RetrogeneDB ID:

retro_cjac_1201

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:14:41744161..41744554(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCJAG00000006748
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:PRDX1
Ensembl ID:ENSCJAG00000004807
Aliases:None
Description:peroxiredoxin 1 [Source:HGNC Symbol;Acc:9352]


Retrocopy-Parental alignment summary:






>retro_cjac_1201
ATGTCTTCAGGAAATGCTAAAATTGGGCACCCTGCCCTCAACTTCAAAGCCATAGCCATTATGCCAGATGGTCAATTTAA
AGATATCAGACTGTCTGACTACAAAGGAAAATATGTTGTATTCTTCTTTTACCCTCTTGACTTTACCTTTGTGTGCCCCA
CGGAGATCATTGCTTTCAGTGATAGGGCAGAAGAATTTAAGAAACTCAACTGCCGAGTGATGGGTGCTTCTGTGGATTCT
CACTTCTATCACCTGGCATGGATCAACATACCTAAGAGACAAGGGGGACTGGGACCCATGAACATTCCTTTGGCGTCAGA
CCCAAAGTGCATCATTGCTCAGGATTATGGGGTGTTAAAGGCTGATGAAGGCGTCTCATTCAGCGGCCTCTAT

ORF - retro_cjac_1201 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 88.55 %
Parental protein coverage: 65.83 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMSSGNAKIGHPAPNFKATAVMPDGQFKDISLSDYKGKYVVFFFYPLDFTFVCPTEIIAFSDRAEEFKKLN
MSSGNAKIGHPA.NFKA.A.MPDGQFKDI.LSDYKGKYVVFFFYPLDFTFVCPTEIIAFSDRAEEFKKLN
RetrocopyMSSGNAKIGHPALNFKAIAIMPDGQFKDIRLSDYKGKYVVFFFYPLDFTFVCPTEIIAFSDRAEEFKKLN
ParentalCQVIGASVDSHFCHLAWINTPKKQGGLGPMNIPLISDPKRTIAQDYGVLKADEGISFRGLF
C.V.GASVDSHF.HLAWIN.PK.QGGLGPMNIPL.SDPK..IAQDYGVLKADEG.SF.GL.
RetrocopyCRVMGASVDSHFYHLAWINIPKRQGGLGPMNIPLASDPKCIIAQDYGVLKADEGVSFSGLY

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 .02 RPM 91 .59 RPM
SRP051959_heart 0 .00 RPM 43 .53 RPM
SRP051959_kidney 0 .07 RPM 79 .96 RPM
SRP051959_liver 0 .06 RPM 130 .09 RPM
SRP051959_lung 0 .03 RPM 36 .81 RPM
SRP051959_lymph_node 0 .05 RPM 36 .16 RPM
SRP051959_skeletal_muscle 0 .00 RPM 27 .28 RPM
SRP051959_spleen 0 .11 RPM 53 .21 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1201 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1201 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_1201 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 32 parental genes, and 91 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000136322 retrocopies
Bos taurus ENSBTAG000000036422 retrocopies
Canis familiaris ENSCAFG000000045675 retrocopies
Choloepus hoffmanni ENSCHOG000000033585 retrocopies
Ciona intestinalis ENSCING000000030021 retrocopy
Callithrix jacchus ENSCJAG00000004807 2 retrocopies
retro_cjac_1201 , retro_cjac_2884,
Callithrix jacchus ENSCJAG000000048824 retrocopies
Callithrix jacchus ENSCJAG000000196363 retrocopies
Cavia porcellus ENSCPOG000000141373 retrocopies
Dasypus novemcinctus ENSDNOG000000184881 retrocopy
Dipodomys ordii ENSDORG000000089751 retrocopy
Equus caballus ENSECAG000000086781 retrocopy
Echinops telfairi ENSETEG0000000792211 retrocopies
Felis catus ENSFCAG000000284841 retrocopy
Homo sapiens ENSG000001174501 retrocopy
Macropus eugenii ENSMEUG000000068204 retrocopies
Macaca mulatta ENSMMUG000000062211 retrocopy
Monodelphis domestica ENSMODG000000023822 retrocopies
Mus musculus ENSMUSG000000286915 retrocopies
Nomascus leucogenys ENSNLEG000000145242 retrocopies
Oryctolagus cuniculus ENSOCUG000000059512 retrocopies
Otolemur garnettii ENSOGAG000000023034 retrocopies
Pongo abelii ENSPPYG000000014111 retrocopy
Pan troglodytes ENSPTRG000000006751 retrocopy
Pteropus vampyrus ENSPVAG000000150011 retrocopy
Rattus norvegicus ENSRNOG000000171948 retrocopies
Sorex araneus ENSSARG000000047035 retrocopies
Sus scrofa ENSSSCG000000039141 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000234132 retrocopies
Tupaia belangeri ENSTBEG000000159974 retrocopies
Tarsius syrichta ENSTSYG000000110311 retrocopy
Tursiops truncatus ENSTTRG000000088584 retrocopies



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