RetrogeneDB ID: retro_cjac_3112

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 8:12091985..12092365(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM230
• Ensembl ID: ENSCJAG00000021275
• Aliases: None
• Description: transmembrane protein 230 [Source:HGNC Symbol;Acc:15876]

Sequence

>retro_cjac_3112
ACTCCTCTCTGCCAGCGTGTTAGGATGCTGTCCGCACCAACTTGGCTACTGGAAGCCCCAGTAGTAAAGTGAAATATTCA
AGGCTCTCCAGCAGAGACGATGGCTACATTGACCTTCAGTTTAAGAAGAGCCCTCCAAAGATCCCTTACAAGGCCATTGC
ACTTGCCACTGTGCTGTTTTTGATTAGCACCTTTCTCATTATTATAGGCTCCCTCCTGCTCTCAGGCTACGTCAGCAAAG
TGGGGGCAGGCCAGGCCGTTCCAGTCCTGATCATTGGCATTCTGGTGTTCCTACCCGGATTTTACCACCTGTGCATCGCT
TTCTGTGCAGCCAAAGCCTACCACGGTTACTCCTATGATGACATTCCAGACTTTGCTGAC

Alignment

ORF - retro_cjac_3112 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.59 %
• Parental protein coverage: 78.4 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SPPYQRVMMPS-RTNLATGIPSSKVKYSRLSSTDDGYIDLQFKKSPPKIPYKAIALATVLFLIGAFLIII
          .P..QRV.M.S.RTNLATG.PSSKVKYSRLSS.DDGYIDLQFKKSPPKIPYKAIALATVLFLI..FLIII
Retrocopy TPLCQRVRMLS<RTNLATGSPSSKVKYSRLSSRDDGYIDLQFKKSPPKIPYKAIALATVLFLISTFLIII

Parental  GSLLLSGYISKGGADRAVPVLIIGILVFLPGFYHLRIAYYASKGYRGYSYDDIPDFDD
          GSLLLSGY.SK.GA..AVPVLIIGILVFLPGFYHL.IA..A.K.Y.GYSYDDIPDF.D
Retrocopy GSLLLSGYVSKVGAGQAVPVLIIGILVFLPGFYHLCIAFCAAKAYHGYSYDDIPDFAD

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	16.77 RPM
SRP051959_heart	0.00 RPM	17.38 RPM
SRP051959_kidney	0.02 RPM	21.25 RPM
SRP051959_liver	0.02 RPM	27.01 RPM
SRP051959_lung	0.02 RPM	21.21 RPM
SRP051959_lymph_node	0.00 RPM	21.28 RPM
SRP051959_skeletal_muscle	0.02 RPM	23.06 RPM
SRP051959_spleen	0.02 RPM	21.70 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3112 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3112 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3112 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 40 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006063	2 retrocopies	retro_btau_1079, retro_btau_147,
Choloepus hoffmanni	ENSCHOG00000010231	12 retrocopies	retro_chof_1228, retro_chof_1463, retro_chof_1812, retro_chof_2199, retro_chof_2210, retro_chof_2400, retro_chof_253, retro_chof_2584, retro_chof_2661, retro_chof_397, retro_chof_884, retro_chof_996,
Callithrix jacchus	ENSCJAG00000021275	2 retrocopies	retro_cjac_3112 , retro_cjac_4206,
Erinaceus europaeus	ENSEEUG00000014992	1 retrocopy	retro_eeur_77,
Homo sapiens	ENSG00000089063	3 retrocopies	retro_hsap_4890, retro_hsap_550, retro_hsap_783,
Loxodonta africana	ENSLAFG00000006412	1 retrocopy	retro_lafr_1033,
Myotis lucifugus	ENSMLUG00000023089	2 retrocopies	retro_mluc_1504, retro_mluc_1759,
Macaca mulatta	ENSMMUG00000013258	4 retrocopies	retro_mmul_1187, retro_mmul_2386, retro_mmul_2626, retro_mmul_856,
Nomascus leucogenys	ENSNLEG00000007719	3 retrocopies	retro_nleu_1256, retro_nleu_199, retro_nleu_723,
Otolemur garnettii	ENSOGAG00000001386	2 retrocopies	retro_ogar_1700, retro_ogar_3108,
Pongo abelii	ENSPPYG00000010796	3 retrocopies	retro_pabe_3801, retro_pabe_507, retro_pabe_916,
Pan troglodytes	ENSPTRG00000013221	4 retrocopies	retro_ptro_3030, retro_ptro_3257, retro_ptro_3258, retro_ptro_413,
Ictidomys tridecemlineatus	ENSSTOG00000019378	1 retrocopy	retro_itri_35,