RetrogeneDB ID:

retro_ptro_2308

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:5:158976002..158976668(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:LXN
Ensembl ID:ENSPTRG00000015571
Aliases:None
Description:latexin [Source:HGNC Symbol;Acc:13347]


Retrocopy-Parental alignment summary:






>retro_ptro_2308
ATAGAAATTTCATGGACCCATGACCCAGCCTCCAAGGCAGCCTCGGTGGCAGTGATCTGCCTCAACTACCAGCAAGGGAC
ACCCCACAAGGTATTTCTGAGGGAGACAGTCAAACAAACCAGCACGGAGGATATCCCAGGAAAAGGACATAAGTATCACC
TCAAATGTTCTGTGGAATAAGTTATTCTAAAACAAGTTGCAGTGAACTGCATAGCTGAATTGCCTTACCCTGCAGTGGGA
CAAGATACTGTACCAGAAATCAACATCACATGTGAAGGAGAAATTTAAAGAGCCCAGATAAAGAAAACAACACGTCTGAT
CAAAAACTCAAGTCCATGAAGGAATCACTAGAAGCACAAAATATTCCAGACATTTTGAGAAATGTATCTCCAAAACATGA
AGCCAGGTCAACATTTAGCCTGGGTTGCCTGTGGTTATGTAACATGGCAAAATTCTGCTGAAAACACGTGATATAAAAGT
GGTAAAAATTAAACTGTCAAGGAAATGCAAAAAAATGATGACTTTATTGAATAGACTATACCATTCCACTTCATGACATT
GCATCCCAGGAGATTGATTCCTTGGGAAATGCAAGTTCTTTGGCACTGACAAGATGGTGCTAAAGTAAAATGTAATCGCT
GTCTGCCAAGGGAAGTACAAGCGGAA

ORF - retro_ptro_2308 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 64.16 %
Parental protein coverage: 100. %
Number of stop codons detected: 4
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalMEIPPTNYPASRAALVAQNYINYQQGTPHRVFEVQKVKQASMEDIPGRGHKYRLKFAVEEIIQKQVKVNC
.EI..T..PAS.AA.VA....NYQQGTPH.VF....VKQ.S.EDIPG.GHKY.LK..VE..I.KQV.VNC
RetrocopyIEISWTHDPASKAASVAVICLNYQQGTPHKVFLRETVKQTSTEDIPGKGHKYHLKCSVE*VILKQVAVNC
ParentalTAEVLYPSTGQETAPEVNFTFEGE-TGKNPDEEDNTFYQRLKSMKEPLEAQNIPDNFGNVSPE-MTLVLH
.AE..YP..GQ.T.PE.N.T.EGE...K.PD.E.NT..Q.LKSMKE.LEAQNIPD...NVSP..M....H
RetrocopyIAELPYPAVGQDTVPEINITCEGE<NLKSPDKENNTSDQKLKSMKESLEAQNIPDILRNVSPK>MKPGQH
ParentalLAWVACGYIIWQNSTEDTWYKMVKIQTVKQVQRNDDFIE-LDYTILLHNIASQEI-IPWQMQVLWHPQYG
LAWVACGY..WQNS.E.T.YK..K..TVK..Q.NDDFIE..DYTI.LH.IASQEI.IPW.MQVLWH.Q.G
RetrocopyLAWVACGYVTWQNSAENT*YKSGKN*TVKEMQKNDDFIE<IDYTIPLHDIASQEI>IPWEMQVLWH*QDG
ParentalTKVKHNSRLPKEVQLE
.KVK.N..LP.EVQ.E
RetrocopyAKVKCNRCLPREVQAE

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 .00 RPM 2 .25 RPM
SRP007412_cerebellum 0 .00 RPM 3 .87 RPM
SRP007412_heart 0 .00 RPM 4 .37 RPM
SRP007412_kidney 0 .00 RPM 9 .44 RPM
SRP007412_liver 0 .00 RPM 3 .90 RPM
SRP007412_testis 0 .00 RPM 1 .48 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_2308 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_2308 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_2308 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_3397
Gorilla gorilla retro_ggor_2300
Pongo abelii retro_pabe_2791
Macaca mulatta retro_mmul_2114

Parental genes homology:
Parental genes homology involve 11 parental genes, and 15 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000093362 retrocopies
Canis familiaris ENSCAFG000000090961 retrocopy
Callithrix jacchus ENSCJAG000000003861 retrocopy
Homo sapiens ENSG000000792571 retrocopy
Gorilla gorilla ENSGGOG000000030921 retrocopy
Macaca mulatta ENSMMUG000000049631 retrocopy
Nomascus leucogenys ENSNLEG000000042291 retrocopy
Pongo abelii ENSPPYG000000142451 retrocopy
Pan troglodytes ENSPTRG00000015571 1 retrocopy
retro_ptro_2308 ,
Pteropus vampyrus ENSPVAG000000136082 retrocopies
Tupaia belangeri ENSTBEG000000176733 retrocopies



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