RetrogeneDB ID:

retro_ptro_1894

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:3:64035960..64037082(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:KRT79
Ensembl ID:ENSPTRG00000004993
Aliases:None
Description:keratin 79 [Source:HGNC Symbol;Acc:28930]


Retrocopy-Parental alignment summary:






>retro_ptro_1894
GGCAGCAGCAGCTTCCGAGGTGGCCTGAGTGGAGGCTATGGTGGGACCAGCGTTGTGGGAGGCATCACCACCGTCCCGGT
CAACCAAAGCCTGCTGAGCCCCCTTAACCTGGAGGTGGACCCCAATATCCAGGCCGTGCGCACCCAGGAGGAGCAGATGG
AGACCCTCAACGAGTTTGCCTCCTTCGTCGACAAGGTAAGGTTCCTAGAGCAGCAGAACAAGATGCTGGAGACCAAGTGG
GGCCTCCTGCAGCAGCAGCAGACGGCTCGGAGCAACATGGACAACATGTTTGAGAGCTATGTCAACAACCTTAGGTGGCA
GCTGGAGACTGGGCCAGGAGAAGCTGAAGCTGGAGGCGCAGCTTGGCAACATGCAGCCGCTGGTAGAGGACTTCAAGACC
AAGTATGAGGATGAGATCAATAAGCGTACAGAGATGGAGAATGAATTTGTCCTCATCAAGAAGGATGCAGATGAAGCTTC
CATGAACAAGGTAGAGTTGGGGTCTCGCCTGGAAGGGCTGACTGACGAGATCAACTTCCTCATGCAGCTATATGAAGAGG
AGATCCGGGAGCTGCAGTCCCAGATCTCAGACACGTCTGTGGTGCTGTCCATGGACAACAGCTGCTCCCTGGACGTGGAC
AGCATCATTGCTGAGGTCAAGGCACAGTAGGAGGAGATCGCCAACTGCAGCCGGGCTGAGGCCGAGAGCATGTACCAGAT
CAAGTATGAGGAGCTGCAGACGCTGGCTGGGAAGCACGGGGATGACCTGCGGCGCACAGAGTGAGATCTCCTAGATACAC
GGGAACATCAGCCAGCTCCAGGCTGATGTTGACCAGAGGGCTTCCCTGGAGGCCGCCATCGCAGATGCCGAGCTGCACGG
GGATTTGGTGGTTAAGGATGCCAACGCCAAGCTGTCCGAGCTGGAGGCCGCCCTGCAGCGGGCCAAGCAGGACATGGCGT
GGCAGCTGCGTGAATACCAGGAGCTGATGAACGTCAAGCTGGCCCTGGACATAGAGATCGCCACCTACAGGAAGCTGCTG
GAGGGCAAGGAGAGCTGGCTGGAATCTGGGATGCAGAACAGGAGTATCCATAGGAAGAACACCAGTGGCTATGGAGGTGT
GC

ORF - retro_ptro_1894 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 54.87 %
Parental protein coverage: 72.34 %
Number of stop codons detected: 2
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalGSRAFMGQGAGRQTFGPACPPGGIQEVTVNQSLLTPLHVEIDPEIQRVRTQEREQIKTLNNKFASFIDKV
GS..F.G...G....G.....GGI..V.VNQSLL.PL..E.DP.IQ.VRTQE.EQ..TLN..FASF.DKV
RetrocopyGSSSFRGGLSGG--YGGTSVVGGITTVPVNQSLLSPLNLEVDPNIQAVRTQE-EQMETLN-EFASFVDKV
ParentalRFLEQQNKVLETKWALLQEQSQN-LGVTRNNLEPLFEAYLDSMWSTLDRLQSERGRLDSELRNVQDLVED
RFLEQQNK.LETKW..L..Q.Q..LG.T...........L...W....RL..E...L...L.N.Q.LVED
RetrocopyRFLEQQNKMLETKWG-LLQQQQT>LGATWTTCLRAMSTTLGGSW----RLGQEKLKLEAQLGNMQPLVED
ParentalFKIKYEDEINKRTAAENEFVVLKKDVDAAYMGRMDLHGKVGTLTQEIDFLQQLYEMELSQVQTHVSNTNV
FK.KYEDEINKRT..ENEFV..KKD.D.A.M....L......LT.EI.FL.QLYE.E....Q...S.T.V
RetrocopyFKTKYEDEINKRTEMENEFVLIKKDADEASMNKVELGSRLEGLTDEINFLMQLYEEEIRELQSQISDTSV
ParentalVLSMDNNRNLDLDSIIAEVKAQYELIAQRSRAEAEAWYQTKYEELQVTAGKHGDNLRDTKNEIAELTR-T
VLSMDN...LD.DSIIAEVKAQ.E.IA..SRAEAE..YQ.KYEELQ..AGKHGD.LR.T.......TR..
RetrocopyVLSMDNSCSLDVDSIIAEVKAQ*EEIANCSRAEAESMYQIKYEELQTLAGKHGDDLRRTE*DLLD-TR>N
ParentalIQRLQGEADAAKKQCQQLQTAIAEAEQRGELALKDAQKKLGDLDVALHQAKEDLTRLLRDYQELMNVKLA
I..LQ...D....Q...L..AIA.AE..G.L..KDA..KL..L..AL..AK.D....LR.YQELMNVKLA
RetrocopyISQLQADVD----QRASLEAAIADAELHGDLVVKDANAKLSELEAALQRAKQDMAWQLREYQELMNVKLA
ParentalLDVEIATYRKLLESEESRMSG-ECPSAVSISVTGNSTTVC
LD.EIATYRKLLE..ES......C...VSI..T.....VC
RetrocopyLDIEIATYRKLLEGKESWLES>GCRTGVSIGRTPVAMEVC

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






RNA-Seq - click to see more details

(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 .00 RPM 0 .02 RPM
SRP007412_cerebellum 0 .00 RPM 0 .00 RPM
SRP007412_heart 0 .00 RPM 0 .00 RPM
SRP007412_kidney 0 .00 RPM 0 .00 RPM
SRP007412_liver 0 .00 RPM 0 .00 RPM
SRP007412_testis 0 .00 RPM 0 .11 RPM

ChIP-Seq - click to see more details

Pan troglodytes was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ptro_1894 retrocopy.

TSS - click to see more details

Pan troglodytes was not studied using FANTOM5 data.

Lab - click to see more details

retro_ptro_1894 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_1894 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_2797
Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species Parental gene accession Retrocopies number
Pan troglodytes ENSPTRG00000004993 1 retrocopy
retro_ptro_1894 ,


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