RetrogeneDB ID: retro_pabe_147

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 10:100743049..100743694(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000002587
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RPS8
• Ensembl ID: ENSPPYG00000001426
• Aliases: None
• Description: ribosomal protein S8 [Source:HGNC Symbol;Acc:10441]

Sequence

>retro_pabe_147
GCTCTTTCCAGCCAGCGCCGAGCGACGGGCATCTCTCGGGACAACTGGCACAAGCGCCGCAAAACCGGGGGCAAGAGAAA
GCCCTACCACAAGAAGCGGAAGTATGAGTTGGGGCACCCAGCTGCCAGCACCAAGATTGGCCCCCGCCGCATCCACACAG
TCCGTGTGCGGGGAGGTAACAAGAAATACCGTGCCCTGAGGTTGGACGTGGGGAATTTCTCCTGGGGCTCAGAGTGTTGT
ACTCGTAAAACAAGGATCATCGATGTTGTCTACAATGCATCTAATAACGAACTGGTTCGTACCAAGACCCTGGTGAAGAA
TTGCATCGTGCTCATCGACAGCACACCGTACCGACAGTGGTACGAGTCCCACTATGCACTGCCCCTGGGCCGCAAGAAGG
GATCCAAGCTGACTCCTGAGGAAGAAGAGATTTTAAACAAAAAACGATCTAAAAAAATTCAGAAGAAATATGATGAAAGG
AAAAAGAATGCCAAAATCAGCAGTCTCCTGGAGGAGCAGTTCCAGCAGGGCAAGCTTCTTGCATGCATCGCTTCAAGGCC
GGGACAGTGTGGCCGAGCAGATGGCTATGTGCTAGAGGGCAAAGAGTTGGAGTTCTATCTTAGGAATAAGGCCCGGAAAG
GCAAA

Alignment

ORF - retro_pabe_147 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.58 %
• Parental protein coverage: 99.52 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GISRDNWHKRRKTGGKRKPYHKKRKYELGRPAANTKIGPRRIHTVRVRGGNKKYRALRLDVGNFSWGSEC
          GISRDNWHKRRKTGGKRKPYHKKRKYELG.PAA.TKIGPRRIHTVRVRGGNKKYRALRLDVGNFSWGSEC
Retrocopy GISRDNWHKRRKTGGKRKPYHKKRKYELGHPAASTKIGPRRIHTVRVRGGNKKYRALRLDVGNFSWGSEC

Parental  CTRKTRIIDVVYNASNNELVRTKTLVKNCIVLIDSTPYRQWYESHYALPLGRKKGAKLTPEEEEILNKKR
          CTRKTRIIDVVYNASNNELVRTKTLVKNCIVLIDSTPYRQWYESHYALPLGRKKG.KLTPEEEEILNKKR
Retrocopy CTRKTRIIDVVYNASNNELVRTKTLVKNCIVLIDSTPYRQWYESHYALPLGRKKGSKLTPEEEEILNKKR

Parental  SKKIQKKYDERKKNAKISSLLEEQFQQGKLLACIASRPGQCGRADGYVLEGKELEFYLRKIKARKGK
          SKKIQKKYDERKKNAKISSLLEEQFQQGKLLACIASRPGQCGRADGYVLEGKELEFYLR..KARKGK
Retrocopy SKKIQKKYDERKKNAKISSLLEEQFQQGKLLACIASRPGQCGRADGYVLEGKELEFYLRN-KARKGK

