RetrogeneDB ID: retro_cjac_563

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:81865570..81866141(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GTPBP10
• Ensembl ID: ENSCJAG00000014212
• Aliases: None
• Description: GTP-binding protein 10 (putative) [Source:HGNC Symbol;Acc:25106]

Sequence

>retro_cjac_563
CAGATATCAGTAGCTGATCTTCCAGGTTTAATAGAAGGAGCACATATGAACAAAGGAATGGGCCACAATTTCTCAAGCAT
ATAGAAAGAACTAGACAACTACTTTTTGTTGTTGATATTTCTGGATTTCAGCTTTCTTATCGCACTCAATACAGAACTGG
TTTTGAAACCATAATAATACAAAAGAATTGGAATTGTACAAAGAGGAGGTTCAGACAAAACCTGCACTTTTGGCAGTTAA
TAAAATGGACTTTCCAGATGCTCAAGATAAGCTCCATGAATTGACGAACCAGCTCCAGAATCCTAAAGATTTTCTGCATT
TATTTGGAAAAAACATGATTCCAGAGAGGACTATAGAGTTCCAACATATCATCCCCATATCTGCAGTTACTGGAGAAGGA
ATTGAAGAATTAAAGAACTGTATAAGAGAGTCACTGGATGAACAGGCCAACCAGGAAAATGATGCATATCATAAGAAACA
GTTGCTTAATTTGTAAATTTCTGATAAAGTATCTTCAAGTGAGCCACCATCATCAAAGCATGCTGTTACTAGTTCCAAAG
TGAATAAATTT

Alignment

ORF - retro_cjac_563 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.72 %
• Parental protein coverage: 61.34 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QISVADLPGLIEGAHMNKGMGH-KFLKHIERTRQLLFVVDISGFQLSYHTQYRTAFETIILL-TKELELY
          QISVADLPGLIEGAHMNKGMGH..FLKHIERTRQLLFVVDISGFQLSY.TQYRT.FET.I...TKELELY
Retrocopy QISVADLPGLIEGAHMNKGMGH<QFLKHIERTRQLLFVVDISGFQLSYRTQYRTGFET-III<TKELELY

Parental  KEELQTKPALLAVNKMDLPDAQDKLHELMNQLQNPKDFLHLFGKNMIPERTVEFQHIIPISAVTGEGIEE
          KEE.QTKPALLAVNKMD.PDAQDKLHEL.NQLQNPKDFLHLFGKNMIPERT.EFQHIIPISAVTGEGIEE
Retrocopy KEEVQTKPALLAVNKMDFPDAQDKLHELTNQLQNPKDFLHLFGKNMIPERTIEFQHIIPISAVTGEGIEE

Parental  LKNCIRKSLDEQANQENDAYHKKQLLNLWISDKVSSSEPPSAKHAVTSSKLGVF
          LKNCIR.SLDEQANQENDAYHKKQLLNL.ISDKVSSSEPPS.KHAVTSSK...F
Retrocopy LKNCIRESLDEQANQENDAYHKKQLLNL*ISDKVSSSEPPSSKHAVTSSKVNKF

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	3.93 RPM
SRP051959_heart	0.00 RPM	6.21 RPM
SRP051959_kidney	0.00 RPM	7.25 RPM
SRP051959_liver	0.00 RPM	5.89 RPM
SRP051959_lung	0.00 RPM	5.11 RPM
SRP051959_lymph_node	0.00 RPM	4.79 RPM
SRP051959_skeletal_muscle	0.00 RPM	3.97 RPM
SRP051959_spleen	0.00 RPM	5.00 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_563 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_563 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_563 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014212	1 retrocopy	retro_cjac_563 ,
Myotis lucifugus	ENSMLUG00000007418	1 retrocopy	retro_mluc_789,
Mus musculus	ENSMUSG00000040464	1 retrocopy	retro_mmus_3183,
Oryctolagus cuniculus	ENSOCUG00000014847	1 retrocopy	retro_ocun_1558,
Otolemur garnettii	ENSOGAG00000010568	1 retrocopy	retro_ogar_431,
Sus scrofa	ENSSSCG00000015305	1 retrocopy	retro_sscr_661,