RetrogeneDB ID: retro_pabe_3004

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6:134590010..134590460(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL15
• Ensembl ID: ENSPPYG00000014065
• Aliases: None
• Description: 60S ribosomal protein L15 [Source:UniProtKB/Swiss-Prot;Acc:Q5NVE0]

Sequence

>retro_pabe_3004
GTGGGTGCATACAAGTACATCCAGGAACTATGGAGAAAGAAGCAGTCTGATGTCATATACTTTCTTCTGAGGGTCCGCTG
CTGGTAGTACTACCAGCTCTCTGCTTTCCACAGGGCTCCCCACCCCACCTGGCCTGATGAAGCACGCCGACTAGGCTACA
AGGCCAAGCAAGATTATAGGAATCGTGTTCGCCGTGGTGGCTGAAAACGTCCAGTTCCTAAGGGTGTAACTTACGGCAAG
CCTGTCCATCATGGTGTTAACCAGCTAAAGTTTGCTCGAAGCCTTCAGTCCTTTGTAGAGGAGCGAGCTGGATGCCACTG
TGGGGCTCTAAGAATCCTCAGTTCTTACTGGGCTGGTGAAGCTTCCACATACAAATTTTTTGAGGTTATCCTCATCAATC
CATTCCATAAAGCTATCAGAAGAAATCCTGACACCCGATGGATCACCAAA

Alignment

ORF - retro_pabe_3004 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.66 %
• Parental protein coverage: 75.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGAYKYIQELWRKKQSDVMRFLLRVRCWQYRQLSALHRAPRPTRPDKARRLGYKAKQGYVIYRIRVRRGG
          .GAYKYIQELWRKKQSDV..FLLRVRCW.Y.QLSA.HRAP.PT.PD.ARRLGYKAKQ....YR.RVRRGG
Retrocopy VGAYKYIQELWRKKQSDVIYFLLRVRCW*YYQLSAFHRAPHPTWPDEARRLGYKAKQD---YRNRVRRGG

Parental  RKRPVPKGATYGKPVHHGVNQLKFARSLQSVAEERAGRHCGALRVLNSYWVGEDSTYKFFEVILIDPFHK
          .KRPVPKG.TYGKPVHHGVNQLKFARSLQS..EERAG.HCGALR.L.SYW.GE.STYKFFEVILI.PFHK
Retrocopy *KRPVPKGVTYGKPVHHGVNQLKFARSLQSFVEERAGCHCGALRILSSYWAGEASTYKFFEVILINPFHK

Parental  AIRRNPDTQWITK
          AIRRNPDT.WITK
Retrocopy AIRRNPDTRWITK

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	280.66 RPM
SRP007412_cerebellum	0.00 RPM	291.84 RPM
SRP007412_heart	0.00 RPM	125.17 RPM
SRP007412_kidney	0.00 RPM	300.97 RPM
SRP007412_liver	0.00 RPM	241.14 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3004 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3004 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3004 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3661
Pan troglodytes	retro_ptro_2483
Gorilla gorilla	retro_ggor_2473

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 84 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003497	6 retrocopies	retro_amel_1281, retro_amel_1470, retro_amel_1519, retro_amel_516, retro_amel_548, retro_amel_712,
Callithrix jacchus	ENSCJAG00000003810	23 retrocopies	retro_cjac_1052, retro_cjac_1270, retro_cjac_1316, retro_cjac_1553, retro_cjac_1578, retro_cjac_1625, retro_cjac_1668, retro_cjac_1741, retro_cjac_2143, retro_cjac_2330, retro_cjac_2518, retro_cjac_2532, retro_cjac_2599, retro_cjac_2821, retro_cjac_2907, retro_cjac_3807, retro_cjac_4185, retro_cjac_506, retro_cjac_585, retro_cjac_712, retro_cjac_734, retro_cjac_783, retro_cjac_890,
Equus caballus	ENSECAG00000010157	1 retrocopy	retro_ecab_38,
Loxodonta africana	ENSLAFG00000004155	1 retrocopy	retro_lafr_677,
Procavia capensis	ENSPCAG00000011995	1 retrocopy	retro_pcap_265,
Pongo abelii	ENSPPYG00000014065	18 retrocopies	retro_pabe_1073, retro_pabe_1201, retro_pabe_1480, retro_pabe_1896, retro_pabe_2049, retro_pabe_2377, retro_pabe_2433, retro_pabe_2467, retro_pabe_2562, retro_pabe_3004 , retro_pabe_3028, retro_pabe_3098, retro_pabe_561, retro_pabe_597, retro_pabe_642, retro_pabe_705, retro_pabe_801, retro_pabe_816,
Pan troglodytes	ENSPTRG00000014695	14 retrocopies	retro_ptro_1178, retro_ptro_1646, retro_ptro_1942, retro_ptro_2064, retro_ptro_2090, retro_ptro_2483, retro_ptro_2572, retro_ptro_435, retro_ptro_459, retro_ptro_550, retro_ptro_646, retro_ptro_663, retro_ptro_886, retro_ptro_991,
Pteropus vampyrus	ENSPVAG00000001771	13 retrocopies	retro_pvam_1016, retro_pvam_1067, retro_pvam_1178, retro_pvam_1280, retro_pvam_1386, retro_pvam_1422, retro_pvam_176, retro_pvam_338, retro_pvam_397, retro_pvam_538, retro_pvam_634, retro_pvam_766, retro_pvam_83,
Tursiops truncatus	ENSTTRG00000007244	5 retrocopies	retro_ttru_1305, retro_ttru_1358, retro_ttru_280, retro_ttru_920, retro_ttru_987,
Vicugna pacos	ENSVPAG00000008573	2 retrocopies	retro_vpac_34, retro_vpac_522,