RetrogeneDB ID: retro_ptro_601

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 11:35967719..35969386(-)
• Located in intron of: ENSPTRG00000003507

Retrocopy information

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

Parental gene information

• Parental gene symbol: WEE2
• Ensembl ID: ENSPTRG00000028383
• Aliases: None
• Description: WEE1 homolog 2 (S. pombe) [Source:HGNC Symbol;Acc:19684]

Sequence

>retro_ptro_601
GAGAAATTAAGCTTTTCCTGTTTGGAAGAAGAGACTCAGAATGAAGGGCAAAAGAAAGCACAAGGAAGCAGGGAGGCCCA
GAGCCAGACCCCAGAGAAGAGTGAAGTGCAGGATTCAGAGGCAATGCTTACATTGCCCAGGACTCCTCTCAGTAACGTGC
ATGAACTCAACACACCTCGGGAAAAAGAAAAAGAAGATCCAGATCAGATTTTGAGGACTCCAGTGTCACACCTTCTCAAA
TATCCTGAGACACCAGGCCAACCAGGCAACAGGAACAAGCTGCCACATGGTGCCAGCCCCTCTGCTCCCAAAAGCCCGCT
GAGCCAGACGTTATTTCTCCAACAGCGAAGCCTCCTTCCAGAGGCTCTAAGCATTTGATGCTCACATCCACTCCTCCCAA
GGATGAGATGACCTCACTGGCTCTGGTCAATACTAATCCCTTCACCCCAAAGTCCTATACAAAATTATTCCTTCAATCCG
GTGTCAAGAGGAAAATTCGAGATGATCTTGAGGAAGCTGGTCCAGAGGAAGGCAAGGAAGAACAAGGGCTGCCTGCTGAG
ACATGTGTTCTATGAGAAACCAACATGGCTTCCTACTATAAAAAAGAATGCTCGGAGGTAGAAAAAATTGGGGTTGGTGA
ATTTGGTACAGTCTACAAGTGCATTAAAAGCCTGGATAGAAGTGTTTATGCAATAAAGCACTATATGAAAACTTTTGCAG
GATTTCACCTGAGTATTTGGCTTTGTGTGAAGTTTATGCTCATACAGTGTTTGGACATCACCCCACCTGGTATATTACTA
CCCCTCACGGGCGGAAGATAACCATATGATCATTCAGAATGAATACTGCAATGGCAGGAGCTTGCAGGCTGCTATATCTG
AAAACACTAAGTCTACTAATCACTTCCAAGAGCCAAAACTCAAGGACATCCTTCTACAGATTTCCCTTGAACTTAAATAC
AGCCACAACTCTGGCATGGTACACCCGGACATGAAACCTTGTAAAACCTTCCTTTGTCACAAGATGCAAAGTGACTCCTC
TGGAGTCACAGAAGTTGAAAATGAAGCTGATTAGTTTCTCTCTGCCCATGTGATATATAAAATTGGTGACCTAGGCCATG
TGACATCAATAAGCAAACTCAAAGTGGAAAAAGGAGATAGTTGCTTCCTAGCAAATGAGATTTTGCAAGAGGATTATTAG
TACCTTCCCAAAGCAGACCTATTTGCCTTGGGATTAATCACTGCAATGGCTGAAGGAGTAAGGACATTACCCATCAACAG
TGCTGCAAGGCACCATAACCATGAGAGTAACTTCCCAGACATTCCTCAGGAGCTCTCAGAAGACTTTTACAGTCTGCTCA
AGCACATGATCCACCCTGATCCAGGAGAGAGACCTTCTGCAGCAGCTCTGGTCAGAAATTGGCCCTGGCCCTCCCTGGGG
AAAGCAGAAGAGCTCTAGCAGCAGCTGAATTTGGAAAAGTCCAAGACAGCTGCACTGGAAAGGGAACTAAGGGAAGCCCA
GCGGGCCCAGTCCCTGCAGGGAGACTTCCATCATGGTGACCCTGGGGTCTCTGGGACCACACGGGATCAGAAAACACCAA
ATGCCTGGTAGGAGGAAAGAGTGCAAGGTCTTCAAGCTTTACCTCAGGACAGCATGAGCCTCTGAAC

Alignment

ORF - retro_ptro_601 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.36 %
• Parental protein coverage: 98.06 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  QKLNFSYCEE-TEIEGQKKVEESREASSQTPEKGEVQDSEAKGTPPWTPLSNMHELDTSSEKDKESPDQI
          .KL.FS..EE.T..EGQKK...SREA.SQTPEK.EVQDSEA..T.P.TPLSN.HEL.T..EK.KE.PDQI
Retrocopy EKLSFSCLEEETQNEGQKKAQGSREAQSQTPEKSEVQDSEAMLTLPRTPLSNVHELNTPREKEKEDPDQI

