RetrogeneDB ID: retro_cjac_936

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 11:99220473..99222071(-)
• Located in intron of: ENSCJAG00000011017

Retrocopy information

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

Parental gene information

• Parental gene symbol: WEE2
• Ensembl ID: ENSCJAG00000013627
• Aliases: None
• Description: None

Sequence

>retro_cjac_936
GGGGGAGAGAGAGCACAAGGAAGCAGGGAGGCCCAGAGCCAGACCCCAGAGAAGAGTGAAGTGCAGGATTGCCACACAAT
GCTTACACTGCTCAGGACTCCTCTCAGTAACATGCATGAACTCAACACACCTCAGGAAAAAGACAAAGAAAATCCAGATC
AGATTTTGAGGACTCCAGTGTCACACCTTCTCAAATGACCTGAGACACTAGGCCAACCAGACAACAGGAACAAACTGCCA
CATGGTGCCAGCCCCTCCACTCCCAAAAGCCCGCTGAGCCAGAGGTTATTTCTCCAAGCAAAGCTTCCTTCCAGAGGCAC
TAAACATTTGACGCTCACATCTACTCCTCCCAAGGATGAGATGACCTCACTGGCTCTGGTCAATATAAGTCCCTTTACCC
CAGAGTCCTATAGAAAATTATTCCTTCAATCCAGTGGTAAGAGGAAAATTCAAGATCTTGAGGAAGCTGGTCCAGAGGAA
GGCAAGGAAGAACAAGGGCTGCCTGCCGAGACATGTGTTCTATGAGAAACCAACATGGCTTCCTGATACAAAAAAAATTA
TCAGAGGTAGAAAAAATTGGGGTTGATGAATTTGGTACAGCCTACAAGTGCACTGAAAGCCTGGATAGAAGCGTTTATGC
AATAAAGCACTCTATGAAAACTTTTGCAGAATTTCACAGGAGAATTTGGCTTTATGTGAAGTATATGCTCATGCAGTGCT
TGGGCATCACCCCAAGTGGTACAATGCCAGTCCTTACAGCAGAAGATGACCATATGATCATTCAGAATGAATACTGCAAT
GGCAGGAGCTTGCAAGCTGCTCTATCTGAAAACACTAAGTCTACTAATCATTTCCAAGAGCCAAAACTCAAGGACATCCT
TCTACAGATTTCCCTTGAACCTAAGTACACCACAACTCTAGCATGATGCACCTGGACATCAAACCTAATAAGACCTTCCT
TGTCACAAGATGCCAAGTGACTCCTCGGGAGTCACGGAAATTGAAAATGAAACTGATTGGTTCCTCTCTGCCCGTGTGAT
ATATAAAATTGGTGACCTAGGCCATGTGACATCAATAAGCAAACTGAAAGTGGAAAGAGATAGTTGCTTACTGGCAAATG
AGATTTTGCAAGAGGATTATTAGTACCTTCTCAAAGCAGACCTATTTGCCTTGGGATTAATCATTGCAATGGCTGCCGGG
GCAGGGACATTATCCATCAACACTGCTGCATGGCACCATAACCCTAAGATTAACTTCCCAGACATTCCTCAGGTGCTCTC
AAAAGACTTTTACAGTCTGCTCAAGAACACGATCCACCCTGATCCAGAAGAGAAACTTGCAATAGCTCTCGTCAGAAATT
GACCCTGGCCCTCCCTGGGGAAAGCAGAAGAACTCTAGCAGCAGCTGAATTTGGAAAAGTCCAAGACAGCCACACCGGAA
GGGGAACTAAGAGAAGCTCAGGAGGCCCAGTCCCCACAGGGAGACTTCCATCATGGTGACCCTGGGGTCTCTGGGACCAC
AAGGGATCAAGAAACCCCAAACGCCTGGTAAAAGGAAAGAATGCAAGGTCTTCAAGCTTCACCTCAGGACAGCATGAG

Alignment

ORF - retro_cjac_936 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.07 %
• Parental protein coverage: 94.89 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  GQKKAQESREASSQTLEKGEVQDSEAKRTPPRTPLSNVHELDTSWEKDKESPDQILRTPVSHPLTCPETP
          G...AQ.SREA.SQT.EK.EVQD.....T..RTPLSN.HEL.T..EKDKE.PDQILRTPVSH.L..PET.
Retrocopy GGERAQGSREAQSQTPEKSEVQDCHTMLTLLRTPLSNMHELNTPQEKDKENPDQILRTPVSHLLK*PETL

