RetrogeneDB ID: retro_cjac_1411

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 15:71164601..71164929(-)
• 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_1411
ATGAAGCCTGCAGGCCTGGGTGAAGGAGTACTTCCGGGCAACCATGGGAACTATGGCTATTGCTAAGAGTGGACAGAGAG
CCTGGGAAGAAGAAAATGAGAGACTCACTGAAAGTCTGAGAAGCAAAGCAGCTACTATAAAATCTCTTTCCATACAAATA
GGCCATAAAGTTAAAACCCAAAATAAATTATTAGCTGAAATGGATTCACAATTTGATTCTACATCTGGATTACGAGGTAA
AACTACAGCCAAACTGAAGAGTTTATCCAGAGGGAGCCAAACAAAGCCACTGTGCTATATGATGCTATTTTCCTTATTTG
TCTTTTTT

Alignment

ORF - retro_cjac_1411 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.09 %
• Parental protein coverage: 92.37 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MRRAGLGEGVPPGNYGNYGY-ANSGYSACEEENERLTESLRSKVTAIKSLSIEIGHEVKTQNNLLAEMDS
          M..AGLGEGV.PGN.GNYGY.A.SG..A.EEENERLTESLRSK...IKSLSI.IGH.VKTQN.LLAEMDS
Retrocopy MKPAGLGEGVLPGNHGNYGY>AKSGQRAWEEENERLTESLRSKAATIKSLSIQIGHKVKTQNKLLAEMDS

Parental  QFDSTTGFLGKTMGKLKILSRGSQTRLLCYMMLFSLFVFF
          QFDST.G..GKT..KLK.LSRGSQT..LCYMMLFSLFVFF
Retrocopy QFDSTSGLRGKTTAKLKSLSRGSQTKPLCYMMLFSLFVFF

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	0.18 RPM	5.84 RPM
SRP051959_heart	0.04 RPM	6.65 RPM
SRP051959_kidney	0.20 RPM	16.35 RPM
SRP051959_liver	0.22 RPM	9.92 RPM
SRP051959_lung	0.11 RPM	8.41 RPM
SRP051959_lymph_node	0.18 RPM	6.32 RPM
SRP051959_skeletal_muscle	0.02 RPM	3.78 RPM
SRP051959_spleen	0.08 RPM	10.04 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1411 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1411 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1411 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,