RetrogeneDB ID: retro_cjac_3644

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: ACFV01191663.1:1636..2209(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000009347
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000019358
• Aliases: None
• Description: None

Sequence

>retro_cjac_3644
ATGGACCCGGCTCCCGGCACCCTGATCTCCTCGCCGCCATGCCCGCGCTCCTGGGCGTCCCACAGGCGGAGGTGCTGGAG
GACGTGTTGCGGGAGCAGTTCGGGCCGCTGCCCCAGCTGGCTGCCATCTGCCGGCTCAAACGGCTGCCCTCAGGTGGCTA
CTCTTCCACCGAAGACCTCCAGTTGGTGCTGGAGTGGCGGTGCATGGCCAACACTAAGGAGCGCGAGCGGATAAAAAATC
TCAACTGTGGTTTTGCCAAATTGAAGGCACTTGTGCCATTTCTTCCCCAAAGCAGGAAGCCCAGCAAAGCTGATATTCTT
AAAGGCACAACTGAATATATATACAAGTTCTCAGTCATGTTTTGGAAGAAGCTGAAGACTCAGAGAAACAAGACCTAGAT
GAGCAGAGCTTGGTAGCAGCACTTCTGAACCACCTATATCCTCCGCTAGAGAGCTATCAAGAAACATCATCCAAGGTATA
GGCTGTGCTTTCAGCTTGAAGAATGAAGAGGAAGAGCTTTGGGCAGATGGCGGCAGTGGTGAGCCCGCACATTCTCATCA
CCAGAGTGTTGTC

Alignment

ORF - retro_cjac_3644 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.08 %
• Parental protein coverage: 87.61 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MDPAPGTL-DLRAATPALLGVPQAEVLEEVLREEFGPLPQLAAICRLKRLPSGGYSSTEDLQLVLERRRV
          MDPAPGTL.DL.AA.PALLGVPQAEVLE.VLRE.FGPLPQLAAICRLKRLPSGGYSSTEDLQLVLE.R..
Retrocopy MDPAPGTL<DLLAAMPALLGVPQAEVLEDVLREQFGPLPQLAAICRLKRLPSGGYSSTEDLQLVLEWRCM

Parental  ANAKEREHIKNLNRGFAKLKALVPFLPQSRKPS-KVDILKGATE-YIQVLSHVLEEAEDSEKQDPDEQS-
          AN.KERE.IKNLN.GFAKLKALVPFLPQSRKPS.K...LK.....YIQVLSHVLEEAEDSEKQD.DEQS.
Retrocopy ANTKERERIKNLNCGFAKLKALVPFLPQSRKPS>KLIFLKAQLN>YIQVLSHVLEEAEDSEKQDLDEQS<

Parental  YSSSTSEPHISSTRELSRNIIQGISCAFSLKNEEEEPWADGGSGEPTHSCRQRVL
          ..SSTSEP.ISS.RELSRNIIQGI.CAFSLKNEEEE.WADGGSGEP.HS..Q.V.
Retrocopy LGSSTSEPPISSARELSRNIIQGIGCAFSLKNEEEELWADGGSGEPAHSHHQSVV

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	0.07 RPM
SRP051959_heart	0.00 RPM	0.07 RPM
SRP051959_kidney	0.00 RPM	0.00 RPM
SRP051959_liver	0.00 RPM	0.13 RPM
SRP051959_lung	0.00 RPM	0.03 RPM
SRP051959_lymph_node	0.00 RPM	0.16 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.00 RPM
SRP051959_spleen	0.00 RPM	0.95 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3644 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3644 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3644 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015931	1 retrocopy	retro_amel_1592,
Callithrix jacchus	ENSCJAG00000019358	1 retrocopy	retro_cjac_3644 ,
Felis catus	ENSFCAG00000013444	1 retrocopy	retro_fcat_159,