RetrogeneDB ID: retro_pabe_1327

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 15:97846667..97847883(-)
• Located in intron of: ENSPPYG00000006821

Retrocopy information

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

Parental gene information

• Parental gene symbol: WDR12
• Ensembl ID: ENSPPYG00000013089
• Aliases: None
• Description: Ribosome biogenesis protein WDR12 [Source:UniProtKB/Swiss-Prot;Acc:Q5REE6]

Sequence

>retro_pabe_1327
ATGGCTCTGTTGCAAACAAGCTTCTACACCGATCACAAGAAATAGGCCATCGATGATGTTCCCTTCTCAATCCCTGCTGT
CTCTGAAAGTGTTGACCTTAGTAACATCACCAATTAATTATTAAAGGGCAGAAATGAGTTCCACAAATATGTGGAGTTTG
ATTTCCTTATTAAGGGTCAGTTTCTGCGAATGCCCCTTGGTCAAACACATGGAACGGGAGAACACCTCATTAGAAGTTGT
GGAAAGAGAATAGACAAAGAAGTATACTGCACCCCAACCAGAATGATGTGTCCGTGATGACTGGACCAGTTCAATTTAAG
GGACAGAGGTATGGATTTTGACTGGTTCTTATAAGACTTCTCGAATCCGGTCCTTGGAAGGAAAGTCAACATTGACAATT
GTGGGACATATGGATGTTGTAAAAGATGTGGCCTGGGTGATAAAAGACAGTTTGCGTTATTATTGAGTGCCTCTATGGAT
CAGACTATTCTCTTATGGGAGTGGAATGTCGAGAGAAACAAAGTGAAAACCCTACACTGCTGCACAAGTGTAGATTCTAC
AGCTATTGATAGCTCAGGAACTAAATTTTGCAGTGGCTCCTGGGATAAGATGCTAAGGATCTGGTCTAGTGTCCCTACAG
AAGAAGATGAAATGGAGGAATCCACAAATCGACCAAGAAAGAAACAGAAAACAGAGCAGTTGGGACTAACAAGGACTCCC
ATAGTGACCCTCTCTGGCCACAAGGAAGCAGTCTCCTCAGTGCTGTGGTCAGATGCTGAAGAAATCTGCAGTGTATCTTG
GGACCATAAGAGTAGTGTGTGGGATGTCATGTTTGGCAATGTTAAGTCAACTTTACAGGAAATAGAGTGTTTAATTGTAT
TTCCTATTCTCTACTTGGTAAATGTTTAGCATCTGGAAGCCCAGATAGGCATATCAGACTGTGGGATCCCCAAACTAAAG
ATGGTTCTTTTGCGTTGCCGTCCCTACCCTCACATACAGTTCGGGAGACATCTTTAACATTGCATTCTACACTTCATTCC
CAGACGTTTTCCGGTTCAATACATTACATTGCCAATACCTGGGATTCACGATGCACTAAGCATCCTTTTTATGATCAGGT
TGCTCTTCAAGTTACATTTCTCAGAGCAGTCCAGACTGCCTCACGGGTCCCTTTGCATGGCGGTGCAGACAATAAACACT
TTCCATCAGATATTCC

Alignment

ORF - retro_pabe_1327 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.6 %
• Parental protein coverage: 98.11 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MAQLQTRFYTDNKKYAIDDVPFSIPAASEIADLSNIINKLLKDKNEFHKHVEFDFLIKGQFLRMPLD-KH
          MA.LQT.FYTD.KK.AIDDVPFSIPA.SE..DLSNI.N.LLK..NEFHK.VEFDFLIKGQFLRMPL..KH
Retrocopy MALLQTSFYTDHKK*AIDDVPFSIPAVSESVDLSNITN*LLKGRNEFHKYVEFDFLIKGQFLRMPLG>KH

