RetrogeneDB ID: retro_ptro_3030

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: GL391837.1:2638862..2639236(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM230
• Ensembl ID: ENSPTRG00000013221
• Aliases: None
• Description: transmembrane protein 230 [Source:HGNC Symbol;Acc:15876]

Sequence

>retro_ptro_3030
CTGTGTCAGCGAGTTATGATGCCGTCCCATACCAACCTGGCTACTGGAATCCCCAGTAGTAAAGTGAAATATTCAAGGCT
CTCCAGCACAGACGATGGCTACATTGACCTTCAGTTTAAGAAAACCCCTCTAAGATCCCTTATAAGGCCATCTCACTTGC
CACTGTGCTATTTTTGATTGGCGCCTTTCTCATTATTATAGGCTCCCTCCTGCTGTCAGGCTACATCAGCAAAGGCGGGG
CAGACGGGGCCGTTCCAGTCCTGATCATTGGCATTCTGGTGTTCCTACCCGGATTTTACCACCTGCGCATCGCTTACTAT
GCATCCAAAGGCTACCGTAGTTACTCCTAAGATGACATTCCAGACTTTGATGAC

Alignment

ORF - retro_ptro_3030 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.65 %
• Parental protein coverage: 68.31 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LWQRVMMPSRTNLATGIPSSKVKYSRLSSTDDGYIDLQFKKTP-PKIPYKAIALATVLFLIGAFLIIIGS
          L.QRVMMPS.TNLATGIPSSKVKYSRLSSTDDGYIDLQFKKTP..KIPYKAI.LATVLFLIGAFLIIIGS
Retrocopy LCQRVMMPSHTNLATGIPSSKVKYSRLSSTDDGYIDLQFKKTP<SKIPYKAISLATVLFLIGAFLIIIGS

Parental  LLLSGYISKGGADRAVPVLIIGILVFLPGFYHLRIAYYASKGYRGYSYDDIPDFDD
          LLLSGYISKGGAD.AVPVLIIGILVFLPGFYHLRIAYYASKGYR.YS.DDIPDFDD
Retrocopy LLLSGYISKGGADGAVPVLIIGILVFLPGFYHLRIAYYASKGYRSYS*DDIPDFDD

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
SRP007412_brain_prefrontal_cortex	0.68 RPM	52.30 RPM
SRP007412_cerebellum	1.90 RPM	33.48 RPM
SRP007412_heart	0.70 RPM	30.69 RPM
SRP007412_kidney	0.99 RPM	54.45 RPM
SRP007412_liver	1.01 RPM	35.71 RPM
SRP007412_testis	0.11 RPM	20.87 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3030 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3030 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3030 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_783

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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,