RetrogeneDB ID: retro_ptro_2018

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 4:136960271..136961415(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PES1
• Ensembl ID: ENSPTRG00000014251
• Aliases: None
• Description: Pan troglodytes pescadillo ribosomal biogenesis factor 1 (PES1), mRNA. [Source:RefSeq mRNA;Acc:NM_001246365]

Sequence

>retro_ptro_2018
GGAGGCCTTGAGAAGCAGCAGCAGGAACGAGGCTCGCCAGCCAACCACAACACCGGAAGCAAAGCCCGAAAGAAGCTCCC
CCTGACCATGGCTGACTGGAGGCGGCCGTGCACCCTGATGGGCATTTATCCCCGTGAACCCAAACACGAGAAGAAGGTTA
ATAAAGGTGCTACTGCGGCCCAAACTTCTTACCTCATCGAAGATATCAGGTTTCTCCTCCAAGAATTCATCGTCAACAAG
GTCCGGGAATGCAAGGTGTCTGTCCGGAAGCCCCGGGAGGCCTATGAGAAGAGCGAGCGGAACACCGTGGAACATCTAAA
GGACAATAAGGCCGACTACAAACATGACCACATCATCAAGGAACGGTACCCCACATTCATCGACGCCCGGGGGTACCTGG
GCGGCGCCGCCTTCTCCTCGTGCTTCCCCTTTTCCACCTTCCCCCGGACTGACAAGTGCCATGTGCAGATCGTTCCGCTG
TGCTGCAGGCTCGCAGCGGAGTTCACGTATTACATCATCGCTGCCTGTGCCCCGAGCAAGGTCTTCCTGTCCATCAAACG
CATTTACTACCAGGCTGAGGTGCTGGCACAGCCCATCGTGTGGATCACCCCCTGTGCTTTCTCCCACGACCACCGGACAG
ACGTGGACTACAGAGTCATGGCCACCTTCACCTAGTTCTACAGCACCCTACTGGGCTTCATCGATGAACTTCAGCCTCTG
CCAGTCGCTCAACTTTCACTATCCCCTCAAGCTGAGGGTCAGGCCCAAGCAGAGGTGAAAGCCAGTGAGGGCACCTACGC
GCTGGACTCAGAGAGCCCAGTGGAGAAACTGGAGGCCCTCAGTGCCAGCCTGGCCCGCGCGGTGGTGCCTACCACAGAGG
AAGAGGCCGAGGTGGATGAGTTTCCCGCCAATGGGGAGTTGGCGGTGCAGGAGGAGGACCACAGGAAGGAGCTGGAGGCG
CAGGAGAAGCACAAGAAGCTTTTTGAGGGCTTGAAGTTCTTCGTTAACTGACAGGTGTCCCCTGAAGCCCTAGCCTTCGT
CATCAGGAGTTTTGGCGGGGGACATATCCTGGGAAAAGCCTTTGTGCATGGGTCCCACCTATGCAGCACCCACCAGATTG
TCGACTGGCCTGGGCAGCAGACCT

Alignment

ORF - retro_ptro_2018 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.97 %
• Parental protein coverage: 64.63 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GGLEKKKYERGSATNYITRNKARKKLQLSLADFRRLCILKGIYPHEPKHKKKVNKGSTAARTFYLIKDIR
          GGLEK...ERGS..N..T..KARKKL.L..AD.RR.C.L.GIYP.EPKH.KKVNKG.TAA.T.YLI.DIR
Retrocopy GGLEKQQQERGSPANHNTGSKARKKLPLTMADWRRPCTLMGIYPREPKHEKKVNKGATAAQTSYLIEDIR

Parental  FLLHEPIVNKFREYKVFVRKLRKAYGKSEWNTVERLKDNKPNYKLDHIIKERYPTFIDALRDLDD-ALSM
          FLL.E.IVNK.RE.KV.VRK.R.AY.KSE.NTVE.LKDNK..YK.DHIIKERYPTFIDA...L...A.S.
Retrocopy FLLQEFIVNKVRECKVSVRKPREAYEKSERNTVEHLKDNKADYKHDHIIKERYPTFIDARGYLGGAAFSS

Parental  CFLFSTFPRTGKCHVQTIQLCRRLTVEFIHYIIAARALRKVFLSIKGIYYQAEVLGQPIVWITPYAFSHD
          CF.FSTFPRT.KCHVQ...LC.RL..EF..YIIAA.A..KVFLSIK.IYYQAEVL.QPIVWITP.AFSHD
Retrocopy CFPFSTFPRTDKCHVQIVPLCCRLAAEFTYYIIAACAPSKVFLSIKRIYYQAEVLAQPIVWITPCAFSHD

Parental  HPTDVDYRVMATFTEFYTTLLGFVN-FRLYQLLNLHYPPKLEGQAQAEAKASEGTYALDSESSMEKLAAL
          H.TDVDYRVMATFT.FY.TLLGF...........L...P..EGQAQAE.KASEGTYALDSES..EKL.AL
Retrocopy HRTDVDYRVMATFT*FYSTLLGFIDELQPLPVAQLSLSPQAEGQAQAEVKASEGTYALDSESPVEKLEAL

Parental  SASLARVVVPATEEEAEVDEFPTDGEMSAQEEDRRKELEAQEKHKKLFEGLKFFLNREVPREALAFIIRS
          SASLAR.VVP.TEEEAEVDEFP..GE...QEED.RKELEAQEKHKKLFEGLKFF.N..V..EALAF.IRS
Retrocopy SASLARAVVPTTEEEAEVDEFPANGELAVQEEDHRKELEAQEKHKKLFEGLKFFVN*QVSPEALAFVIRS

Parental  FG-GEVSWDKSLCIGATYDVTDSRITHQIVDRP
          FG.G..SW.K.LC.G.TY.....R.......RP
Retrocopy FG>GDISWEKPLCMGPTY-AAPTRLSTGLGSRP

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	38.14 RPM
SRP007412_cerebellum	0.00 RPM	48.40 RPM
SRP007412_heart	0.00 RPM	12.94 RPM
SRP007412_kidney	0.00 RPM	43.67 RPM
SRP007412_liver	0.00 RPM	87.40 RPM
SRP007412_testis	0.63 RPM	72.61 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2018 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2018 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2018 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010617	1 retrocopy	retro_cjac_3182,
Cavia porcellus	ENSCPOG00000003565	1 retrocopy	retro_cpor_986,
Homo sapiens	ENSG00000100029	1 retrocopy	retro_hsap_4133,
Otolemur garnettii	ENSOGAG00000005804	1 retrocopy	retro_ogar_1719,
Pongo abelii	ENSPPYG00000011716	1 retrocopy	retro_pabe_3471,
Pan troglodytes	ENSPTRG00000014251	2 retrocopies	retro_ptro_2018 , retro_ptro_2809,
Rattus norvegicus	ENSRNOG00000004515	2 retrocopies	retro_rnor_2953, retro_rnor_824,
Tupaia belangeri	ENSTBEG00000009825	1 retrocopy	retro_tbel_1000,