Parental  MEMENISSEEVVEIEYVEKYTAPQPEQCMFHDDWISSIKGAEEWILTGSYDKTSRIWSLEGKSIMTIVGH
          ME.EN..S.EVVE.E...KYTAPQPE.C...DDW.SSI.G.E.WILTGSY.KTSRI.SLEGKS..TIVGH
Retrocopy MEREN-TSLEVVERE*TKKYTAPQPE*CV-RDDWTSSI*GTEVWILTGSY-KTSRIRSLEGKSTLTIVGH

Parental  TDVVKDVAWVKKDSL-SCLLLSASMDQTILLWEWNVERNKVKALHCCRGHAGSVDSIAVDGSGTKFCSGS
          .DVVKDVAWV.KDSL...LL.SASMDQTILLWEWNVERNKVK.LHCC.....SVDS.A.D.SGTKFCSGS
Retrocopy MDVVKDVAWVIKDSL<ALLL-SASMDQTILLWEWNVERNKVKTLHCCT----SVDSTAIDSSGTKFCSGS

Parental  WDKMLKIWSTVPTDEEDEMEESTNRPRKKQKTEQLGLTRTPVVTLSGHMEAVSSVLWSDAEEICSASWDH
          WDKML.IWS.VPT.EEDEMEESTNRPRKKQKTEQLGLTRTP.VTLSGH.EAVSSVLWSDAEEICS.SWDH
Retrocopy WDKMLRIWSSVPT-EEDEMEESTNRPRKKQKTEQLGLTRTPIVTLSGHKEAVSSVLWSDAEEICSVSWDH

Parental  TIRVWDVESGSLKSTL-TGNKVFNCISYSPLCKRLASGSTDRHIRLWDPRTKDGSLVSLSLTSHTGWVTS
          ...VWDV..G..KSTL.TGN.VFNCISYS.L.K.LASGS.DRHIRLWDP.TKDGS....SL.SHT...TS
Retrocopy KSSVWDVMFGNVKSTL<TGNRVFNCISYSLLGKCLASGSPDRHIRLWDPQTKDGSFALPSLPSHTVRETS

Parental  VKWSPTHEQQLISGSLDNIVKLWDTRSCKAPLYDLAAHEDKVLSVDWTDTGLLLSGGADNKLY-SYRYS
          .....T...Q..SGS...I...WD.R..K.P.YD..A.....L....T.....L.GGADNK...S.RYS
Retrocopy LTLHSTLHSQTFSGSIHYIANTWDSRCTKHPFYDQVALQVTFLRAVQTASRVPLHGGADNKHF<SIRYS

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	0.17 RPM	28.36 RPM
SRP007412_cerebellum	0.61 RPM	27.97 RPM
SRP007412_heart	0.09 RPM	9.06 RPM
SRP007412_kidney	0.36 RPM	12.20 RPM
SRP007412_liver	0.15 RPM	7.90 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1327 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1327 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1327 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1615
Pan troglodytes	retro_ptro_1083
Gorilla gorilla	retro_ggor_1222

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012519	1 retrocopy	retro_cfam_1759,
Choloepus hoffmanni	ENSCHOG00000013851	1 retrocopy	retro_chof_118,
Callithrix jacchus	ENSCJAG00000005171	1 retrocopy	retro_cjac_2690,
Cavia porcellus	ENSCPOG00000008824	1 retrocopy	retro_cpor_1107,
Homo sapiens	ENSG00000138442	1 retrocopy	retro_hsap_1615,
Gorilla gorilla	ENSGGOG00000026073	1 retrocopy	retro_ggor_1222,
Loxodonta africana	ENSLAFG00000011955	1 retrocopy	retro_lafr_1102,
Mus musculus	ENSMUSG00000026019	3 retrocopies	retro_mmus_1394, retro_mmus_2649, retro_mmus_2897,
Nomascus leucogenys	ENSNLEG00000007018	1 retrocopy	retro_nleu_2743,
Pongo abelii	ENSPPYG00000013089	1 retrocopy	retro_pabe_1327 ,
Pan troglodytes	ENSPTRG00000012823	1 retrocopy	retro_ptro_1083,
Tursiops truncatus	ENSTTRG00000001231	1 retrocopy	retro_ttru_1380,