RetrogeneDB ID: retro_cjac_3992

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL286665.1:8972..9405(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000004933
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PERP
• Ensembl ID: ENSCJAG00000019024
• Aliases: None
• Description: PERP, TP53 apoptosis effector [Source:HGNC Symbol;Acc:17637]

Sequence

>retro_cjac_3992
CCGCTGCGGCCTGGCCTGCGAGCGCTGCCGCGGGATCCTGCCCCTGCTCCTGCTCAGCGCCATCGCCTTCGACATCACTG
CGCTGGCCGGCCGCGGCTGGCTGCAGTCGAACGACCACGTCCAGACGTCCTCGCTGTGGTGGAGATGCTTCCACGAGGGT
GGCGGCAGTGGGTCCTACGAGGACGGCTGTCAGAGCCTCATGGAGTATGCGTGGGGTAGAGCAGCAGCTGCCATGCTCTT
CTGCGGCTTCATCATCCTGGTGATCTGTTTCATCTTCTCCTTCTTCGCCCTCATTAGACCCCAGATGCTTGTCTTCCTAA
GAGTGATTGGAGGTCTCCTTGCCTTGGCTGCTGTGTTCCAGATCATCTCCCTGGTAATTTACCCCGTGAACTACACCCAG
ACCTTCGGCCTTCACGCCAACCCAGCTGTCACA

Alignment

ORF - retro_cjac_3992 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.48 %
• Parental protein coverage: 75.13 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  PLR-LACERCRWILP-CS-AQRHR-FDIIALAGRGWLQSNDHVQTSSLWWRCFHEGGGSG-YEDGCQSLM
          PLR.LACERCR.ILP.CS.AQRHR.FDI.ALAGRGWLQSNDHVQTSSLWWRCFHEGGGSG.YEDGCQSLM
Retrocopy PLR>LACERCRGILP>CS>AQRHR>FDITALAGRGWLQSNDHVQTSSLWWRCFHEGGGSGSYEDGCQSLM

Parental  DYAWGRAAAAMLFCGFIILVICFILSFFALCGPQMLVFLRVIGGLLALAAVFQIISLVIYPVKYTQTFNL
          .YAWGRAAAAMLFCGFIILVICFI.SFFAL..PQMLVFLRVIGGLLALAAVFQIISLVIYPV.YTQTF.L
Retrocopy EYAWGRAAAAMLFCGFIILVICFIFSFFALIRPQMLVFLRVIGGLLALAAVFQIISLVIYPVNYTQTFGL

Parental  HANPAIT
          HANPA.T
Retrocopy HANPAVT

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	0.80 RPM	68.76 RPM
SRP051959_heart	0.70 RPM	29.68 RPM
SRP051959_kidney	0.55 RPM	22.96 RPM
SRP051959_liver	0.41 RPM	15.51 RPM
SRP051959_lung	0.68 RPM	17.37 RPM
SRP051959_lymph_node	0.34 RPM	1.76 RPM
SRP051959_skeletal_muscle	0.52 RPM	4.63 RPM
SRP051959_spleen	0.13 RPM	2.44 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3992 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3992 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3992 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020097	1 retrocopy	retro_btau_165,
Callithrix jacchus	ENSCJAG00000019024	1 retrocopy	retro_cjac_3992 ,
Homo sapiens	ENSG00000112378	2 retrocopies	retro_hsap_1523, retro_hsap_2901,
Gorilla gorilla	ENSGGOG00000028340	1 retrocopy	retro_ggor_1165,
Macropus eugenii	ENSMEUG00000004872	1 retrocopy	retro_meug_845,
Microcebus murinus	ENSMICG00000013979	1 retrocopy	retro_mmur_353,
Myotis lucifugus	ENSMLUG00000001473	1 retrocopy	retro_mluc_2287,
Macaca mulatta	ENSMMUG00000000997	1 retrocopy	retro_mmul_2156,
Nomascus leucogenys	ENSNLEG00000014930	2 retrocopies	retro_nleu_1934, retro_nleu_631,
Oryctolagus cuniculus	ENSOCUG00000004238	1 retrocopy	retro_ocun_170,
Otolemur garnettii	ENSOGAG00000011669	1 retrocopy	retro_ogar_631,
Pongo abelii	ENSPPYG00000017043	3 retrocopies	retro_pabe_1267, retro_pabe_2400, retro_pabe_2416,