RetrogeneDB ID: retro_ptro_330

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:111396372..111397775(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRAMEF10
• Ensembl ID: ENSPTRG00000029629
• Aliases: None
• Description: PRAME family member 10 [Source:HGNC Symbol;Acc:27997]

Sequence

>retro_ptro_330
ATGAGCCTCCAGGCCACACCCAGACTCCTGGAGCTGGTGGGGCAGAGCCTGCTGAGGAACCGGTTCTTGGCCATCTTCAC
CCTGGAGGAGCTGCCCAAGGAGGTCTTCTGTCTGCTGTTCACTGAGGCCTCCACCAGGAGATGCTGTGAGATTCTAAAGG
CCATGGTGCAGGCCTGGCCCTTCCCTCGCCTCCCTCTGGGTTCCCTGATGAAGACACCTCATCTGGAGACCTTGCGAGCT
ATGCTGAAGAGACTTGATACACTACTGGCCAGAAGGTTCGCCACAGGAGGTAGAAACTTCAAGTGCTGGATTTGCGGGAT
GTTGATGAGAATTTCTGGACCATATGGTCTGGAGCCAGGGCCCTGTCCTGCTCCCCAGAGGCCATGAGTATGAGGCAGAC
AGTGGTGGACTGTCCAAGGACAGGAAAGCACCAGCCCTTGAAGGTGTTCATAGACCTCTACCTAAAGGAAAACACCCTGG
ATGAATGTCTGCGCTACCTCTGTGGGTGGATCCACTACAGAAGAGGTTTAGTACACCTGTGTTGTAGTAAGGTACAGAAT
TACTCAATGCCCACTTCAAATTTCAGAAATTTATTGGAAAAGGTATACCCAGACAGCAGTATCCATGATTTGGAAGTCTG
GAAAAAGTGCTCGCTGAATAGAACAGGAAAGTTTGCCCCTTACCTGGGCCAGATGAGCAATCTTCACAAACTCTTTTTAG
CCTTCAGTTATGGGTGTGAGTTATACATGTGCGGCCAACAGCAGTTCATTCCTGACTTGGACTCTCCATTCCTCTGCCTG
GAATCCCCAGATGCTTTGTATAAGAAAGGTCAATAATATCAAAGAGCACCTGCTCAGGTGCCTCAAGAACCCCTTGGAGG
CCTTTACATTCTGTCATGCTTACCTAGCTGATCGGGACATGGGGTGTCAGTACCCAAGCCTCAGTCAGCTAAAGCAGCTG
CATCTGATTCATATCCTAATGTGGACCACCAATCTTGAGCCCCTTGGAGCTCTGCTAGAGAAAGCTGCTGCTACTATCGA
GACCCTCGTCTTAGAGGACTGTCGGATCCAGGACTCCCAACTCATGGTCATCCTACCTGCCCTGAGCTGCTGCTCCCAGC
TCACCACCTTCTACTTTCATGGAAATGAGACCTCCATGAATGCTCTGAAAGTTCTGTTGCATCACACAGGTGAACTGAGC
AAGTTAGGCCTGGAGACATATCCTGCCCCTCTGGAGAGTCTTAACAACAGGGGTCATGTCAGTTGGGAGATCCTCGCCCC
AATTCAGGCTGAGCTGATGCGTACACTCAGGGAAGTAAGGCAGCCCAAGAGGATCTTCTTGGTCCTGCCCCCTGCCCTTC
CTGTGGCTCATGGCCATCTGAGAAACTGGAGCTCCATCTTTGC

Alignment

ORF - retro_ptro_330 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.94 %
• Parental protein coverage: 99.79 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSLQSPSRLLELAGQSLLRNQFLTIFTLDELPREVFPLMFMEAFSMRRFEALKLMVQAWPFLCLPLGSLM
          MSLQ...RLLEL.GQSLLRN.FL.IFTL.ELP.EVF.L.F.EA...R..E.LK.MVQAWPF..LPLGSLM
Retrocopy MSLQATPRLLELVGQSLLRNRFLAIFTLEELPKEVFCLLFTEASTRRCCEILKAMVQAWPFPRLPLGSLM

