RetrogeneDB ID: retro_pabe_3680

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:103726399..103726919(+)
• Located in intron of: ENSPPYG00000020597

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL18A
• Ensembl ID: ENSPPYG00000009725
• Aliases: None
• Description: ribosomal protein L18a [Source:HGNC Symbol;Acc:10311]

Sequence

>retro_pabe_3680
GCCTCTGTCACACTGCAAGAGTAAAAGGTGGCAGAGCACTGCCTGCCCACTCCCAAATGCTGCATGCTTCCCCTCTACCA
CATGCAAATCTTTGCACTTAATCATGTCATTGCCAAGTCCCGCTTCTGGTACTTTGTATCTCAGCTAAGGAAGATGAAGA
AGTCTTTGGGGGAAATTGTCTTGTGTGGGTAGGTATTTGAGCAATTCTGCCTGCAGGTGAAGAACTTCAGCTTGTGGCTG
CACCACAACTCATGCAGTGGCATCCACAACATGTACCAGGAATACCTGGACTTGGCCACTGGGGGTGCTGTCACCCAGTA
CTACAGAGAAACGGGTTCCCAGCAATGTGGTTGGGCCCACTGGATCCAGATTGTGAAGGTAGAAGGGATCTCGGCCAGCA
GGTGCCAGCAATCAAACAGTTCCACAGCTCCAAGATCAAGTTTGTGCTGTCCCATCGCATCCTGCATTGTCAGCACAAGC
CACACTTCACCACCAAGATGCCCAGCCCAACACCTTCTTT

Alignment

ORF - retro_pabe_3680 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.71 %
• Parental protein coverage: 98.86 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ASGTLREYKVVGRCLPTPKCHTPPLYRMRIFAPNHVVAKSRFWYFVSQLKKMKKSSGEIVYCGQVFEKSP
          AS.TL.E.KV...CLPTPKC...PLY.M.IFA.NHV.AKSRFWYFVSQL.KMKKS.GEIV.CG.VFE...
Retrocopy ASVTLQE*KVAEHCLPTPKCCMLPLYHMQIFALNHVIAKSRFWYFVSQLRKMKKSLGEIVLCG*VFEQFC

Parental  LRVKNFGIWLRYDSRSGTHNMYREYRDLTTAGAVTQCYRDMGARHRARAHSIQIMKVEEIAASKCRR-PA
          L.VKNF..WL...S.SG.HNMY.EY.DL.T.GAVTQ.YR..G......AH.IQI.KVE.I.AS.C.....
Retrocopy LQVKNFSLWLHHNSCSGIHNMYQEYLDLATGGAVTQYYRETGSQQCGWAHWIQIVKVEGISASRCQQ>QT

Parental  VKQFHDSKIKFPLPHRVLRRQHKPRFTTKRPNTFF
          V.Q..D.....P..H..L..Q.........PNTFF
Retrocopy VPQLQDQVCAVP-SHPALSAQATLHHQDAQPNTFF

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	83.71 RPM
SRP007412_cerebellum	0.00 RPM	50.95 RPM
SRP007412_heart	0.00 RPM	66.02 RPM
SRP007412_kidney	0.00 RPM	149.33 RPM
SRP007412_liver	0.00 RPM	162.89 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3680 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3680 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3680 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4734
Gorilla gorilla	retro_ggor_2940

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Parental genes homology:

Parental genes homology involve 27 parental genes, and 120 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000003125	1 retrocopy	retro_acar_86,
Ailuropoda melanoleuca	ENSAMEG00000010878	5 retrocopies	retro_amel_1046, retro_amel_1476, retro_amel_1601, retro_amel_280, retro_amel_461,
Bos taurus	ENSBTAG00000015831	5 retrocopies	retro_btau_145, retro_btau_1586, retro_btau_842, retro_btau_917, retro_btau_922,
Canis familiaris	ENSCAFG00000015122	1 retrocopy	retro_cfam_231,
Callithrix jacchus	ENSCJAG00000014006	7 retrocopies	retro_cjac_1628, retro_cjac_2814, retro_cjac_3192, retro_cjac_3906, retro_cjac_4134, retro_cjac_441, retro_cjac_642,
Cavia porcellus	ENSCPOG00000015205	1 retrocopy	retro_cpor_1478,
Equus caballus	ENSECAG00000015258	1 retrocopy	retro_ecab_745,
Felis catus	ENSFCAG00000007518	6 retrocopies	retro_fcat_1190, retro_fcat_1213, retro_fcat_1716, retro_fcat_1848, retro_fcat_267, retro_fcat_831,
Homo sapiens	ENSG00000105640	11 retrocopies	retro_hsap_1053, retro_hsap_128, retro_hsap_135, retro_hsap_1610, retro_hsap_1961, retro_hsap_2254, retro_hsap_2676, retro_hsap_2776, retro_hsap_4129, retro_hsap_4734, retro_hsap_4776,
Gorilla gorilla	ENSGGOG00000002870	8 retrocopies	retro_ggor_1215, retro_ggor_1680, retro_ggor_1868, retro_ggor_1933, retro_ggor_195, retro_ggor_227, retro_ggor_2775, retro_ggor_2940,
Macropus eugenii	ENSMEUG00000003228	2 retrocopies	retro_meug_36, retro_meug_49,
Myotis lucifugus	ENSMLUG00000006701	4 retrocopies	retro_mluc_1671, retro_mluc_1893, retro_mluc_1978, retro_mluc_2191,
Macaca mulatta	ENSMMUG00000028844	6 retrocopies	retro_mmul_1416, retro_mmul_1591, retro_mmul_2233, retro_mmul_2547, retro_mmul_292, retro_mmul_364,
Monodelphis domestica	ENSMODG00000019167	2 retrocopies	retro_mdom_349, retro_mdom_680,
Mustela putorius furo	ENSMPUG00000015786	4 retrocopies	retro_mputfur_1007, retro_mputfur_1189, retro_mputfur_1574, retro_mputfur_457,
Mus musculus	ENSMUSG00000045128	8 retrocopies	retro_mmus_1606, retro_mmus_260, retro_mmus_2910, retro_mmus_2924, retro_mmus_326, retro_mmus_346, retro_mmus_937, retro_mmus_951,
Nomascus leucogenys	ENSNLEG00000005889	7 retrocopies	retro_nleu_1087, retro_nleu_1180, retro_nleu_1940, retro_nleu_2261, retro_nleu_2605, retro_nleu_2672, retro_nleu_680,
Otolemur garnettii	ENSOGAG00000031828	4 retrocopies	retro_ogar_1016, retro_ogar_1891, retro_ogar_2226, retro_ogar_2564,
Pongo abelii	ENSPPYG00000009725	10 retrocopies	retro_pabe_1200, retro_pabe_1319, retro_pabe_1620, retro_pabe_2239, retro_pabe_2302, retro_pabe_3680 , retro_pabe_3717, retro_pabe_3802, retro_pabe_482, retro_pabe_487,
Pan troglodytes	ENSPTRG00000010686	3 retrocopies	retro_ptro_1078, retro_ptro_1803, retro_ptro_27,
Pteropus vampyrus	ENSPVAG00000017378	6 retrocopies	retro_pvam_1314, retro_pvam_133, retro_pvam_155, retro_pvam_200, retro_pvam_607, retro_pvam_828,
Rattus norvegicus	ENSRNOG00000018795	6 retrocopies	retro_rnor_108, retro_rnor_1655, retro_rnor_2279, retro_rnor_2362, retro_rnor_2821, retro_rnor_888,
Sarcophilus harrisii	ENSSHAG00000000406	3 retrocopies	retro_shar_435, retro_shar_474, retro_shar_706,
Sus scrofa	ENSSSCG00000013889	2 retrocopies	retro_sscr_1103, retro_sscr_184,
Ictidomys tridecemlineatus	ENSSTOG00000007788	1 retrocopy	retro_itri_694,
Tupaia belangeri	ENSTBEG00000010488	4 retrocopies	retro_tbel_2865, retro_tbel_2925, retro_tbel_635, retro_tbel_919,
Tursiops truncatus	ENSTTRG00000008977	2 retrocopies	retro_ttru_151, retro_ttru_508,