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	0.22 RPM	74.97 RPM
SRP007412_cerebellum	0.12 RPM	45.24 RPM
SRP007412_heart	0.45 RPM	67.04 RPM
SRP007412_kidney	0.93 RPM	144.02 RPM
SRP007412_liver	0.67 RPM	136.79 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_147 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_147 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_147 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 26 parental genes, and 175 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000015697	1 retrocopy	retro_acar_124,
Ailuropoda melanoleuca	ENSAMEG00000014147	3 retrocopies	retro_amel_1883, retro_amel_373, retro_amel_972,
Bos taurus	ENSBTAG00000015285	2 retrocopies	retro_btau_1388, retro_btau_1593,
Choloepus hoffmanni	ENSCHOG00000008785	10 retrocopies	retro_chof_1197, retro_chof_1258, retro_chof_1466, retro_chof_1638, retro_chof_2066, retro_chof_2617, retro_chof_2633, retro_chof_274, retro_chof_331, retro_chof_951,
Callithrix jacchus	ENSCJAG00000004197	5 retrocopies	retro_cjac_1068, retro_cjac_181, retro_cjac_3138, retro_cjac_6, retro_cjac_951,
Cavia porcellus	ENSCPOG00000000723	3 retrocopies	retro_cpor_1099, retro_cpor_335, retro_cpor_621,
Dipodomys ordii	ENSDORG00000009287	1 retrocopy	retro_dord_429,
Felis catus	ENSFCAG00000022996	4 retrocopies	retro_fcat_1222, retro_fcat_200, retro_fcat_456, retro_fcat_962,
Gorilla gorilla	ENSGGOG00000005645	5 retrocopies	retro_ggor_1127, retro_ggor_1170, retro_ggor_1357, retro_ggor_1465, retro_ggor_556,
Loxodonta africana	ENSLAFG00000027596	3 retrocopies	retro_lafr_531, retro_lafr_647, retro_lafr_904,
Macropus eugenii	ENSMEUG00000001388	1 retrocopy	retro_meug_119,
Myotis lucifugus	ENSMLUG00000001559	30 retrocopies	retro_mluc_1114, retro_mluc_1132, retro_mluc_1165, retro_mluc_1277, retro_mluc_1288, retro_mluc_1418, retro_mluc_1467, retro_mluc_1476, retro_mluc_1486, retro_mluc_1634, retro_mluc_1656, retro_mluc_1689, retro_mluc_1808, retro_mluc_1911, retro_mluc_1938, retro_mluc_2043, retro_mluc_2055, retro_mluc_2085, retro_mluc_2111, retro_mluc_2153, retro_mluc_2182, retro_mluc_2209, retro_mluc_2414, retro_mluc_460, retro_mluc_662, retro_mluc_730, retro_mluc_773, retro_mluc_820, retro_mluc_821, retro_mluc_906,
Macaca mulatta	ENSMMUG00000015270	2 retrocopies	retro_mmul_275, retro_mmul_70,
Monodelphis domestica	ENSMODG00000028389	1 retrocopy	retro_mdom_998,
Mustela putorius furo	ENSMPUG00000013485	6 retrocopies	retro_mputfur_334, retro_mputfur_337, retro_mputfur_493, retro_mputfur_780, retro_mputfur_908, retro_mputfur_986,
Mus musculus	ENSMUSG00000047675	33 retrocopies	retro_mmus_1003, retro_mmus_1067, retro_mmus_1184, retro_mmus_1694, retro_mmus_1755, retro_mmus_1796, retro_mmus_2001, retro_mmus_2002, retro_mmus_2003, retro_mmus_2031, retro_mmus_2132, retro_mmus_2173, retro_mmus_2264, retro_mmus_2732, retro_mmus_2772, retro_mmus_2847, retro_mmus_2861, retro_mmus_293, retro_mmus_2956, retro_mmus_2998, retro_mmus_3018, retro_mmus_3052, retro_mmus_3057, retro_mmus_3279, retro_mmus_3307, retro_mmus_3521, retro_mmus_364, retro_mmus_392, retro_mmus_548, retro_mmus_559, retro_mmus_596, retro_mmus_646, retro_mmus_876,
Nomascus leucogenys	ENSNLEG00000014147	1 retrocopy	retro_nleu_34,
Oryctolagus cuniculus	ENSOCUG00000012476	1 retrocopy	retro_ocun_168,
Otolemur garnettii	ENSOGAG00000006922	16 retrocopies	retro_ogar_1156, retro_ogar_1746, retro_ogar_1895, retro_ogar_2501, retro_ogar_2529, retro_ogar_2556, retro_ogar_2699, retro_ogar_2723, retro_ogar_2947, retro_ogar_308, retro_ogar_3291, retro_ogar_3436, retro_ogar_394, retro_ogar_521, retro_ogar_730, retro_ogar_805,
Pongo abelii	ENSPPYG00000001426	1 retrocopy	retro_pabe_147 ,
Pteropus vampyrus	ENSPVAG00000009859	10 retrocopies	retro_pvam_1285, retro_pvam_1315, retro_pvam_1345, retro_pvam_403, retro_pvam_419, retro_pvam_463, retro_pvam_514, retro_pvam_578, retro_pvam_685, retro_pvam_991,
Rattus norvegicus	ENSRNOG00000018768	2 retrocopies	retro_rnor_222, retro_rnor_235,
Sarcophilus harrisii	ENSSHAG00000000111	5 retrocopies	retro_shar_408, retro_shar_472, retro_shar_480, retro_shar_636, retro_shar_667,
Sus scrofa	ENSSSCG00000003930	4 retrocopies	retro_sscr_353, retro_sscr_550, retro_sscr_607, retro_sscr_919,
Tupaia belangeri	ENSTBEG00000000418	20 retrocopies	retro_tbel_1066, retro_tbel_1537, retro_tbel_1538, retro_tbel_163, retro_tbel_1699, retro_tbel_2356, retro_tbel_244, retro_tbel_2580, retro_tbel_3058, retro_tbel_3230, retro_tbel_3478, retro_tbel_3905, retro_tbel_3950, retro_tbel_4241, retro_tbel_4250, retro_tbel_4530, retro_tbel_552, retro_tbel_803, retro_tbel_827, retro_tbel_934,
Tarsius syrichta	ENSTSYG00000005525	5 retrocopies	retro_tsyr_1412, retro_tsyr_1507, retro_tsyr_2176, retro_tsyr_552, retro_tsyr_734,