RetrogeneDB ID:

retro_amel_1805

Retrocopy
location
Organism:Panda (Ailuropoda melanoleuca)
Coordinates:GL194478.1:138427..139540(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSAMEG00000017346
Aliases:None
Description:Aspartate aminotransferase [Source:UniProtKB/TrEMBL;Acc:G1MG53]


Retrocopy-Parental alignment summary:






>retro_amel_1805
AATCTGGGATTTTGTGCCCACCAGGATGATAATGGAAAGGCTTATGTGCTCCCTAGTGTCCAGAATGCAAAGGCCCAGAT
TGCTGCAAAAAGTTTGGACAAAGAATATCTGCCCATTGTGGGACTTGCTGAATTTTGTAAGGCATCAGCAGAACTAGCCC
TGGGTGAGAATAATGAAGTGTTGAAAAGTAGCCAGTATGTCACTGTGCAGACCATTTCTGGAACCAGGACCTTGAGGATT
GGAGACAGGTTATTGTGAAGATTTTTTAAGTTTGGCCGAGATGTCTTTCTGCCCAAACCATCCTAGGGAAATCGTACACA
CATCTTCAGGGACGTTGGCATATAGCTACATGGTTATCGATACTAAGACCCCAAGACATGCAGCTGTGACTTCATAGGCA
CTATAGAGGACATTTCAAAAATGCTACAGCAAAATGTTCTTTTGCATGTCTGTGCCCACAATCCCACAGGAATGTGCTTT
TGCCCTGAGCAATGGAAGGAAGTAGCAACAGTGGTGAAGAAAAACAATCTTTTTGCATTCTTTGGTATGGCTTACCAAGG
CTTTGTCAGTGGTGATGGCAACAAGGATGCCTGGGCTATGTGCCACTTCATCTTCACTGAACAGGGCATTAATATTTGTC
TCTACCAATCCGATGCCAAGAACATGGGCTTATACAGTGAGCACGTGGGAAGCTTCACTGTGGTCTGCAAAGATACTGAT
GAAGCCAAAAGGGTGGAGTCACAGTTGAAGATCTTGATCTGTCCCATGTATTCCAACCCTCCAATCAGTGGGGCCTGCAT
TGCCTTGACCATCCTGACCAGCCCTGACCTGTGATAACAATGGTTGCAGGAAGTAAAAGGCATGGCCCACCCCATCATTA
GCATGTGGATTCAGCTGGTCTCCAACCTCCAGAAGGAGGGCTTCCCCCACTACTGACAGCACATCACTGACCAGATTGGC
ATGTTTTGTTTCACAGGACTAAAGCCTGAACAGGTGGAGAGGCTGACCAAGGAGTTCTCCATCCACATGACAAAGGATGG
CCACATCTCTGTGGCAGGGGTCACCTTGGACAATGTAGGCTATCTTACCCATGCCATTCACCAGGTCTCCAAG

