RetrogeneDB ID: retro_cjac_2967

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:19690373..19691920(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000008042
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: APEX2
• Ensembl ID: ENSCJAG00000016584
• Aliases: None
• Description: None

Sequence

>retro_cjac_2967
ATGTTGTGTGTGGTGAGCTGGAACATCAATGGGATGCAGAGACCCCTGCAAGGGGTGGCAAATCAGGAAACCAACAACTG
GGCTGCCATGGCCGTGGGGCGCATTTTGGATGAGCTGGATGCCGATACCGTCTGTCTCCAGGAGACCAAAGTGACCAGGG
ATGCACTGACAGAACCCCTGGCTATCGCTGAGGTTTATAACTCCTATTTCAGCTTCAGCCGCAACCGTAGTGGCTATTCT
GGTGTAGCCACCTTCTGAAAGGACAGTGCTACCCAGTGGCTGCTGAAGAGGGCCTGAGTGGCCTGTTTGCCACCCAGAAT
GGGGATGTGGGTTGCTATGGAAACATGGATGAGTTTACCCAAGAGGAACTCCGGGCTCTGGATAGTGAGGGCCGGGCCCT
CCTCAAACAGCACAAGATCCGCACCTGGGAAGGAAAGGAGAGGACCTTGACCCTAATCAACGTGTACTGCCCCCACACAG
ACCCTGGGAGGCCTGAGCGGCTGGTCTTTAAGATGTGCTTCTATCGCTTGCTGCAAATCCGAGCTGAAGCCCTCCTGGCG
GCAGGCAGCCATGTGATCATTCTGGGTGACCTGAATACAGCCCACCGCCCCATTGACCAATGGGATTCAGTCAACCTGGA
ATGCTTTGAAGAGGACCCAGGGCGCAAGTGGATAAACGGCTTGCTCAGTAACTTGGGGTGTCAGTCTGCCTCTCATGTAG
GGCCCTTCATCGATAGCTACCGCTGCTTCCAACCAAAGCAGGAGGGGGCCTTCACCTGCTGGTCAGCAGTCATGGGCGCC
GCCATCTCAACTATGGCTCCTGGATTGACTATGTGCTGGGGGACAGGACCCTGGTCATAGACACCTTACACGCCTCTTTC
CTGCTGCCTGAGGTGATGGGCTCTGACCACTGCCCTGTGGGTGGTCTTGAGTGTGTCCTCTATGCCTGCAAAACAGTGCC
CACTTCTGTGCACTCGCTTCCCCCCAAGTTTGCAGGCACCCAGCTCAAGATCCTTCGCTTCCTAGTTCCTCTCAAACACG
GTCCTGTGTTGGAGCAGTCAGCACCGCAGCATAACAGTCAAACCCGGGTACAGACATGCCAAAACAAAGCCCGCGTGCAC
TCAACCAGGCCTCGGCCCAGTCAGCTTGGCTCTAGCAGAGGCCAGAAAAACCTGAAGAGCTACTTTCAGCCCTCCCCTAC
CTTTTCCCAAGCCTCTCCTGACATAGAGATGCCTAGCCTGCCACTGATGAGTGCCCTCATGACCCCAAAGACTTCAGAAG
AGGAGGCTGTGGCCAAAGTGGTGAAGGGCAGGCCAAGGCTTCGAAGCCAAAGATGAGAAGGAAGTAGGGACCTCATTCTG
GAAGTCTTTGCTGGTGGGGTGCTTGCGCGTACCTCTCTGTGGGGGCCACAGGGAACCATGTGTGATGCCTACTGTGAAGA
AGCCAGGACCCAACCTGGGCCACCGCTTCTACATGTGTGCCAGGCCCAGGGGTCCTCCTAATGACCCCTCCTCCTGCTGC
AACTTTTTCCTCTGGAGCAGGCCCAGC

Alignment

ORF - retro_cjac_2967 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.48 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  MLRVVSWNINGIRRPLQGMANQEPNNCAAVAVGRILDELDADIVCLQETKVTRDALTEPLAIVEGYNSYF
          ML.VVSWNING..RPLQG.ANQE.NN.AA.AVGRILDELDAD.VCLQETKVTRDALTEPLAI.E.YNSYF
Retrocopy MLCVVSWNINGMQRPLQGVANQETNNWAAMAVGRILDELDADTVCLQETKVTRDALTEPLAIAEVYNSYF

