RetrogeneDB ID:

retro_cjac_307

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:19:26381362..26381773(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCJAG00000021926
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCJAG00000012702
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_307
ATGGCTCGTACAAAGCAGACTGCCCGCAAATCTACCAGTGGTAAAGCACCCAGGAAGCAACTGGCTACAAAAGCCGCTCG
CAAGAGTACGCCCTCTACCGGAGGGGTGAAGAAACCTCATCGTTACAGGCCTGGTACTGTGGCACTCCGTGAAATTAGAC
GTTATCAGAAGTCCACTGAACTTCTGATTCGCAAACTTCCCTTCCAGCATCTATTGCGAGAAATTGCTCAGGACTTTAAA
ACAGATCTGCGCTTCCAGAGCGCAGCTATTGGTGCTTTGCAGGAGGCAAGTGAGGCCTATCTGGTTGGCCTTTTTGAAGA
CACCAACCTTTGTGCTATCCATGCCAAACGTGTAACAATTATGCCAAAAGACATCCAGCTAGCACACCGCATACGTGGAG
AGTGTGCTTAA

ORF - retro_cjac_307 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 95.59 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQR
MARTKQTARKST.GKAPRKQLATKAARKS.PSTGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQ.
RetrocopyMARTKQTARKSTSGKAPRKQLATKAARKSTPSTGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQH
ParentalLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA
L.REIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLA.RIRGE.A
RetrocopyLLREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAHRIRGECA

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP051959_colon 0 .69 RPM 17 .53 RPM
SRP051959_heart 0 .18 RPM 7 .95 RPM
SRP051959_kidney 0 .09 RPM 9 .07 RPM
SRP051959_liver 0 .09 RPM 7 .99 RPM
SRP051959_lung 0 .07 RPM 13 .16 RPM
SRP051959_lymph_node 0 .48 RPM 12 .81 RPM
SRP051959_skeletal_muscle 0 .09 RPM 6 .16 RPM
SRP051959_spleen 0 .19 RPM 11 .11 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_307 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_307 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_307 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 13 parental genes, and 60 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG00000012702 10 retrocopies
Dasypus novemcinctus ENSDNOG000000248432 retrocopies
Equus caballus ENSECAG000000069041 retrocopy
Equus caballus ENSECAG000000169481 retrocopy
Homo sapiens ENSG0000013247511 retrocopies
Latimeria chalumnae ENSLACG000000041181 retrocopy
Loxodonta africana ENSLAFG000000080833 retrocopies
Microcebus murinus ENSMICG000000021392 retrocopies
Mustela putorius furoENSMPUG000000045554 retrocopies
Oreochromis niloticus ENSONIG000000199755 retrocopies
Pongo abelii ENSPPYG000000086361 retrocopy
Pan troglodytes ENSPTRG0000000965512 retrocopies
Tupaia belangeri ENSTBEG000000161717 retrocopies



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