RetrogeneDB ID: retro_cjac_3155

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 8:96098210..96098444(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BET1
• Ensembl ID: ENSCJAG00000013720
• Aliases: None
• Description: Bet1 golgi vesicular membrane trafficking protein [Source:HGNC Symbol;Acc:14562]

Sequence

>retro_cjac_3155
ATGAGGCGTGCAGGCTTGGGTGAAGCAGGACCTCCTGGCAACTCTGGGAACGACGGCTAAGCTAACAGCAGGTATAGCAC
CTGTGAAGAAGAAAATGAGAGACTCGCTGAAAGTCTGAGAAGCAAAGTAGCTGCTATAAAATCTTTTCCCGTGGAAATAG
GCCATGGAGTTAAAACCCAAAATAAATTATCAGCTGAAACGGATTCACAACTGGATTCTACAATTGGATGTCTA

Alignment

ORF - retro_cjac_3155 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.64 %
• Parental protein coverage: 66.1 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MRRAGLGEGVPPGNYGNYGYANSGYSACEEENERLTESLRSKVTAIKSLSIEIGHEVKTQNNLLAEMDSQ
          MRRAGLGE..PPGN.GN.G.ANS.YS.CEEENERL.ESLRSKV.AIKS...EIGH.VKTQN.L.AE.DSQ
Retrocopy MRRAGLGEAGPPGNSGNDG*ANSRYSTCEEENERLAESLRSKVAAIKSFPVEIGHGVKTQNKLSAETDSQ

Parental  FDSTTGFL
          .DST.G.L
Retrocopy LDSTIGCL

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	5.84 RPM
SRP051959_heart	0.02 RPM	6.65 RPM
SRP051959_kidney	0.00 RPM	16.35 RPM
SRP051959_liver	0.00 RPM	9.92 RPM
SRP051959_lung	0.03 RPM	8.41 RPM
SRP051959_lymph_node	0.09 RPM	6.32 RPM
SRP051959_skeletal_muscle	0.02 RPM	3.78 RPM
SRP051959_spleen	0.02 RPM	10.04 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3155 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3155 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3155 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003424	1 retrocopy	retro_btau_1054,
Choloepus hoffmanni	ENSCHOG00000001276	1 retrocopy	retro_chof_2211,
Callithrix jacchus	ENSCJAG00000000895	1 retrocopy	retro_cjac_3988,
Callithrix jacchus	ENSCJAG00000013720	3 retrocopies	retro_cjac_1411, retro_cjac_2019, retro_cjac_3155 ,
Dasypus novemcinctus	ENSDNOG00000001012	3 retrocopies	retro_dnov_1683, retro_dnov_393, retro_dnov_60,
Homo sapiens	ENSG00000105829	1 retrocopy	retro_hsap_3809,
Gorilla gorilla	ENSGGOG00000002176	1 retrocopy	retro_ggor_2560,
Loxodonta africana	ENSLAFG00000000587	1 retrocopy	retro_lafr_1023,
Macaca mulatta	ENSMMUG00000000007	1 retrocopy	retro_mmul_1656,
Nomascus leucogenys	ENSNLEG00000015441	1 retrocopy	retro_nleu_2151,
Oryctolagus cuniculus	ENSOCUG00000017029	2 retrocopies	retro_ocun_1116, retro_ocun_355,
Ochotona princeps	ENSOPRG00000004536	4 retrocopies	retro_opri_201, retro_opri_249, retro_opri_388, retro_opri_880,
Pan troglodytes	ENSPTRG00000019408	1 retrocopy	retro_ptro_2584,
Rattus norvegicus	ENSRNOG00000011008	2 retrocopies	retro_rnor_2195, retro_rnor_2196,
Sus scrofa	ENSSSCG00000015325	2 retrocopies	retro_sscr_455, retro_sscr_516,
Tupaia belangeri	ENSTBEG00000000765	2 retrocopies	retro_tbel_3115, retro_tbel_4272,
Tarsius syrichta	ENSTSYG00000009729	2 retrocopies	retro_tsyr_136, retro_tsyr_1843,