RetrogeneDB ID: retro_cjac_573

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:82779658..82780267(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: STK33
• Ensembl ID: ENSCJAG00000011801
• Aliases: None
• Description: None

Sequence

>retro_cjac_573
AAAAGTAGAAAATGTGAACACATCACACATCTGGAGCAAGTGTTTGAGACCCCTAAGTGAATGGACCTTGTGATGGGGCT
TTGTGAACAGGGAGAATTCGAAGAAATTCTGAATAGGAGAGGGCACATCCAGAGAATGAGTCAAGGTAGGTCATCGTAAG
CCTCACATCTGCTGTAGTGTGTCTTCACAATAAAGTACATAGAAACCTGAAACTGGAGAGCATAATGGTTCAAAGCAGCT
TTACTGATGCTAACAACAAACTGAACTTCAACATAAAGGTGATGCTGGCTTCGCAGGGAGGAAGCCATGCTGGGCACCAC
ATGTGGGCCTCCTGTCTACACGACCCCTGAAGTTATTGATGCCCATAGCTGTAGCCAGCAATGTGACATTGGGGCCATCA
GGTTACAAGGACATATCATTATATGGGAACCCCCTTCATGGCAAGTTCAGAAGAGACATTTTTGAATTAACAAAAAGAGA
GAACTACATTTTGACGGCCCACTTTGGGATTCTATAAGTGATTGCACTAAAAGCATTTTGAAACGACTTATCAAAGTGGA
TCCTGCTCCCAAAATCACAGCTAAGGAACTGCTTGATGCCCAACGGCTA

Alignment

ORF - retro_cjac_573 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.21 %
• Parental protein coverage: 73.68 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  KSVKHEHIIHLEQVFETPKKMYLVMELCEDGELKKILDRKGHFS-ENETRWIIQSLASAIAYLHNNDIAH
          KS.K.EHI.HLEQVFETPK.M.LVM.LCE.GE...IL.R.GH...ENE.R..I.SL.SA...LHN....H
Retrocopy KSRKCEHITHLEQVFETPK*MDLVMGLCEQGEFEEILNRRGHIQ<ENESR*VIVSLTSAVVCLHNK--VH

Parental  RDLKLENILVKSSLIDDNNEINVTDFGLAVKKQS-RREAMLQATCGTPIYMAPEVINAHDYSQQCDIWSI
          R.LKLE.I.V.SS..D.NN......F...V...S.R.EAML..TCG.P.Y..PEVI.AH..SQQCDI..I
Retrocopy RNLKLESIMVQSSFTDANNKL---NFNIKVMLAS>REEAMLGTTCGPPVYTTPEVIDAHSCSQQCDIGAI

Parental  GVIMYMLLCGEPP-FLASSEEK-LFELIR-KGELHFENPVWNFISDCAKRVLKQLMKVDPAHRITAKELL
          ..........EPP.F.ASSEE...FEL...K.ELHF..P.W..ISDC.K..LK.L.KVDPA..ITAKELL
Retrocopy RLQGHIIIW-EPP<FMASSEET<IFELTK<KRELHFDGPLWDSISDCTKSILKRLIKVDPAPKITAKELL

Parental  DNQWL
          D.Q.L
Retrocopy DAQRL

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	0.69 RPM
SRP051959_heart	0.00 RPM	3.47 RPM
SRP051959_kidney	0.00 RPM	1.51 RPM
SRP051959_liver	0.00 RPM	0.37 RPM
SRP051959_lung	0.00 RPM	1.84 RPM
SRP051959_lymph_node	0.00 RPM	0.21 RPM
SRP051959_skeletal_muscle	0.00 RPM	3.06 RPM
SRP051959_spleen	0.00 RPM	0.92 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_573 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_573 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_573 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	ENSCJAG00000003965	1 retrocopy	retro_cjac_995,
Callithrix jacchus	ENSCJAG00000011801	1 retrocopy	retro_cjac_573 ,