RetrogeneDB ID: retro_cjac_2925

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:105614179..105614553(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000017666
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PIN1
• Ensembl ID: ENSCJAG00000006079
• Aliases: None
• Description: None

Sequence

>retro_cjac_2925
GAAGAGAAGCTGCAGCCCGGCTGGGAGAAGCGCTACAGCCGCAGCCGCAGCTCAGGCCGTGTGTACTACTTCAACCACAT
CGCCAACGCCAGCAGTGGGAGCGACCCAGCGACCACAGCAGCAGTGGCGGCAAAAACAGGCAGAGGGAGCCCGCCACGGT
CCGCTGCTCACACCTGCTGGGGAAGCACAGCCAGTCAAGGCCCTCACCCCGGCGGCAGGAGATCACCTGGCCCAAGGAGG
AGGCCCTGGAGCTGATCAGCGGCTACATCCAGAAGATCAAGTCGGGAGAGGAGGGCTTTGAGTCTCTGCGCTCACAATTC
AGCGACTGCAGCTCGGCCAAGGCCAGGGGAGACCCGGGTGCTGTCAGCAAAGGT

Alignment

ORF - retro_cjac_2925 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.25 %
• Parental protein coverage: 86.21 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EEKLPPGWEKRMSRS--SGRVYYFNHITNAS-QWERPSGNSSSGGKNGQGEPARVRCSHLLVKHSQSRRP
          EEKL.PGWEKR.SRS..SGRVYYFNHI.NAS.QWERPS..SSSGGKN.Q.EPA.VRCSHLL.KHSQSR.P
Retrocopy EEKLQPGWEKRYSRSRSSGRVYYFNHIANAS<QWERPSDHSSSGGKNRQREPATVRCSHLLGKHSQSR-P

Parental  SSWRQEKITRTKEEALELINGYIQKIKSGEEDFESLASQFSDCSSAKARGDLGAFSRG
          S..RQE.IT..KEEALELI.GYIQKIKSGEE.FESL.SQFSDCSSAKARGD.GA.S.G
Retrocopy SPRRQE-ITWPKEEALELISGYIQKIKSGEEGFESLRSQFSDCSSAKARGDPGAVSKG

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	5.10 RPM
SRP051959_heart	0.00 RPM	11.52 RPM
SRP051959_kidney	0.00 RPM	12.60 RPM
SRP051959_liver	0.00 RPM	7.99 RPM
SRP051959_lung	0.00 RPM	6.93 RPM
SRP051959_lymph_node	0.00 RPM	5.87 RPM
SRP051959_skeletal_muscle	0.00 RPM	13.65 RPM
SRP051959_spleen	0.00 RPM	4.73 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2925 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2925 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2925 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_168
Pan troglodytes	retro_ptro_159
Gorilla gorilla	retro_ggor_252
Pongo abelii	retro_pabe_462

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006079	1 retrocopy	retro_cjac_2925 ,
Homo sapiens	ENSG00000127445	1 retrocopy	retro_hsap_168,
Gorilla gorilla	ENSGGOG00000006008	1 retrocopy	retro_ggor_252,
Microcebus murinus	ENSMICG00000001996	1 retrocopy	retro_mmur_1157,
Mus musculus	ENSMUSG00000032171	1 retrocopy	retro_mmus_2072,
Nomascus leucogenys	ENSNLEG00000011999	1 retrocopy	retro_nleu_980,
Pongo abelii	ENSPPYG00000009537	1 retrocopy	retro_pabe_462,
Pan troglodytes	ENSPTRG00000010452	1 retrocopy	retro_ptro_159,
Rattus norvegicus	ENSRNOG00000020474	1 retrocopy	retro_rnor_1220,
Tupaia belangeri	ENSTBEG00000003793	1 retrocopy	retro_tbel_1546,