RetrogeneDB ID: retro_cjac_2380

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:135600858..135601315(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000033406
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CLPP
• Ensembl ID: ENSCJAG00000016699
• Aliases: None
• Description: ClpP caseinolytic peptidase, ATP-dependent, proteolytic subunit homolog (E. coli) [Source:HGNC Symbol;Acc:2084]

Sequence

>retro_cjac_2380
ATATTGGGGGAGGGGGGGCAGGGTGGCGGAGGCAGGTACCCCGCGCTGGGGCTTCGCCTCGCCTCGCCTCTCGCTTTCCA
GAGCAGCGGAAGCCCCAGAGCGGCCTGGCCCTGTAGCAGAGCCTGCACGTTCGGCCCGAGCTCTCCCGCTCATACCCATC
GCGGTGGAGCAGACCCGTCGCGGGTAGCGCGCCTATGACATCTACTCGCGGCTGCTGCGGGAGCGCATCGTGTGCGAAAT
GGGCCCGATAGATGACAGCGTTGCCCTCCTGGTTATTGCACAGCTCCTCTTCCTGCAATCCGAGAGCAACAAGAAGCCCA
TCCACATGTACATCAACAGCCCTGGTGGTGTGGTGACCGCGGGCATGGCCATCTACGATACGATGCTGTATATCCTCAAT
CCAATCTGCACATGGTGCGTGGGCCAGGCAGCCAGCATGGGCTCCCTGCTTCTAGCC

Alignment

ORF - retro_cjac_2380 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.74 %
• Parental protein coverage: 55.68 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ILVGGGRVAAGRYPALGLRLASRFAAQRTPQSGPALQRSLHVT-AARALPLIPIVVEQTGRGERAYDIYS
          IL..GG....GRYPALGLRLAS..A.Q.......A...S...T..ARALPLIPI.VEQT.RG.RAYDIYS
Retrocopy ILGEGGQGGGGRYPALGLRLASPLAFQSSGSPRAAWPCSRACT>SARALPLIPIAVEQTRRG*RAYDIYS

Parental  RLLRERIVCVMGPIDDSVASLVIAQLLFLQSESNKKPIHMYINSPGGVVTAGLAIYDTMQYILNPICTWC
          RLLRERIVC.MGPIDDSVA.LVIAQLLFLQSESNKKPIHMYINSPGGVVTAG.AIYDTM.YILNPICTWC
Retrocopy RLLRERIVCEMGPIDDSVALLVIAQLLFLQSESNKKPIHMYINSPGGVVTAGMAIYDTMLYILNPICTWC

Parental  VGQAASMGSLLLA
          VGQAASMGSLLLA
Retrocopy VGQAASMGSLLLA

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	3.64 RPM
SRP051959_heart	0.02 RPM	4.19 RPM
SRP051959_kidney	0.00 RPM	6.15 RPM
SRP051959_liver	0.00 RPM	7.34 RPM
SRP051959_lung	0.00 RPM	3.43 RPM
SRP051959_lymph_node	0.00 RPM	4.18 RPM
SRP051959_skeletal_muscle	0.00 RPM	6.57 RPM
SRP051959_spleen	0.00 RPM	3.55 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2380 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2380 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2380 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016699	1 retrocopy	retro_cjac_2380 ,
Microcebus murinus	ENSMICG00000006284	1 retrocopy	retro_mmur_1142,
Myotis lucifugus	ENSMLUG00000007981	1 retrocopy	retro_mluc_2501,
Xenopus tropicalis	ENSXETG00000005576	1 retrocopy	retro_xtro_53,