RetrogeneDB ID: retro_cjac_744

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 10:125268482..125269148(+)
• Located in intron of: ENSCJAG00000006717

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: REEP4
• Ensembl ID: ENSCJAG00000020323
• Aliases: None
• Description: receptor accessory protein 4 [Source:HGNC Symbol;Acc:26176]

Sequence

>retro_cjac_744
GTGCGGTGGATGATGTACTGGATCGTTTTTGCACTCTTCATGGTAGCAGAGATCGTCACCGACATTTTTATCTCCTGGTT
CCCTTTCTACTATGAGATCAAGATGGCCTTTGTGCTGTGGCTGCTCTCGCCCTACACCAAGGGCGCCAGCCTGCTTTACC
TCAAGTTTGTCCACCCATCCCTGTCCCGCCACGAGAAGGAGATCGACGCATACCTCGTGGAGGCCAAGGAGCGCAGCTAC
GAGACCATGCTTAGCTTCGGGAAGCGGGGCCTCAACATTGCCGCCTCGGCTGCTGTGCAGGCTGCCAGCAAGAGTCAGGG
GGCGCTGGCCGGCAGGCTGCTGAGCTTCTCCATGCAGGACCTGCGCTCCATCCCCGATGCACCCGCTCCTGCCTAACAGG
ACGCCCTCTACCCAGAGGACCAGGTGCTCCACCGGAGGCCACCCATTGGGTACCGGGACGGGGGCCTGCAGGACAGCAAC
ACGGAGGATGACTGTTGGTCAGATACTGAGGCGGTCCCCCGGATGCCAGCCCGGCCCCGAGAGAAGCCCCTGAGCCGCAG
CCAGAGCCTGCGTGTGATCAAGAGGAAGCCACTGGTGCGGGAGGGCACCTCGCGCTCCCTAAAGGTTCGGACGAGGAAAA
AGACTGTGCCCTCAGACATGGACAGC

Alignment

ORF - retro_cjac_744 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.85 %
• Parental protein coverage: 86.38 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VRWMMYWIVFALFMAAEIVTDIFISWFPFYYEIKMAFVLWLLSPYTKGASLLYRKFVHPSLSRHEKEIDA
          VRWMMYWIVFALFM.AEIVTDIFISWFPFYYEIKMAFVLWLLSPYTKGASLLY.KFVHPSLSRHEKEIDA
Retrocopy VRWMMYWIVFALFMVAEIVTDIFISWFPFYYEIKMAFVLWLLSPYTKGASLLYLKFVHPSLSRHEKEIDA

Parental  YLVQAKERSYETMLSFGKRGLNMAASAAVQAATKSQGALAGRLRSFSMQDLRSIPDAPAPAYQDALYPED
          YLV.AKERSYETMLSFGKRGLN.AASAAVQAA.KSQGALAGRL.SFSMQDLRSIPDAPAPA.QDALYPED
Retrocopy YLVEAKERSYETMLSFGKRGLNIAASAAVQAASKSQGALAGRLLSFSMQDLRSIPDAPAPA*QDALYPED

Parental  QVLHRRPPIGYRDGGLQDSNTEDDCWSDTEAVPRMPARPREKPLSRSQSLRVIKRKPLVREGTSRSLKVR
          QVLHRRPPIGYRDGGLQDSNTEDDCWSDTEAVPRMPARPREKPLSRSQSLRVIKRKPLVREGTSRSLKVR
Retrocopy QVLHRRPPIGYRDGGLQDSNTEDDCWSDTEAVPRMPARPREKPLSRSQSLRVIKRKPLVREGTSRSLKVR

Parental  TRKKTVPSDMDS
          TRKKTVPSDMDS
Retrocopy TRKKTVPSDMDS

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	0.87 RPM	3.15 RPM
SRP051959_heart	0.53 RPM	0.89 RPM
SRP051959_kidney	0.98 RPM	1.44 RPM
SRP051959_liver	0.48 RPM	1.86 RPM
SRP051959_lung	0.99 RPM	3.07 RPM
SRP051959_lymph_node	0.94 RPM	2.81 RPM
SRP051959_skeletal_muscle	0.46 RPM	0.63 RPM
SRP051959_spleen	0.74 RPM	2.00 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_744 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_744 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_744 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020323	1 retrocopy	retro_cjac_744 ,
Felis catus	ENSFCAG00000009632	1 retrocopy	retro_fcat_1195,