RetrogeneDB ID: retro_cjac_3861

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL285268.1:47863..49144(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000021874
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ZFP64
• Ensembl ID: ENSCJAG00000000596
• Aliases: None
• Description: ZFP64 zinc finger protein [Source:HGNC Symbol;Acc:15940]

Sequence

>retro_cjac_3861
ATGTCACGGCGCAAGCAGGCCAAGCCTCAGCATCTCAACTCCGAGGAGCCGCGGCCTGTGCGCCGGGAGTGCGCGGAGGT
GGCCCCGCAGGTGGGGGGGGCGGGGAGCCCGCTTCGGAACTTGATAATGATGTTCCAAAAGCGACCTGCCTCTCCACTGA
AGGCAGTGACCCTCAGAAGGCCCCTGTCATCACTCTTGCCTCAGAGTCAAGGGAACAAACCGCCACCCTTGGAGAGAGGA
CATTCAACTGTTGCTACCCAGGTCGCCACTTCAAAACTATGCATGGCATGAAAGACTTGGACCGCCATCTTAGAATCCAC
ACGGGAGACAAACCGCACAAGTGTGACTTCTGTGACAAGTTCTTCAGCCGGAAGGACAACCTGATCATGCACGTGCGGTG
CCACACCAGTGTGAAGCCACACAAGCGTGACGTGTGCGACTGCACCGCCGTGGACAGTGGCAGCCTCAAGAAGCACCTGG
GGATCCACTCGGAGGAGCGGCCATACAAATGCCAGCTCTGCCCCTATGCCAGCCGCAACTCCAGCCAGCTCACCGTCCAC
CTGCGGTCCCACACGGGGGATACCCCCTTCCAGTGCTGGCTGTGTAGTGCCAAGTTCAAAATCAGCTCGACTTGAAAAAG
CACATGATCGTGCACTCTGGGGAGCAGCCTTTCACGTGCGAGTTCTGTGACGTCCACTGCACCATGAAGGCGAACCTCAA
ATCGCACATCCGCATCAAGCACACCTTCAAGTGTCTGCACTGTGCCTTCCAGGTCCGGGACCGGGCTGACCTCCTGGAGC
ACAGCCGGCTGCACCAGGCTGACCACCCGGAGAAGTGTCCTGAGTGCAGCTACTCCTGCTCCAGCGCGGCCATCCTGCGC
GTGCACAGCAGAGTCCACTGTAAGGACCATCCCTTCAAGTGTGACTTCTGCAGCTTTGACATAAAGCGGCCCAGCAGCCT
GGCCAAGCACATGGACAAGGTGCACAGGGACGAGGCCAAGATGGAGAACTGGGCCCCTCTGGGCAAAGAAGTGCCCAGAT
AGAGCAGCTCCCAACACAAGGCCAAGATCGTGACACAGAGAGCTTTTCGCTGTGAGACCCGTGGCGCCTCCTTCGCCAGG
GATGAGTCTCTGAGATGCCCCAAGCAGCAGCATAGTGATCAGAGTGAGAACAGGAACTCAGACTTGGTCACCTTCCCACC
CGAAAGCTGCGCCTCAGGGCAGCTCAGCACCCTGGTCTCTGTGGGCAGCTCGAGGCCCCCCTAGAACCCAGCTAAGACCT
C

Alignment

ORF - retro_cjac_3861 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.33 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSRRKQANPQHLNSEEPRPARRECAEVAPQV--AGEP-ASELDNDVPKATCLSTEGSDPQKAPVIALASE
          MSRRKQA.PQHLNSEEPRP.RRECAEVAPQV..AG.P.ASELDNDVPKATCLSTEGSDPQKAPVI.LASE
Retrocopy MSRRKQAKPQHLNSEEPRPVRRECAEVAPQVGGAGSP<ASELDNDVPKATCLSTEGSDPQKAPVITLASE

Parental  SREQTATLGERTFNCCYPGCHFKTVHGMKDLDRHLRIHTGDKPHKCEFCDKCFSRKDNLTMHMRCHTSVK
          SREQTATLGERTFNCCYPG.HFKT.HGMKDLDRHLRIHTGDKPHKC.FCDK.FSRKDNL.MH.RCHTSVK
Retrocopy SREQTATLGERTFNCCYPGRHFKTMHGMKDLDRHLRIHTGDKPHKCDFCDKFFSRKDNLIMHVRCHTSVK

Parental  PHKCHLCDYAAVDSSSLKKHLRIHSDERPYKCQLCPYASRNSSQLTVHLRSHTGDTPFQCWLCSAKFKIS
          PHK...CD..AVDS.SLKKHL.IHS.ERPYKCQLCPYASRNSSQLTVHLRSHTGDTPFQCWLCSAKFKIS
Retrocopy PHKRDVCDCTAVDSGSLKKHLGIHSEERPYKCQLCPYASRNSSQLTVHLRSHTGDTPFQCWLCSAKFKIS

Parental  S-DLKRHMIVHSGEKPFKCEFCDVRCTMKANLKSHIRIKHTFKCLHCAFQGRDRADLLEHSRLHQADHPE
          S.DLK.HMIVHSGE.PF.CEFCDV.CTMKANLKSHIRIKHTFKCLHCAFQ.RDRADLLEHSRLHQADHPE
Retrocopy S<DLKKHMIVHSGEQPFTCEFCDVHCTMKANLKSHIRIKHTFKCLHCAFQVRDRADLLEHSRLHQADHPE

Parental  KCPECSYSCSSAAALRVHSRVHCKDRPFKCDFCSFDTKRPSSLAKHIDKVHRDETKTENWAPPGKEVPRE
          KCPECSYSCSSAA.LRVHSRVHCKD.PFKCDFCSFD.KRPSSLAKH.DKVHRDE.K.ENWAP.GKEVPR.
Retrocopy KCPECSYSCSSAAILRVHSRVHCKDHPFKCDFCSFDIKRPSSLAKHMDKVHRDEAKMENWAPLGKEVPR*

Parental  SSSQHMAKIVTQRAFRCETCGASFVRDDSLRCHKKQHSDQSENRNSDLVTFPPESSASGQLSTLVSV-GQ
          SSSQH.AKIVTQRAFRCET.GASF.RD.SLRC.K.QHSDQSENRNSDLVTFPPES.ASGQLSTLVSV.GQ
Retrocopy SSSQHKAKIVTQRAFRCETRGASFARDESLRCPKQQHSDQSENRNSDLVTFPPESCASGQLSTLVSV<GQ

Parental  LEVPLESSQDL
          LE.PLE.S.DL
Retrocopy LEAPLEPS*DL

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	4.64 RPM
SRP051959_heart	0.00 RPM	5.02 RPM
SRP051959_kidney	0.00 RPM	5.17 RPM
SRP051959_liver	0.00 RPM	2.38 RPM
SRP051959_lung	0.00 RPM	6.36 RPM
SRP051959_lymph_node	0.02 RPM	5.05 RPM
SRP051959_skeletal_muscle	0.00 RPM	1.53 RPM
SRP051959_spleen	0.17 RPM	5.32 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3861 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3861 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3861 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000596	1 retrocopy	retro_cjac_3861 ,