RetrogeneDB ID: retro_pabe_684

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 11:33325979..33327644(+)
• Located in intron of: ENSPPYG00000003354

Retrocopy information

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

Parental gene information

• Parental gene symbol: WEE2
• Ensembl ID: ENSPPYG00000018066
• Aliases: None
• Description: WEE1 homolog 2 (S. pombe) [Source:HGNC Symbol;Acc:19684]

Sequence

>retro_pabe_684
GAGAAAGTAAGCTTTTCCTGTTTTGAAGAAGAGACTCAGAATGAAGGGCAAAAGAAAGCACCAGGAAGCAGGGAGGCCCA
GAGCCAGACCCCAGAGAAAGAGTGAAGTGCAGGATTCAGAGGCAATGCTTACATTGCCCAGGACTCCTCTCAGTAACGTG
CATGAACTCAACACACCTCGGGAAAAAGAAAAAGAAAATCCAGATCAGATTTTGAGGACTCCAGTGTCACACCTTCTCAA
ATATCCTGAGACACAAGGCCAACAAGGCAACAGGAACAAGCTGCCACATGGTGCCAGCCCCTCTACTCCCAAAAGCCTAC
TGAGCAAGACGTTATTTCTCCAACAGCGAAGCTTCCTTCCAGAGGCTCTAAGCATTTGATGCTCACATCCACTCCTCCCA
AGGATGAGATGACCTCACTGGCTCTGGTCAGTACTAATCCCTTCACCCCAAAGTCCTATAGAAAATTATTCCTTCAATCC
GGTGTCAAGAGGAAAATTTGAGATGATCTGGAGGAAGCTGGTCCAGAGGAAGGCAAGGAAGAACAAGGGCTGCCTGCTGA
GACATGCGTTCTATGAGAAACCAACATGGCTTCCTACTATAAAAAAGAATGCTCGGAGGTAGAAAAAATTGGGGTTGGTG
AATTTGGTACAGTCTACAAGTGCATTAAAAGCCTGGATAGAAGTGTTTATGCAATAAAGCACTATATGAAAACTTTTGCA
GGATTTCACCTGAGAATTTGGCTTTGCATGAAGTTTATGCTCATACAGTGTTTGGACACCACCCCACCTGGTACATTGCT
ACCCCTCACGGGCGGAAGATAACCATATGATCATTCAGAATGAATACTGAAATGGCAGGAGCCTGCAGGCTGCTATATCT
GAAAACACTAAGTCTACTAATCACTTCCAAGAGCCAAAACTCAAGGACATCCTTCTACAGATTTCCCTTGAACTTAAGCA
CAGCCACAACTCTGGCATGGTATACCCGGACATCAAACCTTGTAAGACCTTCCTTTGTCACAGGATGCAAAATGACTCCT
CTGGAGTCACAGAAGTTGAAAATGAAGCTGATTAGTTTCTCTCTGCCCGTGTGATATATAAAATTGGTGACCTAGGCCAT
GTGACATCAATAAGCAAACTCAAAGTGGAAAAAGGAGATAGTTGCTTCCTGGCAAATGAGATTTTGCAAGAGGATTATTA
GTACCTTCCCAAAGCAGACCTATTTGCCTTGGGATTAATCACTGCAGTGGCTGAAGGAGTAAGGACATTACCCATCAACA
GTGCTGCATGGCACCATAACAATGAGAGTAACTTCCCAGACATTCCTCAGGAGCTCTCAGAAGACTTTTACAGTCTGCTC
AAGCACATGATCCACCCTGATCCAGGAGAGAGACCTTCTGCAGCAGCTCTGGTCAGAAATTGGCCCTGGCCCTCCCTGGG
GAAAGCAGAAGAGCTCTAGCAGCAGCTGAATTTGGAAAAGTCCAAGACAGCTGCACTGGAAAGGGAACTAAGGGAAGCCC
AGCAGGCCCAGTCCCTGAAGGGAGACTTCCATCATGGTGACCCTGGGGTCTCTGGGACCACACGGGATCGGGAAACACCA
AATGCCTGGTAGAAGGAAAGAGTGCAAGGTCTTCAAGCTTTACCTCAGGACAGCATGAGCCTCTG

Alignment

ORF - retro_pabe_684 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.82 %
• Parental protein coverage: 97.88 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  QKLNFS-YCEETEIEEQKKVEKSREALSQTPEK-GEVQDSEAKGTPPRTPLSNVHELDTSSEKDKESPDQ
          .K..FS...EET..E.QKK...SREA.SQTPEK..EVQDSEA..T.PRTPLSNVHEL.T..EK.KE.PDQ
Retrocopy EKVSFSCFEEETQNEGQKKAPGSREAQSQTPEK>SEVQDSEAMLTLPRTPLSNVHELNTPREKEKENPDQ

