RetrogeneDB ID: retro_cjac_2993

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:78917702..78918283(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000017658
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_cjac_2993
ATGCCAGTGGCCCGGAGCTGGGTTTGTCGCAAAACTTATGTGACCCCGCGGAGACCCTTCGAGAAACCTCGTCTCGACCA
AGAGCTGAAGCTGATCAGCGAGTATGGGCTTCGGAACAAACGTGAGGTCTGGAGGGTCAAGTTTACCCTGGCCAAGATCC
GCAAGGCCGCTGGAGAGCTGCTGACACTTGACGAGAAGGATCCACGGCGTCTTTTCGAAGGCAACACCCTGCTGCGGTGG
CTGGTCCGCATTGGGGTGTTGGATGAGGGCAAGATGAAGCTGGATTACATCCTGGGCCTGAAGATTGAGGATTTCTTAGA
GAGACGCCTGCAGACCCAGGTCTTCAAGCTGGGCTTGGCCAAGTCCATCCACCACGCACGTGTACTGATCCGCCAGCGCC
ATATCAGGGTCCGCAAGCAGGTGGTGAACATCCGTCCTTCATTGTCCGCCTGGATTCCCAGAAGCACATCGACTTCTCCC
TCCGCTCTCCCTACGGGGGTGGCCGCCCGGGCCGCGTGAAGAGGAAGAATGCCAAGAAGGGTCAGGGCGGGGCTGGGGCT
GGGGATGACGAGGAGGAGGAT

Alignment

ORF - retro_cjac_2993 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.92 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPVARSWVCRKTYVTPRRPFEKSRLDQELKLIGEYGLRNKREVWRVKFTLAKIRKAARELLTLDEKDPRR
          MPVARSWVCRKTYVTPRRPFEK.RLDQELKLI.EYGLRNKREVWRVKFTLAKIRKAA.ELLTLDEKDPRR
Retrocopy MPVARSWVCRKTYVTPRRPFEKPRLDQELKLISEYGLRNKREVWRVKFTLAKIRKAAGELLTLDEKDPRR

Parental  LFEGNALLRRLVRIGVLDEGKMKLDYILGLKIEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHIRVRKQ
          LFEGN.LLR.LVRIGVLDEGKMKLDYILGLKIEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHIRVRKQ
Retrocopy LFEGNTLLRWLVRIGVLDEGKMKLDYILGLKIEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHIRVRKQ

Parental  VVNI-PSFIVRLDSQKHIDFSLRSPYGGGRPGRVKRKNAKKGQGGAGAGDDEEED
          VVNI.PSFIVRLDSQKHIDFSLRSPYGGGRPGRVKRKNAKKGQGGAGAGDDEEED
Retrocopy VVNI<PSFIVRLDSQKHIDFSLRSPYGGGRPGRVKRKNAKKGQGGAGAGDDEEED

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	0.51 RPM	102.42 RPM
SRP051959_heart	0.51 RPM	104.40 RPM
SRP051959_kidney	0.60 RPM	78.69 RPM
SRP051959_liver	0.76 RPM	114.06 RPM
SRP051959_lung	0.99 RPM	111.63 RPM
SRP051959_lymph_node	2.26 RPM	225.97 RPM
SRP051959_skeletal_muscle	0.85 RPM	146.97 RPM
SRP051959_spleen	0.97 RPM	154.60 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2993 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2993 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2993 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,