RetrogeneDB ID: retro_cjac_3460

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: ACFV01180616.1:4459..5324(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: WLS
• Ensembl ID: ENSCJAG00000017517
• Aliases: None
• Description: None

Sequence

>retro_cjac_3460
TTTTTTTGGAGGAGGATCACCATGATGTCCCGACCCCCAGTGCTTCTGGAAAAAGTTATCTTTGCCCTTGGGATTTCCAT
GACCTTTATCAATATCCCAGTGGAATGATTTTCCATTGGTTTTGACTGGACTTGGACGCTGCTGTTTGGTGACATCCAAC
AGGACATTTTCTATGCGATGCTTCTGTCCTTCTGGATCATCTTCTGTAGCAAGCACATGATGGATCAGCACGAGCGGAAC
CATATTGCAGAGTATTGGAAGCAAGTCGAACCCATTGCCCTTGGCTCCTTCTGCCTCTTCATATTTGACATATGTGAGAG
AGGAGTACAACTCACAAATCCCTTCTATAGTATCTGGACTACAGATGTTGGAACAGAGCTGGCCATGGCCTTCATTATGG
TGGCTGGAATCTGCCTCTGCCTCTACTTCCTGTTTCTATGCTTCATGGTATTTCAGGTGTTTCGGAGCATCAGTGGGAAG
CAGTCCAGCCTGCCAGCTATGAGCAAAGTCCGGCCGCTACACTATGAGGGGCTAATTTTTAGATTCAAGTTCCTCATGCT
TATCACCTTAGCCTTTGCTGCCATGACTGTCATCTTCATAGTTAGGTAACGGAAGGCCATTGGAAATGGGGCGGCGGCAC
AGTCCAAGGGAACAGGGCCTTTTTCATGGGCATCTATGGAATGTGGATCCTGTACCTCTTTGCTCTGATATTCTTGTATG
CACCATCCCATAAAAACTATGGGAAAGACCAGTCCAATGGTGATCTGGGTGTCCACAGTGGGGAAGAACTGCAGCTCACC
ACCACCATCACCCATGTGGACGACCCACTGAGATCTACAAGTTGACCCGCAAGGAGGCCCAGGAG

Alignment

ORF - retro_cjac_3460 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.42 %
• Parental protein coverage: 55.81 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  WYWRRITMMSRPPVLLENIRVIFALGISMTFINIPVEWFSIGFDWTWMLLFGDIRQGIFYAMLLSFWIIF
          ..WRRITMMSRPPVLLE...VIFALGISMTFINIPVE.FSIGFDWTW.LLFGDI.Q.IFYAMLLSFWIIF
Retrocopy FFWRRITMMSRPPVLLE--KVIFALGISMTFINIPVE*FSIGFDWTWTLLFGDIQQDIFYAMLLSFWIIF

Parental  CGEHMMDQHERNHIAGYWKQVGPIAVGSFCLFIFDMCERGVQLTNPFYSIWTTDVGTELAMAFIIVAGIC
          C..HMMDQHERNHIA.YWKQV.PIA.GSFCLFIFD.CERGVQLTNPFYSIWTTDVGTELAMAFI.VAGIC
Retrocopy CSKHMMDQHERNHIAEYWKQVEPIALGSFCLFIFDICERGVQLTNPFYSIWTTDVGTELAMAFIMVAGIC

Parental  LCLYFLFLCFMVFQVFRNISGKQSSLPAMSKVRRLHYEGLIFRFKFLMLITLACAAMTVIFFIVSQVTEG
          LCLYFLFLCFMVFQVFR.ISGKQSSLPAMSKVR.LHYEGLIFRFKFLMLITLA.AAMTVIF........G
Retrocopy LCLYFLFLCFMVFQVFRSISGKQSSLPAMSKVRPLHYEGLIFRFKFLMLITLAFAAMTVIFIVR*RKAIG

Parental  H-WKWGGVTVQVNSAFFTGIYGMWNLYVFALMFLYAPSHKNYGEDQSNGDLGVHSGEELQLTTTITHVDG
          ..W..G.V..Q.N.AFF.GIYGMW.LY.FAL.FLYAPSHKNYG.DQSNGDLGVHSGEELQLTTTITHVD.
Retrocopy N<WGGGTV--QGNRAFFMGIYGMWILYLFALIFLYAPSHKNYGKDQSNGDLGVHSGEELQLTTTITHVDD

Parental  -PTEIYKLTRKEAQE
          .PTEIYKLTRKEAQE
Retrocopy <PTEIYKLTRKEAQE

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	13.91 RPM
SRP051959_heart	0.00 RPM	25.22 RPM
SRP051959_kidney	0.02 RPM	15.06 RPM
SRP051959_liver	0.00 RPM	9.49 RPM
SRP051959_lung	0.00 RPM	31.98 RPM
SRP051959_lymph_node	0.00 RPM	3.24 RPM
SRP051959_skeletal_muscle	0.00 RPM	3.17 RPM
SRP051959_spleen	0.00 RPM	15.61 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3460 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3460 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3460 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017517	1 retrocopy	retro_cjac_3460 ,