Parental  ILRTPVSHPLKCPETPAQPDSRSKLLPSDSPSTPKSMLSRL-AISPTGKLPSRGPKHLKLTPAPLKDEMT
          ILRTPVSH.LK.PET..Q...R.KL....SPSTPKS.LS....ISPT.KLPSRG.KHL.LT..P.KDEMT
Retrocopy ILRTPVSHLLKYPETQGQQGNRNKLPHGASPSTPKSLLSKT<VISPTAKLPSRGSKHLMLTSTPPKDEMT

Parental  SLALVNINPFTPESYKKLFLQSGGKRKMRGDLEEAGPEEGKG--GLPAKRCVLRETNMASRYEKEFLEVE
          SLALV..NPFTP.SY.KLFLQSG.KRK...DLEEAGPEEGK...GLPA..CVL.ETNMAS.Y.KE..EVE
Retrocopy SLALVSTNPFTPKSYRKLFLQSGVKRKI*DDLEEAGPEEGKEEQGLPAETCVL*ETNMASYYKKECSEVE

Parental  KIGVGEFGTVYKCIKRLDGCVYAIKRSMKTFA-ELSNENSALHEVYAHAVLGHHP-HVVRYYSSWAEDDH
          KIGVGEFGTVYKCIK.LD..VYAIK..MKTFA...S.EN.ALHEVYAH.V.GHHP.H.V..Y.S.AED.H
Retrocopy KIGVGEFGTVYKCIKSLDRSVYAIKHYMKTFA<RISPENLALHEVYAHTVFGHHP<HLVHCYPSRAEDNH

Parental  MIIQNEYCNGGSLQAAISENTKSGNHFEEPKLKDILLQISLGLNYIHNSSMVHLDIKPSNIFICHKMQSE
          MIIQNEY.NG.SLQAAISENTKS.NHF.EPKLKDILLQISL.L...HNS.MV..DIKP...F.CH.MQ..
Retrocopy MIIQNEY*NGRSLQAAISENTKSTNHFQEPKLKDILLQISLELKHSHNSGMVYPDIKPCKTFLCHRMQND

Parental  SSGVIEEVENEADWFLSANVMYKIGDLGHATSINKPKVEEGDSRFLANEILQEDYRHLPKADIFALGLTI
          SSGV.E.VENEAD.FLSA.V.YKIGDLGH.TSI.K.KVE.GDS.FLANEILQEDY..LPKAD.FALGL..
Retrocopy SSGVTE-VENEAD*FLSARVIYKIGDLGHVTSISKLKVEKGDSCFLANEILQEDY*YLPKADLFALGLIT

Parental  AVAAGAESLPTNGAAWHHIRKGNFPDVPQELSESFSSLLKNMIHPDAEQRPSAAALARNTVLRPSLGKTE
          AVA.G...LP.N.AAWHH....NFPD.PQELSE.F.SLLK.MIHPD...RPSAAAL.RN....PSLGK.E
Retrocopy AVAEGVRTLPINSAAWHHNNESNFPDIPQELSEDFYSLLKHMIHPDPGERPSAAALVRNWPW-PSLGKAE

Parental  ELQQQLNLEKFKTATLERELREAQQAQSPQGDTHHGDTGVSGT-HTGSRSTKRLVGGKSARSSSFTSGER
          EL.QQLNLEK.KTA.LERELREAQQAQS..GD.HHGD.GVSGT.HTGS..TK.LV.GKSARSSSFTSG..
Retrocopy EL*QQLNLEKSKTAALERELREAQQAQSLKGDFHHGDPGVSGT<HTGSGNTKCLVEGKSARSSSFTSGQH

Parental  EPL
          EPL
Retrocopy EPL

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	0.06 RPM
SRP007412_cerebellum	0.12 RPM	0.73 RPM
SRP007412_heart	0.06 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.36 RPM
SRP007412_liver	0.00 RPM	0.12 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_684 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_684 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_684 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_867
Pan troglodytes	retro_ptro_601
Gorilla gorilla	retro_ggor_705

---

Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 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	ENSPPYG00000003494	1 retrocopy	retro_pabe_3571,
Pongo abelii	ENSPPYG00000018066	1 retrocopy	retro_pabe_684 ,
Pan troglodytes	ENSPTRG00000028383	1 retrocopy	retro_ptro_601,