RetrogeneDB ID: retro_pabe_3507

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 9:119880191..119880565(-)
• Located in intron of: ENSPPYG00000019586

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS25
• Ensembl ID: ENSPPYG00000025915
• Aliases: None
• Description: ribosomal protein S25 [Source:HGNC Symbol;Acc:10413]

Sequence

>retro_pabe_3507
ATGCCACCCAAGGACTACAAGAAGAAGAAAGACACTGGAAAGTCAGCCAAGAAAGACAAAGACTCACTGAACAAACCCGG
GGGCAAGGCCAAAAAGAAGAAATGGTCCAAAGGCAAAGTTAGGGACAAGCTCAATACCTTGTCTTGTTTGACGAAGCTAC
CTATGACAAACTCTGTAAATAAGTTCCCAACTATAAACTTACAACTCCAGCTGTGGTCTCTAAGAGACTGAAGATTTGAG
GTTCCCTGGCCAGGGCAGCCCTTCTGGAGCTCCTTAGTAAAGGACTTATCAAACTGGTTTCAAAGCACAGAGCTCAAGTA
ATTTACACCAGAAATACCAAGGGCAGAGATGCTCCAGCTGCTGGTGAAGATGCA

Alignment

ORF - retro_pabe_3507 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.89 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPPKDDKKKKDAGKSAKKDKDPVNKSGGKAKKKKWSKGKVRDKLNNL-VLFDKATYDKLCKEVPNYKLIT
          MPPKD.KKKKD.GKSAKKDKD..NK.GGKAKKKKWSKGKVRDKLN.L.VLFD.ATYDKLCK.VPNYKL.T
Retrocopy MPPKDYKKKKDTGKSAKKDKDSLNKPGGKAKKKKWSKGKVRDKLNTL<VLFDEATYDKLCK*VPNYKLTT

Parental  PAVVSERLKIRGSLARAALQELLSKGLIKLVSKHRAQVIYTRNTKGGDAPAAGEDA
          PAVVS.RLKI.GSLARAAL.ELLSKGLIKLVSKHRAQVIYTRNTKG.DAPAAGEDA
Retrocopy PAVVSKRLKI*GSLARAALLELLSKGLIKLVSKHRAQVIYTRNTKGRDAPAAGEDA

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	63.53 RPM
SRP007412_cerebellum	0.24 RPM	76.24 RPM
SRP007412_heart	0.03 RPM	100.58 RPM
SRP007412_kidney	0.00 RPM	140.58 RPM
SRP007412_liver	0.03 RPM	145.20 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3507 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3507 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3507 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4310
Pan troglodytes	retro_ptro_2918
Gorilla gorilla	retro_ggor_2880

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 110 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000027772	2 retrocopies	retro_btau_203, retro_btau_9,
Callithrix jacchus	ENSCJAG00000013691	1 retrocopy	retro_cjac_208,
Dasypus novemcinctus	ENSDNOG00000007880	7 retrocopies	retro_dnov_1092, retro_dnov_1566, retro_dnov_2219, retro_dnov_2593, retro_dnov_346, retro_dnov_877, retro_dnov_973,
Homo sapiens	ENSG00000118181	3 retrocopies	retro_hsap_3371, retro_hsap_3547, retro_hsap_4310,
Gorilla gorilla	ENSGGOG00000025540	7 retrocopies	retro_ggor_1601, retro_ggor_1666, retro_ggor_1979, retro_ggor_2395, retro_ggor_2880, retro_ggor_337, retro_ggor_634,
Latimeria chalumnae	ENSLACG00000017531	4 retrocopies	retro_lcha_101, retro_lcha_118, retro_lcha_50, retro_lcha_72,
Macropus eugenii	ENSMEUG00000014185	3 retrocopies	retro_meug_1181, retro_meug_1562, retro_meug_174,
Mus musculus	ENSMUSG00000009927	15 retrocopies	retro_mmus_128, retro_mmus_1368, retro_mmus_1455, retro_mmus_1760, retro_mmus_1769, retro_mmus_1788, retro_mmus_2375, retro_mmus_2393, retro_mmus_2641, retro_mmus_2700, retro_mmus_2797, retro_mmus_3218, retro_mmus_336, retro_mmus_3523, retro_mmus_880,
Oryctolagus cuniculus	ENSOCUG00000017256	11 retrocopies	retro_ocun_1166, retro_ocun_1231, retro_ocun_1319, retro_ocun_1553, retro_ocun_1761, retro_ocun_291, retro_ocun_298, retro_ocun_548, retro_ocun_623, retro_ocun_856, retro_ocun_978,
Otolemur garnettii	ENSOGAG00000007265	3 retrocopies	retro_ogar_220, retro_ogar_257, retro_ogar_32,
Ochotona princeps	ENSOPRG00000016194	9 retrocopies	retro_opri_1099, retro_opri_1204, retro_opri_256, retro_opri_320, retro_opri_393, retro_opri_493, retro_opri_64, retro_opri_854, retro_opri_873,
Pongo abelii	ENSPPYG00000025915	6 retrocopies	retro_pabe_1889, retro_pabe_1971, retro_pabe_2930, retro_pabe_3507 , retro_pabe_71, retro_pabe_94,
Sorex araneus	ENSSARG00000002284	4 retrocopies	retro_sara_21, retro_sara_212, retro_sara_43, retro_sara_542,
Tupaia belangeri	ENSTBEG00000010244	16 retrocopies	retro_tbel_1592, retro_tbel_1823, retro_tbel_1849, retro_tbel_22, retro_tbel_2651, retro_tbel_2744, retro_tbel_3106, retro_tbel_3107, retro_tbel_3499, retro_tbel_374, retro_tbel_3871, retro_tbel_3877, retro_tbel_4239, retro_tbel_4434, retro_tbel_444, retro_tbel_4464,
Tarsius syrichta	ENSTSYG00000005422	15 retrocopies	retro_tsyr_1050, retro_tsyr_1098, retro_tsyr_1125, retro_tsyr_1230, retro_tsyr_1252, retro_tsyr_1454, retro_tsyr_154, retro_tsyr_1558, retro_tsyr_2081, retro_tsyr_358, retro_tsyr_414, retro_tsyr_428, retro_tsyr_570, retro_tsyr_859, retro_tsyr_873,
Vicugna pacos	ENSVPAG00000000266	4 retrocopies	retro_vpac_106, retro_vpac_118, retro_vpac_337, retro_vpac_546,