RetrogeneDB ID: retro_cjac_2520

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 5:60473303..60474356(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000012272
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GTPBP6
• Ensembl ID: ENSCJAG00000013056
• Aliases: None
• Description: GTP binding protein 6 (putative) [Source:HGNC Symbol;Acc:30189]

Sequence

>retro_cjac_2520
AGATCTCTGGACATCACGTGCGTCTTCCTGAATGTAGAGAGGATGGCTGCCCCAACCAAAAAAGAACTGGAAGCCGCCTG
GAGGGTGGAGGTGTTTGACCACTTCACCGTCGTCCTGCACATTTTCCGCTGCAACGCCCGCATGAAGGAGGCCTGGCTGC
AGGTGGCCCTGGCAGAGATCCCGCTCCTCAGGTCGAACCTGCAAAGGGAGGTCGCCCACCTTCACCGAGGAGGATCCGGC
TCCTGCTACATCATGGGGTCAGGAGAATCGTTCATGCAGCTGCAGCAGCGTCTCCTGAAAAAGAAGGAGGCCAAGATCAG
GAAGGCCCTGGACGGGCTTCGGAAGAAGAGGCACCTGCTGCGGCGGCAGCTCAAGAGGCGCAAGTTCCCCATGGTCTCCG
TGGTGGGGTACACCAACTGTGGGAAGACCACGCTGATCAAGGCGCTGATGGGAGACGCCGCCCTGCAGCCGCGGAACCAG
CTGTTTGCCATGCTGGACGTCACAGCCCACGCGGGCACGCTGTCCTCACGCCTGCGCGTCCTGTATGTGGGCATCATCGG
GTTCTTGTCCCAGCTGCCACACGGCCTCATCAAGTCCTTCTCCACTATCCTAGAAGACGTGGCCCACTCGGACCTGATCC
TGCAGGTGAGGGACGTCAGCCACCCCGAGGCGGAGCTCCAGAAAGTCAGCGTCATATCCACACTGCGTGGCCTTCAGCTG
CCCGCCCCGCTCCTGGACTGCATGCTGGAGGTTCACAACAAGGTGGACCTGGTTCCCGGGTACCACCCCACGAAACCGAA
CGTTGTGCTTGTGTCTGCCCTGCTGGGGCATGGGCTCCAGGAGCTGAAAGCTGAACTTGAGGCAGCATTGTTAAAGGCCG
CGGGGAGACAGGTCCTCACCCTCCGCATCAGGCTGGCCAGGGCCCAGCTCAGCTGGCTGCATAAGGAGACCACAGTTCAG
CAGGTGGACATGATCCCCGAGGAAGGAGCAGCCGACGTCAGGGTCATCATCAGCCACTCGGCCTATGGCAAATTCCGGAA
GCTCTTTCCAGGA

Alignment

ORF - retro_cjac_2520 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.75 %
• Parental protein coverage: 98.87 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RSPDITCVFLNVERMAAPTKKELEAAWGLEVFDRFTVVLHIFRCNARTEEARLQVALAEIPLLRSNLQRD
          RS.DITCVFLNVERMAAPTKKELEAAW..EVFD.FTVVLHIFRCNAR..EA.LQVALAEIPLLRSNLQR.
Retrocopy RSLDITCVFLNVERMAAPTKKELEAAWRVEVFDHFTVVLHIFRCNARMKEAWLQVALAEIPLLRSNLQRE

Parental  VAHLHRGGSGSRYIMGSGESFMQLQQRLLKEKEAKIRKALDGLRKKRHLLRRQRTRREFPVVSVVGYTNC
          VAHLHRGGSGS.YIMGSGESFMQLQQRLLK.KEAKIRKALDGLRKKRHLLRRQ..RR.FP.VSVVGYTNC
Retrocopy VAHLHRGGSGSCYIMGSGESFMQLQQRLLKKKEAKIRKALDGLRKKRHLLRRQLKRRKFPMVSVVGYTNC

Parental  GKTTLIKALTGDAALQPRDQLFATLDVTAHAGTLPSRLTVLYVDTIGFLSQLPHGLIESFSATLEDVAHS
          GKTTLIKAL.GDAALQPR.QLFA.LDVTAHAGTL.SRL.VLYV..IGFLSQLPHGLI.SFS..LEDVAHS
Retrocopy GKTTLIKALMGDAALQPRNQLFAMLDVTAHAGTLSSRLRVLYVGIIGFLSQLPHGLIKSFSTILEDVAHS

Parental  DLILHVRDVSHPEAELQKASVVSTLRGLRLPAPLLDSMLEVHNKVDLVPGYHATEPNVVPVSALLGHGLQ
          DLIL.VRDVSHPEAELQK.SV.STLRGL.LPAPLLD.MLEVHNKVDLVPGYH.T.PNVV.VSALLGHGLQ
Retrocopy DLILQVRDVSHPEAELQKVSVISTLRGLQLPAPLLDCMLEVHNKVDLVPGYHPTKPNVVLVSALLGHGLQ

Parental  ELKAELDAAVLKATGRQVLTLRVRLAGAQLSWLHEEATVQQVDVIPQDGAADVRVVISHSAYGKFRKLFP
          ELKAEL.AA.LKA.GRQVLTLR.RLA.AQLSWLH.E.TVQQVD.IP..GAADVRV.ISHSAYGKFRKLFP
Retrocopy ELKAELEAALLKAAGRQVLTLRIRLARAQLSWLHKETTVQQVDMIPEEGAADVRVIISHSAYGKFRKLFP

Parental  G
          G
Retrocopy G

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	1.24 RPM	2.60 RPM
SRP051959_heart	0.02 RPM	4.40 RPM
SRP051959_kidney	0.13 RPM	4.22 RPM
SRP051959_liver	0.11 RPM	4.14 RPM
SRP051959_lung	0.41 RPM	3.22 RPM
SRP051959_lymph_node	0.41 RPM	3.81 RPM
SRP051959_skeletal_muscle	0.09 RPM	6.64 RPM
SRP051959_spleen	0.25 RPM	2.58 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2520 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2520 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2520 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	ENSCJAG00000013056	1 retrocopy	retro_cjac_2520 ,