RetrogeneDB ID: retro_cjac_577

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:85974169..85975039(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PCBP4
• Ensembl ID: ENSCJAG00000005783
• Aliases: None
• Description: None

Sequence

>retro_cjac_577
GTCTTGGGCCGAAAAGCTACATGTTTGCAAGAGAAAATCACCCAAGAGACTACGGGTGCCCAGGTACAGGTGGCAGGGGA
CCTGTTCCCCAACTCCACAGAGCAAGCTGTTACACTGTCGGAGGTGCCTGATGCCATCATCTTGTGTGTGCGCCAGATCT
GCGCTGTTATCCTGGAGTCCCCACCCAAAGGAGCCACTATCCCCTACCACCCAAGCCTCTCCCTAGGGTACTGTCCTTCT
CTCCACCAACCAGGGCTTCTCTGTCCAGGGTCAGTATGGGGCTGTGACCACAGCTGAGGTCACCAAGCTCCAGCAGCTCT
CAAGCCATGCGGTCCCTTTTGCCACACCCAGCGTGGTGCCAGCACTGGATCCCGGCACATAGACCAGCTCACAGGAGTTC
TTGGTTCCCAATGATCTGATTTGCTGTGTGATGGGGCGCCAGGGCAGCAAGATCAGCGAGATCTGGCAGATGTCAGGGCA
CATATCAAGATCGGGAACCAAGCAGAGGGCGCTGGGGAGCAGCATGTGACCATCACTGGGTCACCGGTCTCCATCGCCCT
GGCCCAGTACCTCATCACTGCCTGTCTAGAGACGGCCAAGTCTACCTCTGGGGGAACACCCGGCTTGGCCCCTACAGACC
TGCCTGCCCCCTTCTCGCCGCCCCTGACGGCCCTGCCCACAGCTCCCCGCGGCCTGCTGGGCACACCCTATGCCATCTCC
CTCTCCAACTTCATTGGCCTCAAGCCCGTGCCCTTCTTGGCTTTACCACCTGCTTCCTCAGGGCCGCTGCCAGGCTTGGC
GGCCTACACTGCCAAGATGGCAGCGGCTAATGGGAGTAAGAAGGCTGAGCGGCAGAAATTCACCCCCTAC

Alignment

ORF - retro_cjac_577 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.7 %
• Parental protein coverage: 71.46 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LIGKAGTKIKE--IRETTGAQVQVAGDLLPNSTERAVTVSGVPDAIILCVRQICAVILESPPKGATIPYH
          ..G...T...E....ETTGAQVQVAGDL.PNSTE.AVT.S.VPDAIILCVRQICAVILESPPKGATIPYH
Retrocopy VLGRKATCLQEKITQETTGAQVQVAGDLFPNSTEQAVTLSEVPDAIILCVRQICAVILESPPKGATIPYH

Parental  PSLSLG-TVLLSANQGFSVQGQYGAVTPAEVTKLQQLSSHAVPFATPSVVPGLDPGTQTSSQEFLVPNDL
          PSLSLG.TVLLS.NQGFSVQGQYGAVT.AEVTKLQQLSSHAVPFATPSVVP.LDPGT.TSSQEFLVPNDL
Retrocopy PSLSLG>TVLLSTNQGFSVQGQYGAVTTAEVTKLQQLSSHAVPFATPSVVPALDPGT*TSSQEFLVPNDL

Parental  IGCVIGRQGSKISEIRQMSG-AHIKIGNQAEGAGERHVTITGSPVSIALAQYLITACLETAKSTSGGTPS
          I.CV.GRQGSKISEI.QMSG.AHIKIGNQAEGAGE.HVTITGSPVSIALAQYLITACLETAKSTSGGTP.
Retrocopy ICCVMGRQGSKISEIWQMSG<AHIKIGNQAEGAGEQHVTITGSPVSIALAQYLITACLETAKSTSGGTPG

Parental  SAPADLPAPFSPPLTALPTAPPGLLGTPYAISLSNFIGLKPVPFLALPPASPGPPPGLAAYTAKMAAANG
          .AP.DLPAPFSPPLTALPTAP.GLLGTPYAISLSNFIGLKPVPFLALPPAS.GP.PGLAAYTAKMAAANG
Retrocopy LAPTDLPAPFSPPLTALPTAPRGLLGTPYAISLSNFIGLKPVPFLALPPASSGPLPGLAAYTAKMAAANG

Parental  SKKAERQKFSPY
          SKKAERQKF.PY
Retrocopy SKKAERQKFTPY

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	3.11 RPM
SRP051959_heart	0.00 RPM	14.52 RPM
SRP051959_kidney	0.00 RPM	6.81 RPM
SRP051959_liver	0.00 RPM	5.35 RPM
SRP051959_lung	0.00 RPM	5.77 RPM
SRP051959_lymph_node	0.00 RPM	5.18 RPM
SRP051959_skeletal_muscle	0.00 RPM	10.48 RPM
SRP051959_spleen	0.00 RPM	5.59 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_577 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_577 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_577 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005783	1 retrocopy	retro_cjac_577 ,
Callithrix jacchus	ENSCJAG00000018590	2 retrocopies	retro_cjac_3253, retro_cjac_754,