RetrogeneDB ID: retro_pabe_1276

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 15:22151622..22152050(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPS18C
• Ensembl ID: ENSPPYG00000025867
• Aliases: None
• Description: mitochondrial ribosomal protein S18C [Source:HGNC Symbol;Acc:16633]

Sequence

>retro_pabe_1276
ATGGCCACTATAGTTGCTGTTTGCAGTGGTCTGGGGAGGAAGAAGTTGACACACCTTGTAATGGCTGCTGTTAGCCTTAC
ACATCCCAGGACTCATATGGTGCTATGAAGAAGAGGTTGTTCACAATATAAACAGATATCCAGCAATGAGGACCTGCCCA
TTCCAATGGAAAATTCTTATAAAGAAGCCCTTAAGAAATGTATCTTGTGTGGAAAGCAGGTAGATTTTAAGAATGTACAG
CGTCCCAGTTTATTTCTCCATTTGTTGGATGCATTTGTGGAAGGCACAAAACAGGTCTTTGTGGGAAGAAACAGAAAGAA
ATCACAAAAGCAATTAAGAGAGCTCAAATAATGGGGTTTATGCCAGTTACATCCAAGGATGCTGCATATCTCAAGGACCC
TAAAATTTGTAACATCAGATATCAGGAG

Alignment

ORF - retro_pabe_1276 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.41 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAMVAACGGLGRKKLTHLVTAAVSLTHPGTHTVLWRRGCSQYKQVSSNEDLPIPMENPYKEPLKKCILC
          MA..VA.C.GLGRKKLTHLV.AAVSLTHP.TH.VL.RRGCSQYKQ.SSNEDLPIPMEN.YKE.LKKCILC
Retrocopy MATIVAVCSGLGRKKLTHLVMAAVSLTHPRTHMVL*RRGCSQYKQISSNEDLPIPMENSYKEALKKCILC

Parental  GKHVDYKNVQLLSQFVSPFTGCIYGRHITGLCGKKQK-EITKAIKRAQIMGFMPVTYKDPAYLKDPKVCN
          GK.VD.KNVQ..S.F.........G.......G...K.EITKAIKRAQIMGFMPVT.KD.AYLKDPK.CN
Retrocopy GKQVDFKNVQRPSLFLHLLDAFVEGTKQV-FVGRNRK<EITKAIKRAQIMGFMPVTSKDAAYLKDPKICN

Parental  IRYRE
          IRY.E
Retrocopy IRYQE

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	0.00 RPM	1.88 RPM
SRP007412_cerebellum	0.00 RPM	1.82 RPM
SRP007412_heart	0.00 RPM	2.08 RPM
SRP007412_kidney	0.00 RPM	3.18 RPM
SRP007412_liver	0.00 RPM	2.75 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1276 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1276 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1276 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1540
Pan troglodytes	retro_ptro_1039
Gorilla gorilla	retro_ggor_1173
Macaca mulatta	retro_mmul_2203

---

Parental genes homology:

Parental genes homology involve 21 parental genes, and 49 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000018155	3 retrocopies	retro_btau_1386, retro_btau_309, retro_btau_502,
Callithrix jacchus	ENSCJAG00000005286	3 retrocopies	retro_cjac_1419, retro_cjac_234, retro_cjac_3970,
Cavia porcellus	ENSCPOG00000009198	1 retrocopy	retro_cpor_178,
Dasypus novemcinctus	ENSDNOG00000018326	2 retrocopies	retro_dnov_1030, retro_dnov_152,
Homo sapiens	ENSG00000163319	5 retrocopies	retro_hsap_1540, retro_hsap_2597, retro_hsap_4019, retro_hsap_4684, retro_hsap_969,
Gorilla gorilla	ENSGGOG00000008603	2 retrocopies	retro_ggor_1173, retro_ggor_2908,
Macropus eugenii	ENSMEUG00000010972	2 retrocopies	retro_meug_104, retro_meug_1113,
Myotis lucifugus	ENSMLUG00000017057	1 retrocopy	retro_mluc_2360,
Macaca mulatta	ENSMMUG00000015353	4 retrocopies	retro_mmul_2203, retro_mmul_2494, retro_mmul_655, retro_mmul_793,
Mus musculus	ENSMUSG00000016833	2 retrocopies	retro_mmus_1546, retro_mmus_2127,
Nomascus leucogenys	ENSNLEG00000009119	4 retrocopies	retro_nleu_111, retro_nleu_1614, retro_nleu_2722, retro_nleu_3010,
Ochotona princeps	ENSOPRG00000004113	2 retrocopies	retro_opri_1041, retro_opri_966,
Pongo abelii	ENSPPYG00000025867	2 retrocopies	retro_pabe_1276 , retro_pabe_70,
Pan troglodytes	ENSPTRG00000016233	3 retrocopies	retro_ptro_1039, retro_ptro_1521, retro_ptro_3113,
Pteropus vampyrus	ENSPVAG00000006439	2 retrocopies	retro_pvam_1326, retro_pvam_1412,
Rattus norvegicus	ENSRNOG00000002178	3 retrocopies	retro_rnor_2264, retro_rnor_2265, retro_rnor_477,
Sarcophilus harrisii	ENSSHAG00000007084	1 retrocopy	retro_shar_718,
Ictidomys tridecemlineatus	ENSSTOG00000007989	1 retrocopy	retro_itri_1231,
Tupaia belangeri	ENSTBEG00000012505	3 retrocopies	retro_tbel_1755, retro_tbel_4724, retro_tbel_508,
Tarsius syrichta	ENSTSYG00000012924	1 retrocopy	retro_tsyr_649,
Tursiops truncatus	ENSTTRG00000004897	2 retrocopies	retro_ttru_144, retro_ttru_1721,