RetrogeneDB ID: retro_cjac_263

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL285286.1:32869..33640(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000012102
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000005620
• Aliases: None
• Description: None

Sequence

>retro_cjac_263
CCAGTCTTCATCTACACCAGCAGCGTAGAGGTGGCCGGGCCCAGCTCCTACAAGGAAGTCATCCAGAACGGTCATGAAGA
TCAGCCTCTGGAAAGCACATTGTCTGCTCCCTATCCACACAGCAAACGGCTTGCTGAGAAGGCTGTGCTGGCGGCTAATG
GGTGGACTCTGAAAAACGGTGGCATCTTGTACACTTGTGCCTTAAGACCCATGTACATCTATGGGGAAGGAAGCCCATTC
CTTTCTGCCACTGTAAATGAAGCCCTCCACAACAGGGGGATCCTGCCAAGTACTGGCAAGTTCTCCACAGTCAACCCAGT
ATATGTTGGCAACGTGGCCTGGGCCCACATTCTGGCCTTGAGGGCCCTGCGGGACCCCAGGAAGGCCCCGAGTGTCCGAG
GACAGTTCTATTACATCTCAGATGACACACCTCACCAAAGCTATGATGGCCTTAATTACACCCTGAGCAAAGAGTTCGGC
CTCTACCTTAATTCCAGTTGGAGCCTTCCTCTATTCCTGATGTACTGGATTGCCTTCCTGCTGGAAGTAGTGAGCTTCCT
GCTCAGCCCAATTTACACCTATCGACCCCCCTTCAACCGGCACACAGTGACGCTGTCAAATAGCACGTACACCTTCTCTT
ACAAGAAGGCTCAGCGAGATCTGGCATACAAGCCGCTCTACAGCTGGGAGGAAGCCAGGCAGAAAACCATGGAGTGGGTT
GGTTCCCTTGTGGACCGGCACAAGGAGACGCTGAAGCCCAAGACTCAGTGA

Alignment

ORF - retro_cjac_263 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.02 %
• Parental protein coverage: 68.73 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PVFIYTSTLEVAGPNSYKEVIQNGHEDQPLENMWSAPYPNSKQLAEKAVLAANGWTLKNGGTLYTCALRP
          PVFIYTS..EVAGP.SYKEVIQNGHEDQPLE...SAPYP.SK.LAEKAVLAANGWTLKNGG.LYTCALRP
Retrocopy PVFIYTSSVEVAGPSSYKEVIQNGHEDQPLESTLSAPYPHSKRLAEKAVLAANGWTLKNGGILYTCALRP

Parental  MYIYGEGGPFLSATVNEALHNMGVLPSVGKFSTVNPVYVGNVAWAHILALRALRDPRNAPSVRGQFYYIS
          MYIYGEG.PFLSATVNEALHN.G.LPS.GKFSTVNPVYVGNVAWAHILALRALRDPR.APSVRGQFYYIS
Retrocopy MYIYGEGSPFLSATVNEALHNRGILPSTGKFSTVNPVYVGNVAWAHILALRALRDPRKAPSVRGQFYYIS

Parental  DDTPHQSYDGL-IILSKEFGLYLNPSWSLPLFLRYWVAFLLEVVSFLLSPIYTYGPPFNRHTVTLSNSTF
          DDTPHQSYDGL...LSKEFGLYLN.SWSLPLFL.YW.AFLLEVVSFLLSPIYTY.PPFNRHTVTLSNST.
Retrocopy DDTPHQSYDGLNYTLSKEFGLYLNSSWSLPLFLMYWIAFLLEVVSFLLSPIYTYRPPFNRHTVTLSNSTY

Parental  TFSYKKAQRDLAYKPLYSWEEARQKTVEWVGSLVDRHKETLKPKTQ
          TFSYKKAQRDLAYKPLYSWEEARQKT.EWVGSLVDRHKETLKPKTQ
Retrocopy TFSYKKAQRDLAYKPLYSWEEARQKTMEWVGSLVDRHKETLKPKTQ

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	0.02 RPM
SRP051959_heart	0.02 RPM	0.11 RPM
SRP051959_kidney	0.02 RPM	0.00 RPM
SRP051959_liver	0.06 RPM	0.74 RPM
SRP051959_lung	0.00 RPM	0.08 RPM
SRP051959_lymph_node	0.00 RPM	0.00 RPM
SRP051959_skeletal_muscle	0.02 RPM	0.00 RPM
SRP051959_spleen	0.02 RPM	0.00 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_263 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_263 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_263 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	ENSCJAG00000005620	1 retrocopy	retro_cjac_263 ,