RetrogeneDB ID: retro_cjac_3013

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:112118746..112119240(-)
• Located in intron of: ENSCJAG00000006823

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000018014
• Aliases: None
• Description: None

Sequence

>retro_cjac_3013
GGGACCCATAATTTCAGCAGTGCCTTTGCAGCCATGGCCCCTGTCATGCTGGGAGATGCTATCCTGGCACTAGTGGTGTT
TTAAAGGGAGCCTGGGAACAAGGTGGACCTGACAGAACTATGCCAGGGAAAGAAGGGTGTGCTGTTCAGAATCGCTGGGG
CTTTCACCCCAACTGTCAAAGACCCACCTGCTTGGGTTTGGGGAGTAGTCTGGGGTTCTGAAGGTCAAGAGGGGCCAGCT
CCATGTCTGAGTGCCACTGTCTTTGTGTCTTTGTGACTGGTGAGTGGGAACAGGCCATAGTGCAGAAGGCCAAGATCAGC
TCATGGGTGGCCACCCTGAGGCCTCTGGGAAGGAGACAGATTTTTACTAGATGATTTGCTGTTGCCACTCTTTGGGGATG
ACGGCTTTTGAGATTCTTCCTGGTGATAGAGGATGGCGTGGTGAAGGCGTTGCATGAGCCTGACCATACAGGCCTCACCT
GCAGCCTGGCCCCA

Alignment

ORF - retro_cjac_3013 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.05 %
• Parental protein coverage: 78.77 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  GVRSFSRVAAAMAPIKVGDAIPAVEVFEGEPGNKVNLAELFKGKKGVLFGVPGAFT-PGCSK-THLPGFV
          G...FS...AAMAP...GDAI.A..VF..EPGNKV.L.EL..GKKGVLF...GAFT.P.C...THL.GF.
Retrocopy GTHNFSSAFAAMAPVMLGDAILALVVF*REPGNKVDLTELCQGKKGVLFRIAGAFT<PNCQR<THLLGFG

Parental  EQAEALKAKGVQVVACLSVNDAFVTGEWGRAHKAEGKVRLLADPTGAFGKETD-LLLDDSLVSIFGNR-R
          E....LK.K..Q................G..H.AEG...L......A.GKETD..LLDD.L...FG...R
Retrocopy E*SGVLKVKRGQLHV*VPLSLCLCDW*VGTGHSAEGQDQLMGGHPEASGKETD<FLLDDLLLPLFGDD<R

Parental  LKRFSMVVQDGIVKALNVEPDGTGLTCSLAP
          L.RF..V..DG.VKAL..EPD.TGLTCSLAP
Retrocopy LLRFFLVIEDGVVKALH-EPDHTGLTCSLAP

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	0.02 RPM	24.10 RPM
SRP051959_heart	0.05 RPM	15.80 RPM
SRP051959_kidney	0.09 RPM	21.17 RPM
SRP051959_liver	0.09 RPM	12.00 RPM
SRP051959_lung	0.05 RPM	7.89 RPM
SRP051959_lymph_node	0.16 RPM	9.68 RPM
SRP051959_skeletal_muscle	0.00 RPM	12.16 RPM
SRP051959_spleen	0.00 RPM	6.62 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3013 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3013 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3013 has 8 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_408
Pan troglodytes	retro_ptro_313
Gorilla gorilla	retro_ggor_404
Pongo abelii	retro_pabe_310
Macaca mulatta	retro_mmul_504
Sus scrofa	retro_sscr_888
Canis familiaris	retro_cfam_1806
Equus caballus	retro_ecab_844

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017959	1 retrocopy	retro_amel_753,
Bos taurus	ENSBTAG00000008648	1 retrocopy	retro_btau_1364,
Callithrix jacchus	ENSCJAG00000018014	1 retrocopy	retro_cjac_3013 ,
Dasypus novemcinctus	ENSDNOG00000004647	1 retrocopy	retro_dnov_2664,
Equus caballus	ENSECAG00000017747	2 retrocopies	retro_ecab_823, retro_ecab_844,
Echinops telfairi	ENSETEG00000000264	3 retrocopies	retro_etel_1821, retro_etel_662, retro_etel_740,
Felis catus	ENSFCAG00000028856	3 retrocopies	retro_fcat_1189, retro_fcat_410, retro_fcat_727,
Homo sapiens	ENSG00000126432	1 retrocopy	retro_hsap_408,
Gorilla gorilla	ENSGGOG00000001337	1 retrocopy	retro_ggor_404,
Loxodonta africana	ENSLAFG00000025661	2 retrocopies	retro_lafr_132, retro_lafr_250,
Macaca mulatta	ENSMMUG00000013397	1 retrocopy	retro_mmul_504,
Mustela putorius furo	ENSMPUG00000012907	1 retrocopy	retro_mputfur_1360,
Nomascus leucogenys	ENSNLEG00000005003	2 retrocopies	retro_nleu_1007, retro_nleu_2228,
Procavia capensis	ENSPCAG00000010811	1 retrocopy	retro_pcap_144,
Pongo abelii	ENSPPYG00000003106	1 retrocopy	retro_pabe_310,
Pan troglodytes	ENSPTRG00000003835	1 retrocopy	retro_ptro_313,
Sus scrofa	ENSSSCG00000013030	2 retrocopies	retro_sscr_1041, retro_sscr_888,