RetrogeneDB ID:

retro_ptro_3097

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:X:25251376..25252064(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PAFAH1B2
Ensembl ID:ENSPTRG00000004318
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_ptro_3097
ATGAACCAAGGAGACTCAAACCCAGCAGCTATTCCGCATGCGGCAGAAGACATTCAAGGAGATGACAGATGGATGTGTCA
GCACAACAGATTTGTTTTGGACTGTAAAGACAAACAGCCTGATGTACCATTTGCGGGAGGCTCCGTGGTGCAGTTACTGC
AGCCATATGAGATATGGCGAGAGCTTTTTTCCCCACTTCATGCACTGAATTTTGGAACTGGGGGAGATACAACAAGACAT
GTTTTGTGGAGACTAAAGAACGGAGAACTGGGGAATACTAAGCCTAAGGTCATTGTTTTCTGGCTAGGAAGAAACAACCA
TGAAAATATGGCAGAAGAGGTAGCAGGTGGTATGGCGGCCATCGTACAACTTATCAACACAAGGCAGCCACAGGCCAAAA
TCATTGTATTTGATCTGTTACCTCAAGGTGAGAAACCCAACCCTTTGAGGCAAAAGAACGCCAAGGTGAACCCACTCGTC
AAGATTTCGCTGCTGAAACTTAACCGACGTGCAGCTCCTGGATACTGACAGGGGTTTCGTGCACTCCGACCGTGCCATCT
CCTGCCACGACATGTTTGATTTTCTGCATTTGACAGGAGGCGGCTACTCAAAGGTCTGCAAACCCTTGAATGAACTGATC
ATGCAGTTGTTGGAGGAAACACCTGAGGAGAAACAAACCACCATTGCC

ORF - retro_ptro_3097 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.65 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMSQGDSNPAAIPHAAEDIQGDDRWMSQHNRFVLDCKDKEPDVLFVGDSMVQLMQQYEIWRELFSPLHALN
M.QGDSNPAAIPHAAEDIQGDDRWM.QHNRFVLDCKDK.PDV.F.G.S.VQL.Q.YEIWRELFSPLHALN
RetrocopyMNQGDSNPAAIPHAAEDIQGDDRWMCQHNRFVLDCKDKQPDVPFAGGSVVQLLQPYEIWRELFSPLHALN
ParentalFGIGGDTTRHVLWRLKNGELENIKPKVIVVWVGTNNHENTAEEVAGGIEAIVQLINTRQPQAKIIVLGLL
FG.GGDTTRHVLWRLKNGEL.N.KPKVIV.W.G.NNHEN.AEEVAGG..AIVQLINTRQPQAKIIV..LL
RetrocopyFGTGGDTTRHVLWRLKNGELGNTKPKVIVFWLGRNNHENMAEEVAGGMAAIVQLINTRQPQAKIIVFDLL
ParentalPRGEKPNPLRQKNAKVNQLLKVSLPK-LANVQLLDTDGGFVHSDGAISCHDMFDFLHLTGGGYAKICKPL
P.GEKPNPLRQKNAKVN.L.K.SL.K.L..VQLLDTD.GFVHSD.AISCHDMFDFLHLTGGGY.K.CKPL
RetrocopyPQGEKPNPLRQKNAKVNPLVKISLLK>LTDVQLLDTDRGFVHSDRAISCHDMFDFLHLTGGGYSKVCKPL
ParentalHELIMQLLEETPEEKQTTIA
.ELIMQLLEETPEEKQTTIA
RetrocopyNELIMQLLEETPEEKQTTIA

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 0 .04 RPM 102 .19 RPM
SRP007412_cerebellum 0 .00 RPM 101 .27 RPM
SRP007412_heart 0 .00 RPM 40 .66 RPM
SRP007412_kidney 0 .00 RPM 55 .42 RPM
SRP007412_liver 0 .00 RPM 33 .72 RPM
SRP007412_testis 0 .00 RPM 69 .76 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_3097 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_3097 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_3097 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_4661
Gorilla gorilla retro_ggor_2893
Pongo abelii retro_pabe_3621
Macaca mulatta retro_mmul_2481

Parental genes homology:
Parental genes homology involve 14 parental genes, and 21 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000086282 retrocopies
Canis familiaris ENSCAFG000000132261 retrocopy
Callithrix jacchus ENSCJAG000000126981 retrocopy
Dipodomys ordii ENSDORG000000112741 retrocopy
Felis catus ENSFCAG000000299451 retrocopy
Homo sapiens ENSG000001680922 retrocopies
Gorilla gorilla ENSGGOG000000281972 retrocopies
Macaca mulatta ENSMMUG000000020502 retrocopies
Mustela putorius furoENSMPUG000000042461 retrocopy
Nomascus leucogenys ENSNLEG000000073372 retrocopies
Pongo abelii ENSPPYG000000039072 retrocopies
Pan troglodytes ENSPTRG00000004318 2 retrocopies
retro_ptro_3097 , retro_ptro_782,
Rattus norvegicus ENSRNOG000000180321 retrocopy
Sarcophilus harrisii ENSSHAG000000114031 retrocopy



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