Parental  SFSRNRSGYSGVATFCKDSAT-PVAAEEGLSGLFATQNGDVGCYGNMDEFTQEELRALDSEGRALLTQHK
          SFSRNRSGYSGVATF.KDSAT.PVAAEEGLSGLFATQNGDVGCYGNMDEFTQEELRALDSEGRALL.QHK
Retrocopy SFSRNRSGYSGVATF*KDSAT<PVAAEEGLSGLFATQNGDVGCYGNMDEFTQEELRALDSEGRALLKQHK

Parental  IRTWEGKERTLTLINVYCPHADPGRPERLVFKMRFYRLLQIRAEALLAAGSHVIILGDLNTAHRPIDHWD
          IRTWEGKERTLTLINVYCPH.DPGRPERLVFKM.FYRLLQIRAEALLAAGSHVIILGDLNTAHRPID.WD
Retrocopy IRTWEGKERTLTLINVYCPHTDPGRPERLVFKMCFYRLLQIRAEALLAAGSHVIILGDLNTAHRPIDQWD

Parental  SVNLECFEEDPGRKWMDGLLSNLGCQSASHVGPFIDSYRCFQPKQEGAFTCWSAVTGA-RHLNYGSRIDY
          SVNLECFEEDPGRKW..GLLSNLGCQSASHVGPFIDSYRCFQPKQEGAFTCWSAV.GA.RHLNYGS.IDY
Retrocopy SVNLECFEEDPGRKWINGLLSNLGCQSASHVGPFIDSYRCFQPKQEGAFTCWSAVMGA<RHLNYGSWIDY

Parental  VLGDRTLVIDTFQASFLLPEVMGSDHC-PVG-AVLSVSSVPAKQCPSLCTRF-LPEFAGTQLKILRFLVP
          VLGDRTLVIDT..ASFLLPEVMGSDHC.P.G..VLSVSS.PAKQCP.LCTRF..P.FAGTQLKILRFLVP
Retrocopy VLGDRTLVIDTLHASFLLPEVMGSDHC<PCG<VVLSVSSMPAKQCPLLCTRF<PPKFAGTQLKILRFLVP

Parental  LKQGPVLEQSAPQHNSQTRVQTCQNKARVRSTRLRPSQLGSSRGQKNLKSYFQPSPSCPQASPDIELPSL
          LK.GPVLEQSAPQHNSQTRVQTCQNKARV.STR.RPSQLGSSRGQKNLKSYFQPSP...QASPDIE.PSL
Retrocopy LKHGPVLEQSAPQHNSQTRVQTCQNKARVHSTRPRPSQLGSSRGQKNLKSYFQPSPTFSQASPDIEMPSL

Parental  PLMSALMTPKTSEEEAVAKVVK-GQAKAS-EAKDEKEVRTSFWKSLLAGPLHIPLCGGHREPCVMRTVKK
          PLMSALMTPKTSEEEAVAKVVK.GQAKAS.EAKDEKEV.TSFWKSLL.G.L..PLCGGHREPCVM.TVKK
Retrocopy PLMSALMTPKTSEEEAVAKVVK<GQAKAS<EAKDEKEVGTSFWKSLLVGCLRVPLCGGHREPCVMPTVKK

Parental  PGPNLGRHFYMCARPRGPPNDPSSRCNFFLWSRPS
          PGPNLG..FYMCARPRGPPNDPSS.CNFFLWSRPS
Retrocopy PGPNLGHRFYMCARPRGPPNDPSSCCNFFLWSRPS

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	0.00 RPM	1.35 RPM
SRP051959_heart	0.00 RPM	0.96 RPM
SRP051959_kidney	0.00 RPM	1.02 RPM
SRP051959_liver	0.00 RPM	0.80 RPM
SRP051959_lung	0.00 RPM	1.61 RPM
SRP051959_lymph_node	0.00 RPM	2.88 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.81 RPM
SRP051959_spleen	0.00 RPM	2.67 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2967 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2967 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2967 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016584	1 retrocopy	retro_cjac_2967 ,
Myotis lucifugus	ENSMLUG00000016298	1 retrocopy	retro_mluc_287,
Mus musculus	ENSMUSG00000025269	1 retrocopy	retro_mmus_2564,
Rattus norvegicus	ENSRNOG00000000166	1 retrocopy	retro_rnor_1061,