Parental  KTPHLETLQAVLRGLDTLVA-QKVRPRRWKLQVLDLRDVDENFWTIWSGAKVLSCSPEVMSKRQTVEDCP
          KTPHLETL.A.L..LDTL.A.QKVR.RR.KLQVLDLRDVDENFWTIWSGA..LSCSPE.MS.RQTV.DCP
Retrocopy KTPHLETLRAMLKRLDTLLA<QKVRHRR*KLQVLDLRDVDENFWTIWSGARALSCSPEAMSMRQTVVDCP

Parental  RMGERQPLKVFIDLCLKESTLDECLSYLCGWIHYRRGLVHLCCNKVQNYSMPTSSFCNLLERIYPD-SIQ
          R.G..QPLKVFIDL.LKE.TLDECL.YLCGWIHYRRGLVHLCC.KVQNYSMPTS.F.NLLE..YPD.SI.
Retrocopy RTGKHQPLKVFIDLYLKENTLDECLRYLCGWIHYRRGLVHLCCSKVQNYSMPTSNFRNLLEKVYPDSSIH

Parental  ELEVWKKSSLNKTGKFAPYLSQMSNLRELFLAFSYERELYVSVQWPCIPDLDSPFLCLYYPQMLYIKK-I
          .LEVWKK.SLN.TGKFAPYL.QMSNL..LFLAFSY..ELY...Q...IPDLDSPFLCL..P..LY.KK..
Retrocopy DLEVWKKCSLNRTGKFAPYLGQMSNLHKLFLAFSYGCELYMCGQQQFIPDLDSPFLCLESPDALY-KK>V

Parental  SNIKEHLEHLLRYLKNPLGAFIFSDAYLTDRDMECLSQYPSLSQLKELRLIHILMWTTNLEPLGVLLEKV
          .NIKEHL...LR.LKNPL.AF.F..AYL.DRDM.C..QYPSLSQLK.L.LIHILMWTTNLEPLG.LLEK.
Retrocopy NNIKEHL---LRCLKNPLEAFTFCHAYLADRDMGC--QYPSLSQLKQLHLIHILMWTTNLEPLGALLEKA

Parental  AVTLKTLVLKDCRIQDPQLRVLLPALSHCSQLTTFNFHGNETSMNALKDLLRHTGGLSKLGLELYPAPLE
          A.T..TLVL.DCRIQD.QL.V.LPALS.CSQLTTF.FHGNETSMNALK.LL.HTG.LSKLGLE.YPAPLE
Retrocopy AATIETLVLEDCRIQDSQLMVILPALSCCSQLTTFYFHGNETSMNALKVLLHHTGELSKLGLETYPAPLE

Parental  SLDYKGHVNWEILTPIRAELMRTLREVRQPKRIF-FGPVPCPTCGSWPSEKVDFHLC
          SL...GHV.WEIL.PI.AELMRTLREVRQPKRIF..GP.PCP.CGSWPSEK...HLC
Retrocopy SLNNRGHVSWEILAPIQAELMRTLREVRQPKRIF<LGPAPCPSCGSWPSEKLELHLC

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	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.08 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	0.00 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_330 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_330 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_330 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_220

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000013324	1 retrocopy	retro_dord_231,
Homo sapiens	ENSG00000187545	1 retrocopy	retro_hsap_220,
Mus musculus	ENSMUSG00000025839	1 retrocopy	retro_mmus_557,
Otolemur garnettii	ENSOGAG00000000273	2 retrocopies	retro_ogar_1100, retro_ogar_1238,
Ochotona princeps	ENSOPRG00000009716	1 retrocopy	retro_opri_661,
Pan troglodytes	ENSPTRG00000029629	1 retrocopy	retro_ptro_330 ,
Rattus norvegicus	ENSRNOG00000042820	1 retrocopy	retro_rnor_1371,
Rattus norvegicus	ENSRNOG00000048835	1 retrocopy	retro_rnor_396,