Parental  AQPDSRSKLLPSDSPSTPKSMLSRLAISPTGKLLSRGPKHLKLTPAPLRDEMTSFALVNINPFTPESYRK
          .QPD.R.KL....SPSTPKS.LS........KL.SRG.KHL.LT..P..DEMTS.ALVNI.PFTPESYRK
Retrocopy GQPDNRNKLPHGASPSTPKSPLSQ-RLFLQAKLPSRGTKHLTLTSTPPKDEMTSLALVNISPFTPESYRK

Parental  LFLQSGGKRKIRGDLEEAGPEEGKG--GLPAKRCVLRETNMASRYEKEFL-EVEKIGVGEFGSVYKCIKR
          LFLQS.GKRKI..DLEEAGPEEGK...GLPA..CVL.ETNMAS.Y.K....EVEKIGV.EFG..YKC...
Retrocopy LFLQSSGKRKIQ-DLEEAGPEEGKEEQGLPAETCVL*ETNMAS*YKKNYQ<EVEKIGVDEFGTAYKCTES

Parental  LDGCVYAIKRSMKTLAE-LSSENLALHEVYAHAVLGHH-PHVVRYYSSW-VEDDHMIIQSEYCNGGSLQA
          LD..VYAIK.SMKT.AE..S.ENLAL.EVYAHAVLGHH.P.VV...S....EDDHMIIQ.EYCNG.SLQA
Retrocopy LDRSVYAIKHSMKTFAE<ISQENLALCEVYAHAVLGHH<PQVVQCQSLQ<AEDDHMIIQNEYCNGRSLQA

Parental  AISENTKFHKHFQEPKLKDILLQISLGLKYI-HNSGMVHLDIKPSNIFI-CHKMQSDSSGVIEEVANEAD
          A.SENTK...HFQEPKLKDILLQISL..KY..HNS.M.HLDIKP...F..CHKM.SDSSGV.E...NE.D
Retrocopy ALSENTKSTNHFQEPKLKDILLQISLEPKYT<HNSSMMHLDIKPNKTFL<CHKMPSDSSGVTE-IENETD

Parental  WFLSANVVYKIGDLGHATSISKPEVEEGDSRFLANEILQEDYRHLPKADIFALGLTIALAAGAESLPTNG
          WFLSA.V.YKIGDLGH.TSISK..VE..DS..LANEILQEDY..L.KAD.FALGL.IA.AAGA..L..N.
Retrocopy WFLSARVIYKIGDLGHVTSISKLKVER-DSCLLANEILQEDY*YLLKADLFALGLIIAMAAGAGTLSINT

Parental  AAWHHIRKGNFPDVPQELSEDFSSLLKNMIQPDPEQRPSAAALASNRVLRPSLGKTEELQQQLNLEKFKT
          AAWHH..K.NFPD.PQ.LS.DF.SLLKN.I...P......A.........PSLGK.EEL.QQLNLEK.KT
Retrocopy AAWHHNPKINFPDIPQVLSKDFYSLLKNTIH--PDPEEKLAIALVRN*PWPSLGKAEEL*QQLNLEKSKT

Parental  ATLERELREAQQAQSPQGDIHYGDTWISRT-HTGSRSTKRLVGGKSARSSSFTSEQLE
          AT.E.ELREAQ.AQSPQGD.H.GD...S.T.H.GSR..KRLV.GK.ARSSSFTS.Q.E
Retrocopy ATPEGELREAQEAQSPQGDFHHGDPGVSGT<HKGSRNPKRLVKGKNARSSSFTSGQHE

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
SRP051959_colon	1.46 RPM	0.13 RPM
SRP051959_heart	0.28 RPM	0.82 RPM
SRP051959_kidney	0.27 RPM	0.22 RPM
SRP051959_liver	0.26 RPM	1.00 RPM
SRP051959_lung	0.21 RPM	0.05 RPM
SRP051959_lymph_node	0.43 RPM	0.09 RPM
SRP051959_skeletal_muscle	0.17 RPM	0.09 RPM
SRP051959_spleen	0.21 RPM	0.02 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_936 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_936 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_936 has 0 orthologous retrocopies within eutheria group .

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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,