RetrogeneDB ID: retro_ptro_217

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:145889013..145889761(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AKR1D1
• Ensembl ID: ENSPTRG00000019740
• Aliases: None
• Description: aldo-keto reductase family 1, member D1 [Source:HGNC Symbol;Acc:388]

Sequence

>retro_ptro_217
GTGAAGGTTGTCATTGGTCTGGGGTGCTGACACACTGATGAAGCCTACATATACCAAAATGAAGACACAGCTGGGGAGGC
CATCAGGGGGAAAATAGCAGAAGGAAAGGTGCAGAGGAAGGATATCTTCTACTGTGGAAAACTGTGGGCTACAAATCACA
ACCCAGAGCTAGTCTGCCCAAGCCTAGAGAGGATGCTCAAGGTCCTCCAGCTAGATTGTGTGGATCTTTACATCATTGAA
ATACCCATGGCTGCTAAGCCAGAAGATGAAATCTACCCTATAGGTGAGAATGGCAAAGGGTTATATCACAAGTCAAATCT
ATGTGCCACTTGGGAGACTTCGGAAGCTTGTAAAGATGCTGGCTTGGTGAAATCCCTCGGAGTATCCAGTTTTAACAGCA
GGCCAGCTGGAGCTCATCCAGAACAACCCAGGACTCAAACCCAAGCCAGTCAGCAACGAGGTTGAGTGCCACCCATATTA
CACCCAGCCAAAACTTTTGAAATTTCGCCAACAACATGACATTGTCATGATTGCATATAGCCCTTTGGGGACCACTAGGA
ATCCAACCTGGACAAATATGTCTTCTCTGCCTTCGTTAAAGGATGCACTTCTAAAAAGGTGCAATAAGATCATAGCTCAA
GTTATTTTGCGTTTCAACATCCAGCAAGGGGTGGTTGTCATTCCTAAAAACTTTAATCCTGAAAAGATCAAGGAAAACCT
TCAGGCCTTTGACTTTTCTCTCACTGAA

Alignment

ORF - retro_ptro_217 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.38 %
• Parental protein coverage: 77.61 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VKVAIDTGYRHIDGAYIYQNEHEVGEAIREKIAEGKVRREDIFYCGKLWATNHVPEMVRPTLERTLRVLQ
          VKV.I..G..H.D.AYIYQNE...GEAIR.KIAEGKV.R.DIFYCGKLWATNH.PE.V.P.LER.L.VLQ
Retrocopy VKVVIGLGC*HTDEAYIYQNEDTAGEAIRGKIAEGKVQRKDIFYCGKLWATNHNPELVCPSLERMLKVLQ

Parental  LDYVDLYIIEVPMAFKPGDEIYPRDENGKWLYHKSNLCATWEAMEACKDAGLVKSLGVSNFNRR-QLELI
          LD.VDLYIIE.PMA.KP.DEIYP..ENGK.LYHKSNLCATWE..EACKDAGLVKSLGVS.FN.R.QLELI
Retrocopy LDCVDLYIIEIPMAAKPEDEIYPIGENGKGLYHKSNLCATWETSEACKDAGLVKSLGVSSFNSR>QLELI

Parental  LNKPGLKHKPVSNQVECHPYFTQPKLLKFCQQHDIVITAYSPLGTSRNPIWVNVSSPPLLKDALLNSLGK
          .N.PGLK.KPVSN.VECHPY.TQPKLLKF.QQHDIV..AYSPLGT.RNP.W.N.SS.P.LKDALL....K
Retrocopy QNNPGLKPKPVSNEVECHPYYTQPKLLKFRQQHDIVMIAYSPLGTTRNPTWTNMSSLPSLKDALL----K

Parental  RYNKTAAQIVLRFNIQRGVVVIPKSFNLERIKENFQIFDFSLTE
          R.NK..AQ..LRFNIQ.GVVVIPK.FN.E.IKEN.Q.FDFSLTE
Retrocopy RCNKIIAQVILRFNIQQGVVVIPKNFNPEKIKENLQAFDFSLTE

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	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.04 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	74.37 RPM
SRP007412_testis	0.00 RPM	0.21 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_217 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_217 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_217 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_257
Gorilla gorilla	retro_ggor_307
Pongo abelii	retro_pabe_406

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012872	1 retrocopy	retro_cjac_1688,
Homo sapiens	ENSG00000122787	1 retrocopy	retro_hsap_257,
Gorilla gorilla	ENSGGOG00000014684	1 retrocopy	retro_ggor_307,
Nomascus leucogenys	ENSNLEG00000013710	1 retrocopy	retro_nleu_860,
Pongo abelii	ENSPPYG00000018037	1 retrocopy	retro_pabe_406,
Pan troglodytes	ENSPTRG00000019716	6 retrocopies	retro_ptro_1365, retro_ptro_1794, retro_ptro_254, retro_ptro_3040, retro_ptro_3160, retro_ptro_972,
Pan troglodytes	ENSPTRG00000019718	1 retrocopy	retro_ptro_428,
Pan troglodytes	ENSPTRG00000019740	1 retrocopy	retro_ptro_217 ,
Rattus norvegicus	ENSRNOG00000013004	1 retrocopy	retro_rnor_2559,