RetrogeneDB ID:

retro_ggor_87

Retrocopy
location
Organism:Gorilla (Gorilla gorilla)
Coordinates:X:88509775..88510924(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSGGOG00000007622
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:PABPC4
Ensembl ID:ENSGGOG00000004002
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_ggor_87
ATGGGGAGCGGGGAGCCTAATCCTGCTGGCAAGAAAAAGAAGTATCTCAAGGCCGCTCTGTACGTGGGTGACTTGGACCC
AGATGTCACCGAGGACATGCTCTATAAGAAGTTCAGGCCTGCTGGCCCTCTGCGATTCACCCGAATCTGCCGTGATCCGG
TGACCCGCAGCCCCCTGGGCTATGGGTATGTTAACTTCCGCTTTCCGGCGGATGCAGAGTGGGCCTTGAACACCATGAAT
TTTGATTTGATTAATGGAAAACCATTCCGCCTTATGTGGTCTCAGCCAGATGACCGCTTAAGAAAGTCTGGAGTGGGAAA
TATATTCATCAAAAACCTGGACAAATCCATAGACAATAGGGCCCTGTTTTACTTATTTTCTGCTTTTGGGAACATTCTGT
CCTGCAAAGTCGTATGCGATGACAACGGCTCTAAGGGTTATGCCTATGTGCACTTTGACAGCCTGGCCGCTGCCAATAGA
GCCATCTGGCACATGAACGGAGTGCGGCTCAACAACCGCCAGGTGTATGTTGGCAGATTCAAATTCCCAGAAGAGCGGGC
GGCTGAGGTCAGAACCAGGGATAGAGCAACTTTCACCAATGTTTTCGTTAAAAACATTGGAGACGACATAGATGACGAAA
AACTGAAGGAACTTTTCTGTGAATATGGGCCAACTGAGAGTGTTAAAGTAATAAGAGATGCCAGTGGGAAATCTAAAGGC
TTTGGATTTGTGAGATATGAGACACACGAGGCTGCCCAAAAGGCTGTGCTAGACTTGCATGGAAAGTCCATCGATGGAAA
AGTCCTGTATGTAGGGCGAGCACAGAAGAAAATTGAACGCCTGGCTGAGTTGAGGCGGAGATTTGAACGGCTGAGGTTAA
AAGAAAAAAGTCGGCCCCCAGGGGTGCCTATCTATATTAAGAACTTGGATGAGACAATCAATGATGAAAAACTGAAGGAG
GAATTTTCTTCCTTTGGGTCAATTAGTCGGGCCAAAGTGATGATGGAAGTGGGGCAAGGCAAAGGATTTGGTGTGGTCTG
CTTTTCCTCTTTTGAAGAGGCTACCAAAGCAGTGGATGAGATGAATGGCCGCATAGTGGGCTCCAAGCCCCTGCATGTCA
CCCTGGGCCAGGCCAGGCGCAGGTGCTGA

ORF - retro_ggor_87 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 66.58 %
Parental protein coverage: 55.15 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalYPMASLYVGDLHSDVTEAMLYEKFSPAGPVLSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVI
Y..A.LYVGDL..DVTE.MLY.KF.PAGP....R.CRD..TR..LGY.YVNF..PADAE.AL.TMNFD.I
RetrocopyYLKAALYVGDLDPDVTEDMLYKKFRPAGPLRFTRICRDPVTRSPLGYGYVNFRFPADAEWALNTMNFDLI
ParentalKGKPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYAFVHFET
.GKP.R.MWSQ.D..LRKSGVGN.FIKNLDKSIDN.AL...FSAFGNILSCKVVCD.NGSKGYA.VHF..
RetrocopyNGKPFRLMWSQPDDRLRKSGVGNIFIKNLDKSIDNRALFYLFSAFGNILSCKVVCDDNGSKGYAYVHFDS
ParentalQEAADKAIEKMNGMLLNDRKVFVGRFKSRKEREAELGAKAK-EFTNVYIKNFGEEVDDESLKELFSQFGK
..AA..AI..MNG..LN.R.V.VGRFK...ER.AE........FTNV..KN.G...DDE.LKELF...G.
RetrocopyLAAANRAIWHMNGVRLNNRQVYVGRFKFPEERAAEVRTRDRATFTNVFVKNIGDDIDDEKLKELFCEYGP
ParentalTLSVKVMRDPNGKSKGFGFVSYEKHEDANKAVEEMNGKEISGKIIFVGRAQKKVERQAELKRKFEQLKQE
T.SVKV.RD..GKSKGFGFV.YE.HE.A.KAV....GK.I.GK...VGRAQKK.ER.AEL.R.FE.L...
RetrocopyTESVKVIRDASGKSKGFGFVRYETHEAAQKAVLDLHGKSIDGKVLYVGRAQKKIERLAELRRRFERLRLK
ParentalRISRYQGVNLYIKNLDDTIDDEKLRKEFSPFGSITSAKVMLEDGRSKGFGFVCFSSPEEATKAVTEMNGR
..SR..GV..YIKNLD.TI.DEKL..EFS.FGSI..AKVM.E.G..KGFG.VCFSS.EEATKAV.EMNGR
RetrocopyEKSRPPGVPIYIKNLDETINDEKLKEEFSSFGSISRAKVMMEVGQGKGFGVVCFSSFEEATKAVDEMNGR
ParentalIVGSKPLYVALAQRK
IVGSKPL.V.L.Q..
RetrocopyIVGSKPLHVTLGQAR

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
SRP007412_brain_prefrontal_cortex 1 .44 RPM 35 .10 RPM
SRP007412_cerebellum 1 .26 RPM 35 .18 RPM
SRP007412_heart 0 .25 RPM 54 .32 RPM
SRP007412_kidney 0 .57 RPM 54 .46 RPM
SRP007412_liver 0 .42 RPM 54 .87 RPM
SRP007412_testis 3 .00 RPM 116 .34 RPM
Gorilla gorilla was not studied using ChIP-Seq data.
Gorilla gorilla was not studied using EST data.
Gorilla gorilla was not studied using FANTOM5 data.
retro_ggor_87 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ggor_87 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 20 parental genes, and 42 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000115352 retrocopies
Callithrix jacchus ENSCJAG000000025123 retrocopies
Cavia porcellus ENSCPOG000000095522 retrocopies
Felis catus ENSFCAG000000152542 retrocopies
Homo sapiens ENSG000000906212 retrocopies
Gorilla gorilla ENSGGOG00000004002 3 retrocopies
retro_ggor_2127, retro_ggor_87 , retro_ggor_916,
Gorilla gorilla ENSGGOG000000067851 retrocopy
Microcebus murinus ENSMICG000000166331 retrocopy
Macaca mulatta ENSMMUG000000074971 retrocopy
Monodelphis domestica ENSMODG000000176572 retrocopies
Mustela putorius furoENSMPUG000000144142 retrocopies
Mus musculus ENSMUSG000000112577 retrocopies
Nomascus leucogenys ENSNLEG000000119282 retrocopies
Oryctolagus cuniculus ENSOCUG000000005622 retrocopies
Otolemur garnettii ENSOGAG000000040671 retrocopy
Ochotona princeps ENSOPRG000000119841 retrocopy
Pongo abelii ENSPPYG000000015062 retrocopies
Pan troglodytes ENSPTRG000000005733 retrocopies
Rattus norvegicus ENSRNOG000000156422 retrocopies
Sarcophilus harrisii ENSSHAG000000181391 retrocopy



Copyright © RetrogeneDB 2014-2017