RetrogeneDB ID: retro_cjac_4206

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:96575028..96575368(-)
• 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_4206
CAGTGTGCTATGATGCCATCCCACACAAACCTGGTTGGAATCCCCAGTAGTAAAGTGAAATACTCAAGGATCTCCAGTAC
AGGTGATGGCTACACTGACCTTCAGTTTAGAAAAGCTCTCCTAAAATCCCTTACAAGGCCACTGCATTTGCCACTGTGCT
TTCTCGATTGGTGCCTTTCTCATTATCACAGGCTCACCTTCTGGCTACATCAGCAAGGTGGGGGCAGACTGGGCAGTTCC
AGTCCTGATCACTAATTCTCCTATTTCTGTTCAGATTTTACCACCTGCACAGAGCCTACTATGCATCCAAAGGATTACTT
CTAGGGCTTACCAGGATTAT

Alignment

ORF - retro_cjac_4206 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.03 %
• Parental protein coverage: 69.75 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QRVMMPSRTNLATGIPSSKVKYSRLSSTDDGYIDLQFK-KSPPKIPYKAIALATVL-FLIGAFLIIIGSL
          Q..MMPS.TNL..GIPSSKVKYSR.SST.DGY.DLQF..KS.PKIPYKA.A.ATVL.F.IGAFLII.GS.
Retrocopy QCAMMPSHTNLV-GIPSSKVKYSRISSTGDGYTDLQFR<KSSPKIPYKATAFATVL<FSIGAFLIITGS-

Parental  LLSGYISKGGADRAVPVLI----IGILVFLPGFYHLRIAYYASKGYRGY
          ..SGYISK.GAD.AVPVLI....I......P....L.I....S..Y..Y
Retrocopy -PSGYISKVGADWAVPVLITNSPISVQILPPAQSLLCIQRITSRAYQDY

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	0.04 RPM	17.38 RPM
SRP051959_kidney	0.00 RPM	21.25 RPM
SRP051959_liver	0.00 RPM	27.01 RPM
SRP051959_lung	0.02 RPM	21.21 RPM
SRP051959_lymph_node	0.00 RPM	21.28 RPM
SRP051959_skeletal_muscle	0.00 RPM	23.06 RPM
SRP051959_spleen	0.04 RPM	21.70 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4206 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4206 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4206 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4890
Pan troglodytes	retro_ptro_3257
Pongo abelii	retro_pabe_3801
Macaca mulatta	retro_mmul_2626

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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,