Parental  LRTPVSHPLKCPETPAQPDSRSKLLPSDSPSTPKTMLSRL-VISPTGKLPSRGPKHLKLTPAPLKDEMTS
          LRTPVSH.LK.PETP.QP..R.KL....SPS.PK..LS...VISPT.K.PSRG.KHL.LT..P.KDEMTS
Retrocopy LRTPVSHLLKYPETPGQPGNRNKLPHGASPSAPKSPLSQT<VISPTAKPPSRGSKHLMLTSTPPKDEMTS

Parental  LALVNINPFTPESYKKLFLQSGGKRKIRGDLEEAGPEEGKG--GLPAKRCVLRETNMASRYEKEFLEVEK
          LALVN.NPFTP.SY.KLFLQSG.KRKIR.DLEEAGPEEGK...GLPA..CVL.ETNMAS.Y.KE..EVEK
Retrocopy LALVNTNPFTPKSYTKLFLQSGVKRKIRDDLEEAGPEEGKEEQGLPAETCVL*ETNMASYYKKECSEVEK

Parental  IGVGEFGTVYKCIKRLDGCVYAIKRSMKTFT-ELSNENSALHEVYAHAVLGHHP-HVVRYYSSWAEDDHM
          IGVGEFGTVYKCIK.LD..VYAIK..MKTF....S.E..AL.EVYAH.V.GHHP.H.V.YY.S.AED.HM
Retrocopy IGVGEFGTVYKCIKSLDRSVYAIKHYMKTFA<RISPEYLALCEVYAHTVFGHHP<HLVYYYPSRAEDNHM

Parental  IIQNEYCNGGSLQAAISENTKSGNHFEEPKLKDILLQISLGLNYIHNSSMVHLDIKPSNIFICHKMQSES
          IIQNEYCNG.SLQAAISENTKS.NHF.EPKLKDILLQISL.L.Y.HNS.MVH.D.KP...F.CHKMQS.S
Retrocopy IIQNEYCNGRSLQAAISENTKSTNHFQEPKLKDILLQISLELKYSHNSGMVHPDMKPCKTFLCHKMQSDS

Parental  SGVIEEVENEADWFLSANVMYKIGDLGHATSINKPKVEEGDSRFLANEILQEDYRHLPKADIFALGLTIA
          SGV.E.VENEAD.FLSA.V.YKIGDLGH.TSI.K.KVE.GDS.FLANEILQEDY..LPKAD.FALGL..A
Retrocopy SGVTE-VENEAD*FLSAHVIYKIGDLGHVTSISKLKVEKGDSCFLANEILQEDY*YLPKADLFALGLITA

Parental  VAAGAESLPTNGAAWHHIRKGNFPDVPQELSESFSSLLKNMIQPDAEQRPSAAALARNTVLRPSLGKTEE
          .A.G...LP.N.AA.HH....NFPD.PQELSE.F.SLLK.MI.PD...RPSAAAL.RN....PSLGK.EE
Retrocopy MAEGVRTLPINSAARHHNHESNFPDIPQELSEDFYSLLKHMIHPDPGERPSAAALVRNWPW-PSLGKAEE

Parental  LQQQLNLEKFKTATLERELREAQQAQSPQGDTHHGDTGVSGT-HTGSRSTKRLVGGKSARSSSFTSGERE
          L.QQLNLEK.KTA.LERELREAQ.AQS.QGD.HHGD.GVSGT.HTGS..TK.LVGGKSARSSSFTSG..E
Retrocopy L*QQLNLEKSKTAALERELREAQRAQSLQGDFHHGDPGVSGT<HTGSENTKCLVGGKSARSSSFTSGQHE

Parental  PLH
          PL.
Retrocopy PLN

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	0.02 RPM	0.11 RPM
SRP007412_cerebellum	0.57 RPM	0.79 RPM
SRP007412_heart	0.00 RPM	0.15 RPM
SRP007412_kidney	0.00 RPM	1.62 RPM
SRP007412_liver	0.00 RPM	0.07 RPM
SRP007412_testis	0.00 RPM	0.84 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_601 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_601 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_601 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_867
Gorilla gorilla	retro_ggor_705
Pongo abelii	retro_pabe_684

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004658	1 retrocopy	retro_btau_932,
Callithrix jacchus	ENSCJAG00000013627	1 retrocopy	retro_cjac_936,
Dipodomys ordii	ENSDORG00000015156	1 retrocopy	retro_dord_559,
Gorilla gorilla	ENSGGOG00000009609	1 retrocopy	retro_ggor_705,
Ochotona princeps	ENSOPRG00000009103	2 retrocopies	retro_opri_358, retro_opri_841,
Pongo abelii	ENSPPYG00000018066	1 retrocopy	retro_pabe_684,
Pan troglodytes	ENSPTRG00000028383	1 retrocopy	retro_ptro_601 ,