RetrogeneDB ID: retro_cjac_2034

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 21:40165052..40165378(+)
• Located in intron of: ENSCJAG00000002793

Retrocopy information

• Ensembl ID: ENSCJAG00000002799
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPS9
• Ensembl ID: ENSCJAG00000001130
• Aliases: None
• Description: None

Sequence

>retro_cjac_2034
ATGTCAGTGGCCAGGAGCTGGGTTTGTGGCAAAAGTTATGTGACCCCACAGAGACCCTTCGAGAAATCTCATCTCTACCA
AGAGCTGAAGCTGATTGGCGAGTATGGGCTCCAGAGCAAACGTGAGGTCTGGAGGGTCACATTTACCCTGGTCAAGATCC
ACAAGGCCGCCCGGGAGCTGCTGACCTTGACAAGAAGGACCCACCGCATCTGTTCGAAGGCAACACCCTGCTGCAGCGGC
TGGTTCGCGCTGGGGTGCTGGATGAGGCCAGGATGAGGCTGGATTACATTTTGGGCCAGAAGATCGATTATTTCTTAGAT
GCTCGC

Alignment

ORF - retro_cjac_2034 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.36 %
• Parental protein coverage: 56.19 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPVARSWVCRKTYVTPRRPFEKSRLDQELKLIGEYGLRNKREVWRVKFTLAKIRKAARELLT-LDEKDPR
          M.VARSWVC.K.YVTP.RPFEKS.L.QELKLIGEYGL..KREVWRV.FTL.KI.KAARELLT.LD.KDP.
Retrocopy MSVARSWVCGKSYVTPQRPFEKSHLYQELKLIGEYGLQSKREVWRVTFTLVKIHKAARELLT<LDKKDPP

Parental  RLFEGNALLRRLVRIGVLDEGKMKLDYILGLKIEDFLERR
          .LFEGN.LL.RLVR.GVLDE..M.LDYILG.KI..FL..R
Retrocopy HLFEGNTLLQRLVRAGVLDEARMRLDYILGQKIDYFLDAR

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	0.04 RPM	102.42 RPM
SRP051959_heart	0.09 RPM	104.40 RPM
SRP051959_kidney	0.07 RPM	78.69 RPM
SRP051959_liver	0.06 RPM	114.06 RPM
SRP051959_lung	0.13 RPM	111.63 RPM
SRP051959_lymph_node	0.07 RPM	225.97 RPM
SRP051959_skeletal_muscle	0.04 RPM	146.97 RPM
SRP051959_spleen	0.04 RPM	154.60 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2034 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2034 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2034 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001130	3 retrocopies	retro_cjac_2034 , retro_cjac_2993, retro_cjac_719,
Cavia porcellus	ENSCPOG00000020893	2 retrocopies	retro_cpor_1457, retro_cpor_407,
Gorilla gorilla	ENSGGOG00000027839	4 retrocopies	retro_ggor_1491, retro_ggor_160, retro_ggor_2190, retro_ggor_32,
Mustela putorius furo	ENSMPUG00000010394	1 retrocopy	retro_mputfur_128,
Nomascus leucogenys	ENSNLEG00000006314	1 retrocopy	retro_nleu_91,
Pan troglodytes	ENSPTRG00000011449	1 retrocopy	retro_ptro_57,
Rattus norvegicus	ENSRNOG00000011355	7 retrocopies	retro_rnor_1298, retro_rnor_2577, retro_rnor_2849, retro_rnor_2902, retro_rnor_635, retro_rnor_663, retro_rnor_892,
Rattus norvegicus	ENSRNOG00000049813	3 retrocopies	retro_rnor_2082, retro_rnor_30, retro_rnor_78,