RetrogeneDB ID: retro_cjac_1940

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:91395966..91396382(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000011188
• Aliases: None
• Description: None

Sequence

>retro_cjac_1940
CCAGGCTCCAGCAAGCACACCCTGTCACTGTGCATCAACAAACCCTTTGAACTGAATCACCTTTCATGTGAGGATCTGCC
CAAAGGCAATATGTGGAGGGACACAGAGATATGTCTGCTGGCCAAGACTTTCATTGACCAGGGGAAGCTCATTCCAGGTG
ATGCCATGATGTAACTGACCTCGTAGGAGCTGAAAAATCTCACCCAGTCTCATTGACTGTTGTATGGTTTCACCAGGACA
CTTCCACAGGCTGAAGGCCTAGATTGACTTTATCAGACACACCTGGTGATGAACTCAAACATGAAATTTGAGGTCATCAA
GCTATGCCTCATTGCTTGCTGGATTCACCCAGTCAATAGCCAAGTCACCAACCTCTAGTTCAACCCTCCAAAACAGTCTG
CATTGATGATCTGACT

Alignment

ORF - retro_cjac_1940 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.14 %
• Parental protein coverage: 61.23 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PGSGKGTVSSRITKHFELKHLSSGDLLRDNMLRGTEIGVLAKAFIDQGKLIPDDVMTRLALHELKNLTQY
          PGS.K.T.S..I.K.FEL.HLS..DL...NM.R.TEI..LAK.FIDQGKLIP.D.M..L...ELKNLTQ.
Retrocopy PGSSKHTLSLCINKPFELNHLSCEDLPKGNMWRDTEICLLAKTFIDQGKLIPGDAMM*LTS*ELKNLTQS

Parental  NWLLDGFPRTLPQAEALDRAYQIDTVINLNVPFEVIKQRLTARWIHPASGRVYNIEFNPP-KTVGIDDLT
          ..LL.GF.RTLPQAE.LD..YQ...V.N.N..FEVIK..L.A.WIHP....V.N..FNPP.KTV.IDDLT
Retrocopy H*LLYGFTRTLPQAEGLD*LYQTHLVMNSNMKFEVIKLCLIACWIHPVNSQVTNL*FNPP<KTVCIDDLT

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	41.49 RPM
SRP051959_heart	0.00 RPM	48.99 RPM
SRP051959_kidney	0.00 RPM	85.13 RPM
SRP051959_liver	0.02 RPM	112.16 RPM
SRP051959_lung	0.00 RPM	24.24 RPM
SRP051959_lymph_node	0.00 RPM	22.76 RPM
SRP051959_skeletal_muscle	0.02 RPM	35.31 RPM
SRP051959_spleen	0.02 RPM	37.35 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1940 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1940 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1940 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Bos taurus	retro_btau_323
Equus caballus	retro_ecab_317

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Parental genes homology:

Parental genes homology involve 25 parental genes, and 48 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002640	3 retrocopies	retro_amel_1009, retro_amel_1916, retro_amel_1931,
Bos taurus	ENSBTAG00000017147	1 retrocopy	retro_btau_323,
Callithrix jacchus	ENSCJAG00000011188	1 retrocopy	retro_cjac_1940 ,
Callithrix jacchus	ENSCJAG00000016835	1 retrocopy	retro_cjac_1856,
Equus caballus	ENSECAG00000011235	2 retrocopies	retro_ecab_317, retro_ecab_914,
Echinops telfairi	ENSETEG00000000829	1 retrocopy	retro_etel_57,
Felis catus	ENSFCAG00000028063	2 retrocopies	retro_fcat_162, retro_fcat_1982,
Homo sapiens	ENSG00000147853	3 retrocopies	retro_hsap_1163, retro_hsap_3228, retro_hsap_555,
Gorilla gorilla	ENSGGOG00000028122	3 retrocopies	retro_ggor_2195, retro_ggor_503, retro_ggor_908,
Loxodonta africana	ENSLAFG00000001126	1 retrocopy	retro_lafr_205,
Microcebus murinus	ENSMICG00000013112	3 retrocopies	retro_mmur_1474, retro_mmur_1559, retro_mmur_1579,
Myotis lucifugus	ENSMLUG00000017272	1 retrocopy	retro_mluc_535,
Macaca mulatta	ENSMMUG00000000143	2 retrocopies	retro_mmul_2032, retro_mmul_898,
Mustela putorius furo	ENSMPUG00000005006	2 retrocopies	retro_mputfur_1163, retro_mputfur_890,
Nomascus leucogenys	ENSNLEG00000008885	3 retrocopies	retro_nleu_2638, retro_nleu_2653, retro_nleu_948,
Oryctolagus cuniculus	ENSOCUG00000011411	1 retrocopy	retro_ocun_716,
Otolemur garnettii	ENSOGAG00000007477	2 retrocopies	retro_ogar_3482, retro_ogar_3492,
Pongo abelii	ENSPPYG00000019245	3 retrocopies	retro_pabe_2676, retro_pabe_3588, retro_pabe_967,
Pan troglodytes	ENSPTRG00000020742	5 retrocopies	retro_ptro_1785, retro_ptro_2180, retro_ptro_2895, retro_ptro_416, retro_ptro_796,
Pteropus vampyrus	ENSPVAG00000015751	1 retrocopy	retro_pvam_269,
Sus scrofa	ENSSSCG00000023595	1 retrocopy	retro_sscr_641,
Ictidomys tridecemlineatus	ENSSTOG00000000021	1 retrocopy	retro_itri_933,
Tupaia belangeri	ENSTBEG00000008054	3 retrocopies	retro_tbel_1463, retro_tbel_3247, retro_tbel_3397,
Tursiops truncatus	ENSTTRG00000016524	1 retrocopy	retro_ttru_1036,
Vicugna pacos	ENSVPAG00000009187	1 retrocopy	retro_vpac_137,