ORF - retro_amel_1805 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 80.11 %
Parental protein coverage: 86.05 %
Number of stop codons detected: 7
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalNLGVGAYRDDNGKPYVLPSVRKAEAQIAAKNLDKEYLPIAGLAEFCKASAELALGENNEVLKSSRYATVQ
NLG..A..DDNGK.YVLPSV..A.AQIAAK.LDKEYLPI.GLAEFCKASAELALGENNEVLKSS.Y.TVQ
RetrocopyNLGFCAHQDDNGKAYVLPSVQNAKAQIAAKSLDKEYLPIVGLAEFCKASAELALGENNEVLKSSQYVTVQ
ParentalTISGTGALRIGASFLQRFFKFSRDVFLPKPSWGNHTPIFRDAGMQLHGYRYYDPKTCGFDFTGAIEDISK
TISGT..LRIG...L.RFFKF.RDVFLPKPS.GN.T.IFRD.G..LHGYRY.DPKTC..DF.G.IEDISK
RetrocopyTISGTRTLRIGDRLL*RFFKFGRDVFLPKPS*GNRTHIFRDVGI*LHGYRY*DPKTCSCDFIGTIEDISK
ParentalMPQQSVLLLHACAHNPTGVDPRPEQWKEMATVVKKNNLFAFFDMAYQGFASGDGNKDAWAVRHFI--EQG
M.QQ.VLL.H.CAHNPTG....PEQWKE.ATVVKKNNLFAFF.MAYQGF.SGDGNKDAWA..HFI..EQG
RetrocopyMLQQNVLL-HVCAHNPTGMCFCPEQWKEVATVVKKNNLFAFFGMAYQGFVSGDGNKDAWAMCHFIFTEQG
ParentalINVCLCQSYAKNMGLYGERVGAFTVVCKDADEAKRVESQLKILIRPMYSNPPVNGARIASTILTSPDLRK
IN.CL.QS.AKNMGLY.E.VG.FTVVCKD.DEAKRVESQLKILI.PMYSNPP..GA.IA.TILTSPDL..
RetrocopyINICLYQSDAKNMGLYSEHVGSFTVVCKDTDEAKRVESQLKILICPMYSNPPISGACIALTILTSPDL**
ParentalQWLQEVKGMADRIISMRTQLVSNLKKEGSSHNWQHITDQIGMFCFTGLKPEQVERLTKEFSIYMTKDGRI
QWLQEVKGMA..IISM..QLVSNL.KEG..H..QHITDQIGMFCFTGLKPEQVERLTKEFSI.MTKDG.I
RetrocopyQWLQEVKGMAHPIISMWIQLVSNLQKEGFPHY*QHITDQIGMFCFTGLKPEQVERLTKEFSIHMTKDGHI
ParentalSVAGVTSGNVGYLAHAIHQVTK
SVAGVT..NVGYL.HAIHQV.K
RetrocopySVAGVTLDNVGYLTHAIHQVSK

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






RNA-Seq - click to see more details

Ailuropoda melanoleuca was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Ailuropoda melanoleuca was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_amel_1805 retrocopy.

TSS - click to see more details

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab - click to see more details

retro_amel_1805 was not experimentally validated.

Retrocopy orthology:
Ailuropoda melanoleuca does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.
Parental genes homology:
Parental genes homology involve 18 parental genes, and 34 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG00000017346 3 retrocopies
retro_amel_1805 , retro_amel_815, retro_amel_846,
Canis familiaris ENSCAFG000000083572 retrocopies
retro_cfam_586, retro_cfam_816,
Callithrix jacchus ENSCJAG000000112341 retrocopy
retro_cjac_2916,
Equus caballus ENSECAG000000165041 retrocopy
retro_ecab_694,
Felis catus ENSFCAG000000255523 retrocopies
retro_fcat_1068, retro_fcat_1888, retro_fcat_381,
Homo sapiens ENSG000001251664 retrocopies
retro_hsap_4687, retro_hsap_473, retro_hsap_960, retro_hsap_971,
Gorilla gorilla ENSGGOG000000057673 retrocopies
retro_ggor_2912, retro_ggor_449, retro_ggor_774,
Macropus eugenii ENSMEUG000000125741 retrocopy
retro_meug_2109,
Microcebus murinus ENSMICG000000089541 retrocopy
retro_mmur_480,
Macaca mulatta ENSMMUG000000060001 retrocopy
retro_mmul_1337,
Mustela putorius furoENSMPUG000000048621 retrocopy
retro_mputfur_567,
Mus musculus ENSMUSG000000316721 retrocopy
retro_mmus_2701,
Oryctolagus cuniculus ENSOCUG000000038711 retrocopy
retro_ocun_1516,
Otolemur garnettii ENSOGAG000000005512 retrocopies
retro_ogar_2182, retro_ogar_827,
Pongo abelii ENSPPYG000000074133 retrocopies
retro_pabe_3640, retro_pabe_823, retro_pabe_901,
Pan troglodytes ENSPTRG000000081854 retrocopies
retro_ptro_3115, retro_ptro_354, retro_ptro_665, retro_ptro_670,
Rattus norvegicus ENSRNOG000000117821 retrocopy
retro_rnor_2695,
Tupaia belangeri ENSTBEG000000018081 retrocopy
retro_tbel_3799,


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