RetrogeneDB ID: retro_cjac_3856

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL285178.1:2939..3725(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000018971
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RCC1
• Ensembl ID: ENSCJAG00000009686
• Aliases: None
• Description: regulator of chromosome condensation [Source:RefSeq peptide;Acc:NP_001192137]

Sequence

>retro_cjac_3856
CCACCCAAGCACATAGCTAAAAGAAGGTCACTCCCAGAAGATGCCATCCCCAAAAACAAGAAGGTGAAGGTCTCACACAG
GTCCCACAGCACAAAACCAGGCTTGGTGCTAACACTGGGCCAAAGCGATGTGGGCCAGCTGGGGCTGAGTGAGAATATGA
TGGAGAGGAAGAAGCCGGCCCTGGTATCCATTCCAGAAAATGTTGTGCAGGCTGAGGCTCGGGGCATGCATACCAAGTGT
TTAAGCAAAAGTGGCCAGGTCTACTCCTTTGGCTGCAATGATGAGGGTGCCCTGGGAAAAGACATGTCAGTGGAGGGCTC
AGAAATGGTCCCTGGGAAAGTGGAGCTGCAAGAGAAGGTGTCAGCAGGAGACAGTCACACAGTAGCCCTCACCCAGGATG
GCTGTGTCTTCCTCTGGGGCTCCTTAGAGGATAATAACAGTGTGATTGGACTGTTGGAGCCCATGAAGAAGAGAATGGTG
CCCGTACCCATCCAGCTGGATGTGCCTGTGGTGAAAGTGGCCTCAGGAAATGACCACTTGGTGATGCTGACAGCTGATGG
TGACCTCTACACCTTGGACTGTGGGAAACAGGGCCAGCTAGGCTGTGTGCCTGAGTTATTTGCCAACTATGGTGGCCGGC
AAGGCCTTGAACGACTCCTGGTTCCCAAGTGTGTGATGCTGAAATCCAGGGGAAGCTGGGGCCATGTGAGATTTCAGGAT
GCCTTCTGTGGTGCCTATTTCACCTTTGCCATCTCTTAAGAGGGCCACATGTACGACTGGCCTCTC

Alignment

ORF - retro_cjac_3856 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.79 %
• Parental protein coverage: 62.95 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PPKRIAKRKSPPEDAIPKNKKVKVSHRSHSTEPGLVLTLGQGDVGQLGLGENVMERKKPALVSIPEDVVQ
          PPK.IAKR.S.PEDAIPKNKKVKVSHRSHST.PGLVLTLGQ.DVGQLGL.EN.MERKKPALVSIPE.VVQ
Retrocopy PPKHIAKRRSLPEDAIPKNKKVKVSHRSHSTKPGLVLTLGQSDVGQLGLSENMMERKKPALVSIPENVVQ

Parental  AEAGGMHTVCLSKSGQVYSFGCNDEGALGRDTSVEGSEMVPGKVELQEKVVQVSAGDSHTAALTEDGRVF
          AEA.GMHT.CLSKSGQVYSFGCNDEGALG.D.SVEGSEMVPGKVELQEK...VSAGDSHT.ALT.DG.VF
Retrocopy AEARGMHTKCLSKSGQVYSFGCNDEGALGKDMSVEGSEMVPGKVELQEK---VSAGDSHTVALTQDGCVF

Parental  LWGSFRDNNGVIGLLEPMKKSMVPVQVQLDVTVVKVASGNDHLVMLTADGDLYTLGCGEQGQLGRVPELF
          LWGS..DNN.VIGLLEPMKK.MVPV..QLDV.VVKVASGNDHLVMLTADGDLYTL.CG.QGQLG.VPELF
Retrocopy LWGSLEDNNSVIGLLEPMKKRMVPVPIQLDVPVVKVASGNDHLVMLTADGDLYTLDCGKQGQLGCVPELF

Parental  ANRGGRQGLERLLVPKCVMLKSRGSRGHVRFQDAFCGAYFTFAISREGHVYGFGL
          AN.GGRQGLERLLVPKCVMLKSRGS.GHVRFQDAFCGAYFTFAIS.EGH.Y...L
Retrocopy ANYGGRQGLERLLVPKCVMLKSRGSWGHVRFQDAFCGAYFTFAIS*EGHMYDWPL

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	7.97 RPM
SRP051959_heart	0.07 RPM	2.26 RPM
SRP051959_kidney	0.00 RPM	4.64 RPM
SRP051959_liver	0.00 RPM	6.39 RPM
SRP051959_lung	0.18 RPM	5.27 RPM
SRP051959_lymph_node	0.05 RPM	9.00 RPM
SRP051959_skeletal_muscle	0.00 RPM	2.25 RPM
SRP051959_spleen	0.06 RPM	5.92 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3856 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3856 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3856 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009686	3 retrocopies	retro_cjac_2440, retro_cjac_3424, retro_cjac_3856 ,
Erinaceus europaeus	ENSEEUG00000004565	1 retrocopy	retro_eeur_418,
Myotis lucifugus	ENSMLUG00000017075	1 retrocopy	retro_mluc_2278,
Rattus norvegicus	ENSRNOG00000050106	1 retrocopy	retro_rnor_2886,