RetrogeneDB ID: retro_cjac_1211

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 14:55044865..55045186(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GGCT
• Ensembl ID: ENSCJAG00000008589
• Aliases: None
• Description: gamma-glutamylcyclotransferase [Source:HGNC Symbol;Acc:21705]

Sequence

>retro_cjac_1211
CTTTGGCAATTCCTAAGGCCTAATTAGTCAAACTTGGTATGGAGGCAAGGAAAGGTAAATAGTGGAATAGATTTTGTAAT
AGCGGTTAAAATTTTATCTCAACAAGAGAGAGAAATAACCTGTCAAAGTTACCTGATGAGAAAGTGTAAGAGTGCTCCTT
CATCAAGACAGTATAAAAAGGTTCTTTGCATGGGTACAAAAGAAAAGAGTTTGCCACTGGAGTATCGAAAGTAGTTAAAA
GCAATAGAACCAAATGACTGTAAAAGAAAGGTCTCAGAAGAAATTAAAGACATTATTGAAAAGGGTGAATGCAAACTCAT
T

Alignment

ORF - retro_cjac_1211 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.21 %
• Parental protein coverage: 56.38 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VWKMNKSNLNSLDEQEG-VKSGTYVVIEVKVSTQEGREITCRSYLMTNYESAPPSPQYKKIICMGAKENG
          .W.....N...L....G.V.SG...VI.VK...Q..REITC.SYLM....SAP.S.QYKK..CMG.KE..
Retrocopy LWQFLRPN*SNLVWRQGKVNSGIDFVIAVKILSQQEREITCQSYLMRKCKSAPSSRQYKKVLCMGTKEKS

Parental  LPLEYQEKLEAIEPNDYTGKVSEEIEDIIKKGETQTL
          LPLEY...L.AIEPND...KVSEEI.DII.KGE....
Retrocopy LPLEYRK*LKAIEPNDCKRKVSEEIKDIIEKGECKLI

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	1.64 RPM
SRP051959_heart	0.00 RPM	1.23 RPM
SRP051959_kidney	0.00 RPM	3.51 RPM
SRP051959_liver	0.00 RPM	4.18 RPM
SRP051959_lung	0.00 RPM	1.29 RPM
SRP051959_lymph_node	0.00 RPM	1.19 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.79 RPM
SRP051959_spleen	0.00 RPM	1.70 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1211 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1211 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1211 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008757	1 retrocopy	retro_chof_467,
Callithrix jacchus	ENSCJAG00000008589	1 retrocopy	retro_cjac_1211 ,
Dasypus novemcinctus	ENSDNOG00000007242	1 retrocopy	retro_dnov_2324,
Mustela putorius furo	ENSMPUG00000005083	1 retrocopy	retro_mputfur_1157,
Otolemur garnettii	ENSOGAG00000013316	1 retrocopy	retro_ogar_2457,
Ochotona princeps	ENSOPRG00000005329	2 retrocopies	retro_opri_170, retro_opri_505,