RetrogeneDB ID: retro_pabe_2933

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6:7559485..7559948(-)
• Located in intron of: ENSPPYG00000016206

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS3
• Ensembl ID: ENSPPYG00000003688
• Aliases: None
• Description: 40S ribosomal protein S3 [Source:RefSeq peptide;Acc:NP_001127020]

Sequence

>retro_pabe_2933
ATGGCCATACAAATTTCCAAGAAGAGGAAGTTTGTCATTGATGGCATCTTCTAAGCTGAAATGAATGAGTTTCTTACTCA
GGAGCTGGCTGAAGATGGCTACTCTGGAGTTGAGGTGCGAGTTACACCAACCAGGACAGAAATCATTATCTTAGCTACCA
GAACACAGAATGTTCTTGGTGAGAAGGGCTGGCGGATTCGGGAACTGACTGCTGTAGTTCAGAAGAGGTTTGGCTCTCCA
GAGGGCAGTGTAGAGCTTTATGCTGAAAAGGTGGCCACTAGGGGTCTGTGTGCATTGCCCAGGCAGAGTCTCTGCGTACA
AACTCCTAGGAGGGCTTGCTGTGTGGAGGGCCTGCTATGGTGTGTTGTGGTTCATCATGGAAAGTGGGGCCAAAGGCTGT
GAGGTCATGGTGTCTGGGAAACTCTGAGGACAGAGGGCTAAATCCATGAAGTTTGTGGATGGC

Alignment

ORF - retro_pabe_2933 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.72 %
• Parental protein coverage: 63.79 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAVQISKKRKFVADGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLGEKGRRIRELT
          MA.QISKKRKFV.DGIF.AE.NEFLT.ELAEDGYSGVEVRVTPTRTEIIILATRTQNVLGEKG.RIRELT
Retrocopy MAIQISKKRKFVIDGIF*AEMNEFLTQELAEDGYSGVEVRVTPTRTEIIILATRTQNVLGEKGWRIRELT

Parental  AVVQKRFGFPEGSVELYAEKVATRGLCA-IAQAESLR-YKLLGGLAVRRACYGVLRFIMESGAKGCEVVV
          AVVQKRFG.PEGSVELYAEKVATRGLCA.IAQAESLR.YKLLGGLAV.RACYGVL.FIMESGAKGCEV.V
Retrocopy AVVQKRFGSPEGSVELYAEKVATRGLCA<IAQAESLR<YKLLGGLAVWRACYGVLWFIMESGAKGCEVMV

Parental  SGKLRGQRAKSMKFVDG
          SGKL.GQRAKSMKFVDG
Retrocopy SGKL*GQRAKSMKFVDG

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	0.11 RPM	229.73 RPM
SRP007412_cerebellum	0.12 RPM	193.10 RPM
SRP007412_heart	0.09 RPM	238.33 RPM
SRP007412_kidney	0.33 RPM	446.55 RPM
SRP007412_liver	0.24 RPM	485.89 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2933 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2933 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2933 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 30 parental genes, and 97 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017051	2 retrocopies	retro_amel_1483, retro_amel_465,
Bos taurus	ENSBTAG00000005620	4 retrocopies	retro_btau_1626, retro_btau_425, retro_btau_909, retro_btau_924,
Canis familiaris	ENSCAFG00000005402	2 retrocopies	retro_cfam_1411, retro_cfam_1569,
Choloepus hoffmanni	ENSCHOG00000005328	8 retrocopies	retro_chof_1301, retro_chof_1369, retro_chof_1492, retro_chof_199, retro_chof_2477, retro_chof_2506, retro_chof_452, retro_chof_571,
Callithrix jacchus	ENSCJAG00000015424	4 retrocopies	retro_cjac_2355, retro_cjac_2593, retro_cjac_388, retro_cjac_3963,
Cavia porcellus	ENSCPOG00000004665	1 retrocopy	retro_cpor_995,
Dipodomys ordii	ENSDORG00000002974	2 retrocopies	retro_dord_608, retro_dord_758,
Equus caballus	ENSECAG00000013915	2 retrocopies	retro_ecab_588, retro_ecab_96,
Echinops telfairi	ENSETEG00000015500	3 retrocopies	retro_etel_1225, retro_etel_1757, retro_etel_857,
Felis catus	ENSFCAG00000011942	3 retrocopies	retro_fcat_1462, retro_fcat_1490, retro_fcat_981,
Homo sapiens	ENSG00000149273	4 retrocopies	retro_hsap_1124, retro_hsap_1655, retro_hsap_2736, retro_hsap_3552,
Gorilla gorilla	ENSGGOG00000006519	4 retrocopies	retro_ggor_1248, retro_ggor_1509, retro_ggor_216, retro_ggor_878,
Loxodonta africana	ENSLAFG00000004297	3 retrocopies	retro_lafr_278, retro_lafr_600, retro_lafr_861,
Macropus eugenii	ENSMEUG00000011581	4 retrocopies	retro_meug_1724, retro_meug_399, retro_meug_431, retro_meug_774,
Myotis lucifugus	ENSMLUG00000004079	3 retrocopies	retro_mluc_1092, retro_mluc_680, retro_mluc_934,
Macaca mulatta	ENSMMUG00000009019	6 retrocopies	retro_mmul_1166, retro_mmul_1634, retro_mmul_1779, retro_mmul_1816, retro_mmul_665, retro_mmul_871,
Monodelphis domestica	ENSMODG00000006945	1 retrocopy	retro_mdom_304,
Mustela putorius furo	ENSMPUG00000009197	3 retrocopies	retro_mputfur_412, retro_mputfur_443, retro_mputfur_936,
Mus musculus	ENSMUSG00000030744	2 retrocopies	retro_mmus_1453, retro_mmus_1776,
Nomascus leucogenys	ENSNLEG00000026915	2 retrocopies	retro_nleu_103, retro_nleu_236,
Oryctolagus cuniculus	ENSOCUG00000022412	3 retrocopies	retro_ocun_11, retro_ocun_1934, retro_ocun_787,
Otolemur garnettii	ENSOGAG00000005318	7 retrocopies	retro_ogar_1180, retro_ogar_1354, retro_ogar_1559, retro_ogar_1574, retro_ogar_2577, retro_ogar_2786, retro_ogar_999,
Pongo abelii	ENSPPYG00000003688	4 retrocopies	retro_pabe_1367, retro_pabe_2274, retro_pabe_2933 , retro_pabe_929,
Pteropus vampyrus	ENSPVAG00000011271	1 retrocopy	retro_pvam_1388,
Rattus norvegicus	ENSRNOG00000017418	3 retrocopies	retro_rnor_2328, retro_rnor_283, retro_rnor_930,
Sarcophilus harrisii	ENSSHAG00000011198	1 retrocopy	retro_shar_705,
Sus scrofa	ENSSSCG00000014855	4 retrocopies	retro_sscr_283, retro_sscr_556, retro_sscr_568, retro_sscr_900,
Tupaia belangeri	ENSTBEG00000007053	4 retrocopies	retro_tbel_1194, retro_tbel_2090, retro_tbel_265, retro_tbel_4262,
Tursiops truncatus	ENSTTRG00000005858	5 retrocopies	retro_ttru_1108, retro_ttru_1413, retro_ttru_1927, retro_ttru_50, retro_ttru_544,
Vicugna pacos	ENSVPAG00000011615	2 retrocopies	retro_vpac_131, retro_vpac_145,