RetrogeneDB ID: retro_cjac_2969

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:23266321..23266853(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GPN3
• Ensembl ID: ENSCJAG00000009339
• Aliases: None
• Description: GPN-loop GTPase 3 [Source:HGNC Symbol;Acc:30186]

Sequence

>retro_cjac_2969
TTCGATTGTCCAGCTTGAACTGAGTCGGGCACTCACCTGCCTGTGACAAAGCAGCTGGTCCTGCAGCTTGAGCAGTGGGG
GTTCTGAGTTTATGGGGTTTTTCTCGTTGAGTCTCAGTTCATGGTGGAGTCATTCAAGTGTATTTCTGGCATCTTGGCAG
CCCTGAGTGCCCTGCTCTCTCTAGAAATTCCACACGTTAACATCGTGATGAAGATGGATCTGTAGAGTAAAAAAGCTAAA
AAGGAAACCGAGAGTTTCTAGATCCAGCCATGAATTCCTTATTTGATGATTCTACAAGTGACTTAAGCAGCAAAAAATTC
AAAAAAGTAACTAAAGCTGCATGTGGACTGATGACTGCCGCATAGTGCTCTTACCTCATCATCAGTCAAATGAAGAAATT
GTGAACATTGTATTACAGCATATTGATTCTGTCATTCAATGTGGAGAAGATTCAAAATTTAAATCACCAAAGGAACATGA
AAATGAGTCTTCTTCTTTGCTTGATGACTATTTTCAACAACGCCAGGATGAG

Alignment

ORF - retro_cjac_2969 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.84 %
• Parental protein coverage: 63.25 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FDCPGQIELYTHLPVMKQLVQQLEQWEFRVCGVFLVDSQFMVESFKFISGILAALSAMVSLEIPQVNIMT
          FDCP...E..THLPV.KQLV.QLEQW.F.V.GVFLV.SQFMVESFK.ISGILAALSA..SLEIP.VNI..
Retrocopy FDCPA*TESGTHLPVTKQLVLQLEQWGF*VYGVFLVESQFMVESFKCISGILAALSALLSLEIPHVNIVM

Parental  KMDLLSKKAKKEIE-KFLDPDMYSLLEDSTSDL-RSKKFKKLTKAICGLIDDYSMVRFLPYDQSDEESMN
          KMDL.SKKAKKE.E..FLDP.M.SL..DSTSDL....K..K.....C...DD...V..LP..QS.EE..N
Retrocopy KMDL*SKKAKKETE<EFLDPAMNSLFDDSTSDL<KQQKIQKSN*S-CMWTDDCRIV-LLPHHQSNEEIVN

Parental  IVLQHIDFAIQYGEDLEFKEPKEREDE-SSMFDEYFQECQGE
          IVLQHID..IQ.GED..FK.PKE.E.E.SS..D.YFQ..Q.E
Retrocopy IVLQHIDSVIQCGEDSKFKSPKEHENESSSLLDDYFQQRQDE

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	5.68 RPM
SRP051959_heart	0.00 RPM	10.24 RPM
SRP051959_kidney	0.00 RPM	11.45 RPM
SRP051959_liver	0.00 RPM	11.85 RPM
SRP051959_lung	0.00 RPM	6.65 RPM
SRP051959_lymph_node	0.00 RPM	7.83 RPM
SRP051959_skeletal_muscle	0.00 RPM	13.85 RPM
SRP051959_spleen	0.00 RPM	7.56 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2969 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2969 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2969 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_652
Gorilla gorilla	retro_ggor_570
Macaca mulatta	retro_mmul_2435

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009339	1 retrocopy	retro_cjac_2969 ,
Dasypus novemcinctus	ENSDNOG00000016646	1 retrocopy	retro_dnov_2095,
Homo sapiens	ENSG00000111231	1 retrocopy	retro_hsap_652,
Gorilla gorilla	ENSGGOG00000001697	1 retrocopy	retro_ggor_570,
Myotis lucifugus	ENSMLUG00000015510	1 retrocopy	retro_mluc_408,
Macaca mulatta	ENSMMUG00000006494	1 retrocopy	retro_mmul_2435,
Nomascus leucogenys	ENSNLEG00000002831	1 retrocopy	retro_nleu_2030,