RetrogeneDB ID: retro_pabe_3413

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 9:58200209..58200815(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS5
• Ensembl ID: ENSPPYG00000010500
• Aliases: None
• Description: ribosomal protein S5 [Source:HGNC Symbol;Acc:10426]

Sequence

>retro_pabe_3413
ATGACCAAGTGGGAGACAGCAGCACCAGAGATGGCAGAGACCCCCAACATCCAGCTCTTTGGGAGGTGGAGCACTGATGA
TGTGCAGATCAATGACATTTCCCTGAAGGATTACATTGCAGTGAAGGAGAAGTATGCCAGGTACCTGCTTCGCAGTACAG
GGTAGTATGCCACCAAGCATTTCCACAAAACACAGTGCCCCATCTTGGAGCACCTCACTAACTCCATGATGATGCATGGC
CACAATAATGGCAAGAAACCCATGACCATGCACATTGTCAAGCATGCCTTTGAGATCATCCACCTGCTCACGAATGAGAA
CACTCTTCGAGTCTTGGTGAATGCCATCATCAACAGTGGTCCCTGGGAGGACTCCACATGCATTGGGTGAGCCAAGACCA
TGAGATGAAAGGCTGTGGATGTGTACCCACTGCATGGCATGAATCAGGCCATCTGGCTGCTGTGCAGAGGCACTTGTGAG
GCTTCCTTCCAGAACATCAAGACCATTGCTGAGTGCCTGGAAGATGAGCTCATCAATGCCACCAGGGACTCCTTCAACTC
CTATGTCATCAAGAAGGATGAGCTAGAGCATGTGGCCAAGTCCAAC

Alignment

ORF - retro_pabe_3413 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.37 %
• Parental protein coverage: 99.51 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTEWETAAPAVAETPDIKAFGKWSTDDVQINDISLQDYIAVKEKYAKYLPHSAGRYAAKRFRKAQCPIVE
          MT.WETAAP..AETP.I..FG.WSTDDVQINDISL.DYIAVKEKYA.YL..S.G.YA.K.F.K.QCPI.E
Retrocopy MTKWETAAPEMAETPNIQLFGRWSTDDVQINDISLKDYIAVKEKYARYLLRSTG*YATKHFHKTQCPILE

Parental  RLTNSMMMHGRNNGKKLMTVRIVKHAFEIIHLLTGENPLQVLVNAIINSGPREDSTRIGRAGTVRRQAVD
          .LTNSMMMHG.NNGKK.MT..IVKHAFEIIHLLT.EN.L.VLVNAIINSGP.EDST.IG.A.T.R..AVD
Retrocopy HLTNSMMMHGHNNGKKPMTMHIVKHAFEIIHLLTNENTLRVLVNAIINSGPWEDSTCIG*AKTMR*KAVD

Parental  VSPLRRVNQAIWLLCTGAREAAFRNIKTIAECLADELINAAKGSSNSYAIKKKDELERVAKSN
          V.PL...NQAIWLLC.G..EA.F.NIKTIAECL.DELINA...S.NSY.I.KKDELE.VAKSN
Retrocopy VYPLHGMNQAIWLLCRGTCEASFQNIKTIAECLEDELINATRDSFNSYVI-KKDELEHVAKSN

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	0.17 RPM	48.82 RPM
SRP007412_cerebellum	0.12 RPM	68.70 RPM
SRP007412_heart	0.03 RPM	81.58 RPM
SRP007412_kidney	0.17 RPM	131.03 RPM
SRP007412_liver	0.03 RPM	155.40 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3413 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3413 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3413 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4224
Gorilla gorilla	retro_ggor_2828

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 49 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000002366	1 retrocopy	retro_cfam_1355,
Callithrix jacchus	ENSCJAG00000000304	6 retrocopies	retro_cjac_1463, retro_cjac_2049, retro_cjac_2050, retro_cjac_2508, retro_cjac_4105, retro_cjac_599,
Echinops telfairi	ENSETEG00000013543	1 retrocopy	retro_etel_912,
Homo sapiens	ENSG00000083845	5 retrocopies	retro_hsap_2524, retro_hsap_2526, retro_hsap_3649, retro_hsap_3976, retro_hsap_4224,
Gorilla gorilla	ENSGGOG00000004258	4 retrocopies	retro_ggor_1577, retro_ggor_2465, retro_ggor_2828, retro_ggor_2942,
Macropus eugenii	ENSMEUG00000015400	3 retrocopies	retro_meug_1075, retro_meug_1792, retro_meug_347,
Myotis lucifugus	ENSMLUG00000012641	1 retrocopy	retro_mluc_2266,
Macaca mulatta	ENSMMUG00000008729	3 retrocopies	retro_mmul_1595, retro_mmul_2525, retro_mmul_77,
Mustela putorius furo	ENSMPUG00000008308	1 retrocopy	retro_mputfur_1316,
Ornithorhynchus anatinus	ENSOANG00000011921	1 retrocopy	retro_oana_83,
Otolemur garnettii	ENSOGAG00000013088	2 retrocopies	retro_ogar_1711, retro_ogar_3461,
Procavia capensis	ENSPCAG00000011034	2 retrocopies	retro_pcap_168, retro_pcap_58,
Pongo abelii	ENSPPYG00000010500	7 retrocopies	retro_pabe_1857, retro_pabe_1858, retro_pabe_2996, retro_pabe_3270, retro_pabe_3413 , retro_pabe_3683, retro_pabe_375,
Pan troglodytes	ENSPTRG00000011591	6 retrocopies	retro_ptro_1469, retro_ptro_1471, retro_ptro_2474, retro_ptro_2700, retro_ptro_2868, retro_ptro_3152,
Ictidomys tridecemlineatus	ENSSTOG00000005935	1 retrocopy	retro_itri_1742,
Tupaia belangeri	ENSTBEG00000016955	2 retrocopies	retro_tbel_1127, retro_tbel_1169,
Tarsius syrichta	ENSTSYG00000000076	2 retrocopies	retro_tsyr_1258, retro_tsyr_1981,
Tursiops truncatus	ENSTTRG00000001991	1 retrocopy	retro_ttru_106,