genes homology involve 25 parental genes, and 62 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009869	2 retrocopies	retro_amel_1810, retro_amel_355,
Bos taurus	ENSBTAG00000008072	1 retrocopy	retro_btau_759,
Choloepus hoffmanni	ENSCHOG00000004836	1 retrocopy	retro_chof_7,
Callithrix jacchus	ENSCJAG00000020883	9 retrocopies	retro_cjac_1126, retro_cjac_1170, retro_cjac_2176 , retro_cjac_2595, retro_cjac_2638, retro_cjac_3852, retro_cjac_628, retro_cjac_705, retro_cjac_864,
Cavia porcellus	ENSCPOG00000024533	1 retrocopy	retro_cpor_1098,
Dasypus novemcinctus	ENSDNOG00000008699	3 retrocopies	retro_dnov_1327, retro_dnov_1809, retro_dnov_2244,
Dipodomys ordii	ENSDORG00000009136	1 retrocopy	retro_dord_667,
Erinaceus europaeus	ENSEEUG00000014286	1 retrocopy	retro_eeur_522,
Homo sapiens	ENSG00000188529	5 retrocopies	retro_hsap_1343, retro_hsap_1940, retro_hsap_2445, retro_hsap_3054, retro_hsap_4295,
Gorilla gorilla	ENSGGOG00000000392	4 retrocopies	retro_ggor_1044, retro_ggor_1411, retro_ggor_1522, retro_ggor_2870,
Loxodonta africana	ENSLAFG00000026905	1 retrocopy	retro_lafr_148,
Myotis lucifugus	ENSMLUG00000028520	1 retrocopy	retro_mluc_89,
Mustela putorius furo	ENSMPUG00000015845	1 retrocopy	retro_mputfur_353,
Mus musculus	ENSMUSG00000028676	5 retrocopies	retro_mmus_1081, retro_mmus_1311, retro_mmus_1814, retro_mmus_3480, retro_mmus_982,
Nomascus leucogenys	ENSNLEG00000013180	3 retrocopies	retro_nleu_1647, retro_nleu_1825, retro_nleu_202,
Oryctolagus cuniculus	ENSOCUG00000029326	1 retrocopy	retro_ocun_717,
Otolemur garnettii	ENSOGAG00000015374	2 retrocopies	retro_ogar_2650, retro_ogar_2987,
Ochotona princeps	ENSOPRG00000018613	3 retrocopies	retro_opri_1067, retro_opri_295, retro_opri_916,
Pongo abelii	ENSPPYG00000001726	4 retrocopies	retro_pabe_1115, retro_pabe_1601, retro_pabe_1796, retro_pabe_2529,
Pan troglodytes	ENSPTRG00000024234	4 retrocopies	retro_ptro_1295, retro_ptro_1413, retro_ptro_1986, retro_ptro_918,
Rattus norvegicus	ENSRNOG00000007992	3 retrocopies	retro_rnor_1657, retro_rnor_2800, retro_rnor_2829,
Sus scrofa	ENSSSCG00000021615	2 retrocopies	retro_sscr_528, retro_sscr_554,
Ictidomys tridecemlineatus	ENSSTOG00000000956	1 retrocopy	retro_itri_1333,
Tupaia belangeri	ENSTBEG00000017716	1 retrocopy	retro_tbel_4154,
Tursiops truncatus	ENSTTRG00000016150	2 retrocopies	retro_ttru_1098, retro_ttru_695,