RetrogeneDB ID: retro_ptro_1648

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2B:143691737..143692510(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPS18B
• Ensembl ID: ENSPTRG00000017932
• Aliases: None
• Description: Pan troglodytes mitochondrial ribosomal protein S18B (MRPS18B), nuclear gene encoding mitochondrial protein, mRNA. [Source:RefSeq mRNA;Acc:NM_001040115]

Sequence

>retro_ptro_1648
ATGGTGATGCCCATATTAAACACCTACTGAGGCAGCTTCCTATCCTTTCTGTCTTCTGAAGTACAAATGGAGTTCAGGTT
CCCCTCCAGACTCTTTCACCAAAGCTCCTTCTGAGAAAGATTCTTTGCCCCCAGTTCCCATTTCACTATATGAGAATGAA
CCCTGGAAATATCTGGAATCAGAAGAATACCAAGAACCATAGGGTTCTCGTCCCAACTGGGTGGACTATTGCCACTACAA
CAAGGGTGGTATACCCCCACAGCAGACTCAAAAGACATGTATACATAGGAAAAAAGTTGCTGGGAATCCCTGCCCCATCT
GCCAAGATCACAAGTTGCATGTTGACTTTAGGAATGTTAAGCTCTTGGAACAGTTTGTCAGTGCCCACACGGGTATTATC
TTCCATGCTCCATACACAGGAGTCTGTATGAAGCAGCACAAGATGTTGACCCATGCCATCCAGAAAGCCAGGGATCATGG
TCTCCTCAGTTACCACATCTCCCAAGTTGAACCCCGGGACCTTGATTTTAGTGCCTCTCATGGAGCTATGAGTACTTCTC
TGCCAGTCCCCACCCTGGTCTCAGGTGAACCATGGTATCTATGGTACAGCTGGAAACAGCCATCAGAGAAAGAACTGTCT
CACCTTTGCCAGCTCTATCAGGATTATCTCGAAGAAGAGAGTGGCCCCCGCACCTGAGTCAATGCCCAAGATGCTCCCCA
CAACACCAGTGGAAGCCTCCTTCACTGAATAGACAGGCCCCTAGAGTGCTCTG

Alignment

ORF - retro_ptro_1648 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.56 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAASVLNT-VLRRLPMLSLFRGSHRVQVPLQTLC-TKAPSEEDSLSSVPISPYKDEPWKYLESEEYQERY
          M....LNT..LR.LP.LS.F.....VQVPLQTL..TKAPSE.DSL..VPIS.Y..EPWKYLESEEYQE..
Retrocopy MVMPILNT<LLRQLPILSVF*STNGVQVPLQTLS<TKAPSEKDSLPPVPISLYENEPWKYLESEEYQEP*

Parental  GSRPVWADYRRNHKGGVPPQRTRKTCIRRNKVVGNPCPICRDHKLHVDFRNVKLLEQFVCAHTGIIFHAP
          GSRP.W.DY....KGG.PPQ.T.KTCI.R.KV.GNPCPIC.DHKLHVDFRNVKLLEQFV.AHTGIIFHAP
Retrocopy GSRPNWVDYCHYNKGGIPPQQTQKTCIHRKKVAGNPCPICQDHKLHVDFRNVKLLEQFVSAHTGIIFHAP

Parental  YTGVCVKQHKRLTQAIQKARDHGLLIYHIPQVEPRDLDFSTSHGAVSATPPAPTLVSGDPWYPWYNWKQP
          YTGVC.KQHK.LT.AIQKARDHGLL.YHI.QVEPRDLDFS.SHGA.S...P.PTLVSG.PWY.WY.WKQP
Retrocopy YTGVCMKQHKMLTHAIQKARDHGLLSYHISQVEPRDLDFSASHGAMSTSLPVPTLVSGEPWYLWYSWKQP

Parental  PERELSRLRRLYQGHLREESG-PPPESMPKMPPRTPAEASSTGQTGPQSAL
          .E.ELS.L..LYQ..L.EESG.P.PESMPKM.P.TP.EAS.T..TGP.SAL
Retrocopy SEKELSHLCQLYQDYLEEESG>PAPESMPKMLPTTPVEASFTE*TGP*SAL

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	20.34 RPM
SRP007412_cerebellum	0.00 RPM	20.94 RPM
SRP007412_heart	0.00 RPM	35.44 RPM
SRP007412_kidney	0.00 RPM	43.28 RPM
SRP007412_liver	0.00 RPM	43.83 RPM
SRP007412_testis	0.00 RPM	16.76 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1648 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1648 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1648 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2162
Pongo abelii	retro_pabe_2050

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005581	1 retrocopy	retro_chof_505,
Macropus eugenii	ENSMEUG00000012457	10 retrocopies	retro_meug_1183, retro_meug_2004, retro_meug_2124, retro_meug_215, retro_meug_610, retro_meug_648, retro_meug_696, retro_meug_712, retro_meug_717, retro_meug_734,
Macaca mulatta	ENSMMUG00000006525	1 retrocopy	retro_mmul_900,
Monodelphis domestica	ENSMODG00000015933	1 retrocopy	retro_mdom_426,
Mus musculus	ENSMUSG00000024436	1 retrocopy	retro_mmus_2036,
Nomascus leucogenys	ENSNLEG00000005224	1 retrocopy	retro_nleu_1811,
Oryctolagus cuniculus	ENSOCUG00000002149	2 retrocopies	retro_ocun_1307, retro_ocun_1641,
Pongo abelii	ENSPPYG00000016412	1 retrocopy	retro_pabe_2050,
Pan troglodytes	ENSPTRG00000017932	1 retrocopy	retro_ptro_1648 ,
Rattus norvegicus	ENSRNOG00000000804	1 retrocopy	retro_rnor_1328,
Ictidomys tridecemlineatus	ENSSTOG00000011853	1 retrocopy	retro_itri_254,
Tarsius syrichta	ENSTSYG00000003333	1 retrocopy	retro_tsyr_1769,