RetrogeneDB ID: retro_ptro_1083

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 15:98177078..98177749(-)
• Located in intron of: ENSPTRG00000007507

Retrocopy information

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

Parental gene information

• Parental gene symbol: WDR12
• Ensembl ID: ENSPTRG00000012823
• Aliases: None
• Description: Pan troglodytes WD repeat domain 12 (WDR12), mRNA. [Source:RefSeq mRNA;Acc:NM_001246511]

Sequence

>retro_ptro_1083
AGTGTAGATTCCACAGCTATTGATAGCTCAGGAACTAAATTTTGCAGCGGCTCCTGAGATAAGGTGCTAAGGATCTGGTC
TACTGTCCCTACAGAAGACGACGAAACGGAGGAATCCACAAACTGACCAAGAAAGAAACAGAAAACAGAGCAGCTGGGAC
TAACAAGGACTCCCATAGTGACCCTCTCTGGCCACAAGGAAGCAATCTCCTCAGTGCTGTGGTCAGATGCTGAAGAAATC
TGCAGCGTATCTTGGGACCATGAAATTAGTGTGTGGGATGTCGCGTTTGGCAATCTGAAGTCAACTTTACAGGAAATAAA
GTGTTTAATTGTATTTCCTATTCTCCACTTTGTAAATGTTTAGCATCTGGAAGCACAGATAGGCATATCAGACTGTGGGA
TCCCCAAACTAAAGATGGCTCTTTCGTGTTGCCGTCCCTAACCTCACATACAGGTTGGGAGACATCAGTAAAATGGTCTC
CTACCCATGAACCACAGCAGATTTCAGGATCCTTATATAACACCGTCAAGCTGTGGGATTCAAGAAGTTGTAAGGCTCCT
CTCTATGATGTGGCTGCTCATGAAGAGAAAGTTCTGAGAGCAGACTAGACAGACGCAGGGCTCCTTCCGAGTGGAGGAGC
AGATAATAAACTGTATTCCTACAGATATTCC

Alignment

ORF - retro_ptro_1083 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.63 %
• Parental protein coverage: 53.19 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SVDSIAVDGSGTKFCSGSWDKMLKIWSTVPTDEEDEMEESTNRPRKKQKTEQLGLTRTPIVTLSGHMEAV
          SVDS.A.D.SGTKFCSGS.DK.L.IWSTVPT.E.DE.EESTN.PRKKQKTEQLGLTRTPIVTLSGH.EA.
Retrocopy SVDSTAIDSSGTKFCSGS*DKVLRIWSTVPT-EDDETEESTN*PRKKQKTEQLGLTRTPIVTLSGHKEAI

Parental  SSVLWSDAEEICSASWDHTIRVWDVESGSLKSTL-TGNKVFNCISYSPLCKRLASGSTDRHIRLWDPRTK
          SSVLWSDAEEICS.SWDH.I.VWDV..G.LKSTL.TGNKVFNCISYSPLCK.LASGSTDRHIRLWDP.TK
Retrocopy SSVLWSDAEEICSVSWDHEISVWDVAFGNLKSTL<TGNKVFNCISYSPLCKCLASGSTDRHIRLWDPQTK

Parental  DGSLVSLSLTSHTGWVTSVKWSPTHEQQLISGSLDNIVKLWDTRSCKAPLYDLAAHEDKVLSVDWTDTGL
          DGS.V..SLTSHTGW.TSVKWSPTHE.Q.ISGSL.N.VKLWD.RSCKAPLYD.AAHE.KVL..D.TD.GL
Retrocopy DGSFVLPSLTSHTGWETSVKWSPTHEPQQISGSLYNTVKLWDSRSCKAPLYDVAAHEEKVLRAD*TDAGL

Parental  LLSGGADNKLYSYRYS
          L.SGGADNKLYSYRYS
Retrocopy LPSGGADNKLYSYRYS

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	0.20 RPM	12.15 RPM
SRP007412_cerebellum	0.22 RPM	16.17 RPM
SRP007412_heart	0.00 RPM	11.95 RPM
SRP007412_kidney	0.24 RPM	14.38 RPM
SRP007412_liver	0.07 RPM	8.41 RPM
SRP007412_testis	0.11 RPM	49.21 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1083 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1083 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1083 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1615
Gorilla gorilla	retro_ggor_1222
Pongo abelii	retro_pabe_1327

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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,