RetrogeneDB ID: retro_cjac_2492

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:159995295..159995622(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000011575
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: YKT6
• Ensembl ID: ENSCJAG00000008053
• Aliases: None
• Description: YKT6 v-SNARE homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:16959]

Sequence

>retro_cjac_2492
ATGAAGCTGGGCAGCCTCAGTGTCCTCTACGAAGGTGAGCCCAAGGCAGTGCCGCCCAAAGCCACCTACGATAATGTGGC
TTCCTTCAGTTTCTCCCAGAGGTCCAGTGTTCAAGAAGTCATGACCTTCATGAGTCAACTGACTGTGGAGGGCTCATGCA
AAGGCACTAGAGCGTCAGTCAAAGAACAAGACTACCTGTGCCATGTCCATGTCCGGAACGACGGTCTTGCAGGTGTGGCC
ATTGCTGACAGTGAACGCCCATCCCAGGTGGCCTGTACCTTGCTGGAGTACTTACTAGATGAATTCTCCAAGCAAGTCAA
CAGGCTC

Alignment

ORF - retro_cjac_2492 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.31 %
• Parental protein coverage: 65.85 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKLYSLSVLYKGDAKVVLLKAAHD-VSSFSFFQRSSVQEFMTFTSQLIVERSSKGTRASVKEQDYLCHVY
          MKL.SLSVLY.G..K.V..KA..D.V.SFSF.QRSSVQE.MTF.SQL.VE.S.KGTRASVKEQDYLCHV.
Retrocopy MKLGSLSVLYEGEPKAVPPKATYDNVASFSFSQRSSVQEVMTFMSQLTVEGSCKGTRASVKEQDYLCHVH

Parental  VRNDSLAGVVIADNEYPSRVAFTLLEKVLDEFSKQVDRI
          VRND.LAGV.IAD.E.PS.VA.TLLE..LDEFSKQV.R.
Retrocopy VRNDGLAGVAIADSERPSQVACTLLEYLLDEFSKQVNRL

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	28.00 RPM
SRP051959_heart	0.00 RPM	22.15 RPM
SRP051959_kidney	0.02 RPM	24.87 RPM
SRP051959_liver	0.00 RPM	11.70 RPM
SRP051959_lung	0.02 RPM	22.40 RPM
SRP051959_lymph_node	0.09 RPM	17.19 RPM
SRP051959_skeletal_muscle	0.00 RPM	23.83 RPM
SRP051959_spleen	0.02 RPM	18.21 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2492 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2492 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2492 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017618	1 retrocopy	retro_amel_967,
Bos taurus	ENSBTAG00000000274	1 retrocopy	retro_btau_601,
Canis familiaris	ENSCAFG00000002903	1 retrocopy	retro_cfam_740,
Choloepus hoffmanni	ENSCHOG00000011207	1 retrocopy	retro_chof_657,
Callithrix jacchus	ENSCJAG00000008053	2 retrocopies	retro_cjac_2394, retro_cjac_2492 ,
Dasypus novemcinctus	ENSDNOG00000015173	1 retrocopy	retro_dnov_1364,
Dipodomys ordii	ENSDORG00000016393	1 retrocopy	retro_dord_621,
Erinaceus europaeus	ENSEEUG00000001247	1 retrocopy	retro_eeur_267,
Felis catus	ENSFCAG00000014362	1 retrocopy	retro_fcat_1327,
Homo sapiens	ENSG00000106636	1 retrocopy	retro_hsap_3687,
Gorilla gorilla	ENSGGOG00000027036	1 retrocopy	retro_ggor_2493,
Macropus eugenii	ENSMEUG00000014769	1 retrocopy	retro_meug_2068,
Mustela putorius furo	ENSMPUG00000018200	2 retrocopies	retro_mputfur_141, retro_mputfur_165,
Mus musculus	ENSMUSG00000002741	1 retrocopy	retro_mmus_825,
Nomascus leucogenys	ENSNLEG00000003689	1 retrocopy	retro_nleu_2275,
Oryctolagus cuniculus	ENSOCUG00000002981	1 retrocopy	retro_ocun_15,
Pongo abelii	ENSPPYG00000017595	1 retrocopy	retro_pabe_3022,
Pan troglodytes	ENSPTRG00000019141	1 retrocopy	retro_ptro_2500,
Sus scrofa	ENSSSCG00000016750	1 retrocopy	retro_sscr_1063,
Tursiops truncatus	ENSTTRG00000006052	2 retrocopies	retro_ttru_1320, retro_ttru_417,