RetrogeneDB ID: retro_cjac_1188

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 14:14916216..14916707(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000011259
• Aliases: None
• Description: None

Sequence

>retro_cjac_1188
ATGAAAGCCTGGGATTGGTGGCCCTGCTTCTGGGGGCCATGCTGGGAACTGCCTGGGCTCGGAGGAGCCAGGATCTCCCC
TATGGAGTGTGCAGGGCTCTGGTGGATGAACTAGAATGGGAAATTGCCAAGGTGGACCCCAAGAAAACCATTCAGATGGG
ACCTTTCCGTATCAATCCAGATGGCAGCCAGTCAGCGGTGGACGTGCCTTATGCCCTCTCAGAGGCCCACCGCACAGAGC
TGCTGGAGGAGATATCTGACCGGATGAAGGAGTATGGGGAACAGATTGATCCTTCCACCCATCGCAAGAACTATGTACGT
GTAGTGAGCCGGAATGGAGAATCCAGTGAACTGGACCTACAAGGCATCTGAATTGACTCAGGTATCAGTGGCACCCTCAA
GTTTGCGTGTGAGAGCGTTGTGGAGGAATACGAGGATGAACTCATTGAATTCTTTTCCCGAGAGGCTGACAATGTTAAAG
ACAAACTTTGC

Alignment

ORF - retro_cjac_1188 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.7 %
• Parental protein coverage: 90.11 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MKGWGW-LALLLGALLGTAWARRSQDLHCGACRALVDELEWEIAKVDPKKTIQMGSFRINPDGSQSVVEV
          MK.W.W..ALLLGA.LGTAWARRSQDL..G.CRALVDELEWEIAKVDPKKTIQMG.FRINPDGSQS.V.V
Retrocopy MKAWDW<VALLLGAMLGTAWARRSQDLPYGVCRALVDELEWEIAKVDPKKTIQMGPFRINPDGSQSAVDV

Parental  PYARSEAHLTELLEEICDRMKEYGEQIDPSTHRKNYVRVVSRNGESSELDLQGIRIDSDISGTLKFACES
          PYA.SEAH.TELLEEI.DRMKEYGEQIDPSTHRKNYVRVVSRNGESSELDLQGI.IDS.ISGTLKFACES
Retrocopy PYALSEAHRTELLEEISDRMKEYGEQIDPSTHRKNYVRVVSRNGESSELDLQGI*IDSGISGTLKFACES

Parental  IVEEYEDELIEFFSREADNVKDKLC
          .VEEYEDELIEFFSREADNVKDKLC
Retrocopy VVEEYEDELIEFFSREADNVKDKLC

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	12.25 RPM
SRP051959_heart	0.00 RPM	11.44 RPM
SRP051959_kidney	0.00 RPM	20.32 RPM
SRP051959_liver	0.00 RPM	21.23 RPM
SRP051959_lung	0.03 RPM	13.63 RPM
SRP051959_lymph_node	0.02 RPM	13.22 RPM
SRP051959_skeletal_muscle	0.02 RPM	7.42 RPM
SRP051959_spleen	0.00 RPM	16.76 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1188 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1188 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1188 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	ENSCJAG00000011259	1 retrocopy	retro_cjac_1188 ,
Dasypus novemcinctus	ENSDNOG00000010925	1 retrocopy	retro_dnov_444,
Mustela putorius furo	ENSMPUG00000001366	1 retrocopy	retro_mputfur_930,
Ictidomys tridecemlineatus	ENSSTOG00000015971	1 retrocopy	retro_itri_928,