RetrogeneDB ID: retro_ptro_1975

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 4:39508877..39509489(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: WDR5
• Ensembl ID: ENSPTRG00000023653
• Aliases: None
• Description: None

Sequence

>retro_ptro_1975
TCTCTAAAGTTCACCCTTGCTGGCCACACCAAAGCAGTGTCCTCCGTGAAATTCAGCCCGAATGGAGAGTGGCTGGCAAG
TTCATCTGCTGATAAACTCATTAAAATTTGGGGGACTCATATGATGGGAAATTTGAGAAAACCGTCTGGTCACAAGCTGG
GAATATCCGATGCAGCCTGGTCGTCAGATTCTAACCTTTTTGTTTCCGCCTCAGATGACAAAACCTTGAAGATACAGGAC
GTGAGCTCGGGAAAGTGTCTGAAAACCCTGAAGGGACACAGTAATTATGTCTTTTGCTGTAACTTCAATCCCCAGTCCAG
CCTTACTGTCTCAGGATCCTTTGATGAAAGTGTGAGGATATGGGTTGTGAAAACAGGGAAGTGCCACAAGACTGCTAGCT
CACTCCGATCCAGTCTCGGCCATTCATTTTAATCGTGATGGATTCTTGATAGTTTCAAGTAGCTATGATGGTCTCTGTCA
CATCTGGGACACCGCCTCAGGCCAGTGCCTGAAAACGCTCACTGATGATGACAACCCCTGGTGTCTTTCGTGAAGCTCTC
CCCAAAGGGCGGATACATCCTGGCTGCCACGCTGGGCAACACTCAAGCTCTG

Alignment

ORF - retro_ptro_1975 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.61 %
• Parental protein coverage: 61.38 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ALKFTLAGHTKAVSSVKFSPNGEWLASSSADKLIKIWGAYDGKFEKTISGHKLGISDVAWSSDSNLLVSA
          .LKFTLAGHTKAVSSVKFSPNGEWLASSSADKLIKIWG..........SGHKLGISD.AWSSDSNL.VSA
Retrocopy SLKFTLAGHTKAVSSVKFSPNGEWLASSSADKLIKIWGTHMMGNLRKPSGHKLGISDAAWSSDSNLFVSA

Parental  SDDKTLKIWDVSSGKCLKTLKGHSNYVFCCNFNPQSNLIVSGSFDESVRIWDVKT-GKCLKTLPAHSDPV
          SDDKTLKI.DVSSGKCLKTLKGHSNYVFCCNFNPQS.L.VSGSFDESVRIW.VKT.G.....L.AHSDPV
Retrocopy SDDKTLKIQDVSSGKCLKTLKGHSNYVFCCNFNPQSSLTVSGSFDESVRIWVVKT>GSATRLL-AHSDPV

Parental  SAVHFNRDGSLIVSSSYDGLCRIWDTASGQCLKTLIDDDN-PPVSFVKFSPNGKYILAATLDNTLKL
          SA.HFNRDG.LIVSSSYDGLC.IWDTASGQCLKTL.DDDN.P.VSFVK.SP.G.YILAATL.NT..L
Retrocopy SAIHFNRDGFLIVSSSYDGLCHIWDTASGQCLKTLTDDDN<PLVSFVKLSPKGGYILAATLGNTQAL

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	0.43 RPM	34.02 RPM
SRP007412_cerebellum	0.61 RPM	45.78 RPM
SRP007412_heart	0.12 RPM	12.12 RPM
SRP007412_kidney	0.42 RPM	39.10 RPM
SRP007412_liver	0.07 RPM	54.63 RPM
SRP007412_testis	0.11 RPM	93.16 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1975 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1975 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1975 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_2023

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Parental genes homology:

Parental genes homology involve 27 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011179	1 retrocopy	retro_amel_29,
Bos taurus	ENSBTAG00000047031	1 retrocopy	retro_btau_299,
Canis familiaris	ENSCAFG00000019830	1 retrocopy	retro_cfam_128,
Callithrix jacchus	ENSCJAG00000010123	1 retrocopy	retro_cjac_1,
Cavia porcellus	ENSCPOG00000014790	1 retrocopy	retro_cpor_12,
Dipodomys ordii	ENSDORG00000015010	1 retrocopy	retro_dord_7,
Equus caballus	ENSECAG00000017389	1 retrocopy	retro_ecab_82,
Echinops telfairi	ENSETEG00000015731	1 retrocopy	retro_etel_15,
Felis catus	ENSFCAG00000005712	1 retrocopy	retro_fcat_119,
Homo sapiens	ENSG00000196363	1 retrocopy	retro_hsap_11,
Gorilla gorilla	ENSGGOG00000004997	2 retrocopies	retro_ggor_171, retro_ggor_2023,
Loxodonta africana	ENSLAFG00000011192	1 retrocopy	retro_lafr_55,
Microcebus murinus	ENSMICG00000008085	1 retrocopy	retro_mmur_34,
Myotis lucifugus	ENSMLUG00000002236	1 retrocopy	retro_mluc_11,
Macaca mulatta	ENSMMUG00000014159	1 retrocopy	retro_mmul_190,
Mustela putorius furo	ENSMPUG00000012184	1 retrocopy	retro_mputfur_2,
Mus musculus	ENSMUSG00000026917	1 retrocopy	retro_mmus_132,
Otolemur garnettii	ENSOGAG00000008960	1 retrocopy	retro_ogar_86,
Procavia capensis	ENSPCAG00000013476	1 retrocopy	retro_pcap_43,
Pan troglodytes	ENSPTRG00000008551	1 retrocopy	retro_ptro_1569,
Pan troglodytes	ENSPTRG00000020853	1 retrocopy	retro_ptro_344,
Pan troglodytes	ENSPTRG00000023653	2 retrocopies	retro_ptro_18, retro_ptro_1975 ,
Pteropus vampyrus	ENSPVAG00000001666	1 retrocopy	retro_pvam_112,
Rattus norvegicus	ENSRNOG00000008212	1 retrocopy	retro_rnor_258,
Sus scrofa	ENSSSCG00000024912	1 retrocopy	retro_sscr_1,
Ictidomys tridecemlineatus	ENSSTOG00000015899	1 retrocopy	retro_itri_117,
Drosophila melanogaster	FBgn0040066	1 retrocopy	retro_dmel_69,