RetrogeneDB ID:

retro_amel_557

Retrocopy
location
Organism:Panda (Ailuropoda melanoleuca)
Coordinates:GL192501.1:76171..77058(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSAMEG00000002366
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSAMEG00000011920
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_amel_557
AAAACTGTTTATTGCTGTCTGAGCTTTGAAACTACAGGTTTAAGAGAACATTTTGAAAAATGGGGCACACTTACAGATTT
TGTGGTGAGGAGAGACCCCCAAACAAAATGTTCCAGGCGTTTTGGTTTTGTGATTTACTCCTGTGTTGAAGAGGTGGTTG
CAGCAATGTGTGCCCCACCACAGAAGGTTGATGGGTGTGTAGTGGAACCAAAGAGAACTGTTTCTAGAAAGGATTCTATA
AAGCCTGGTGCCCATCTAACAGTGAAGAAAATTTTCTTTGGTGGTATTAAAGAAGATACAGAAGAATATAATTTGAAAGA
CTACTTTGAAAAGTATGGCAAGACTGAAACCATAGTATGGAAGACAGGCACAGTGGAAAAAAGAGGATTTGCTTTTGTAA
TTTTTAATGATCATGATACAGTTGATAAAACTATTGTTCAGAAATACCACACTATTAATGGGCATAACTATGAAGAGAAA
AAGGCCCTTTCTAACCAAGAAATGCAGTCTGCTGGATCACAGAGAGGTCATGGAGGTGGATCTGGCAACTTCATGGGTCA
TGGAGGAAACTCTAGAGATGGTGGTAACTTTGGCCGTGGTGGGAACTTCGTGGAAGAAGAGGCTACAGTGGTGGAGGTGG
CGGTAGCAGAGATAGTTCTGGAGGCGGTGATGGTGGATATAACGGATTTGGAGGTGATGGTGGCAATTGTGGTGGTGGTC
CTGGTTATAGTAGTAGAGGAGGCTATGGTGGTGGTGGACCAGGATATGGAAACCAAGGAGGCAGATGTGGTGGTGGAGGA
GGATAGGATGATTACCATGAAGGAGGAAACTTTGGAGGTAACTATGGTGGTGGTGGGAACTATAATGATTTTGGAAATTA
TAGTGGA

ORF - retro_amel_557 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 74.0 %
Parental protein coverage: 82.09 %
Number of stop codons detected: 1
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalRKLFIALSFETTGLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAAMCARPHKVDGRVVEP
......LSFETTGLREHFEKWGTLTD.VV.RDPQTK.SR.FGFV.YSCVEEV.AAMCA.P.KVDG.VVEP
RetrocopyKTVYCCLSFETTGLREHFEKWGTLTDFVVRRDPQTKCSRRFGFVIYSCVEEVVAAMCAPPQKVDGCVVEP
ParentalKRAVSREDSVKPGAHLTVKKIFVGGIKEDTEEYNLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDDH
KR.VSR.DS.KPGAHLTVKKIF.GGIKEDTEEYNL.DYFEKYGK.ET...........KRGFAFV.F.DH
RetrocopyKRTVSRKDSIKPGAHLTVKKIFFGGIKEDTEEYNLKDYFEKYGKTET--IVWKTGTVEKRGFAFVIFNDH
ParentalDTVDKIVVQKYHTINGHNCEVKKALSKQEMQSAGSQRGRGGGSGNFMGRGGNFGGGGNFGRGGNF-GGRG
DTVDK..VQKYHTINGHN.E.KKALS.QEMQSAGSQRG.GGGSGNFMG.GGN...GGNFGRGGNF..GR.
RetrocopyDTVDKTIVQKYHTINGHNYEEKKALSNQEMQSAGSQRGHGGGSGNFMGHGGNSRDGGNFGRGGNF<RGRR
ParentalGYGGGGGGSRGSYGGGDGGYNGFGGDGGNYGGGPGYSSRGGYGGCGGPGYSSRGGYGASGHQGGRYGGGG
GY.GGGGGSR.S.GGGDGGYNGFGGDGGN.GGGPGYSSRGGYGG.GGPGY...GG....G.....Y..GG
RetrocopyGYSGGGGGSRDSSGGGDGGYNGFGGDGGNCGGGPGYSSRGGYGG-GGPGYGNQGGRCGGGGG*DDYHEGG
ParentalGGYDGYNEGGNFGG-GNYGG
.....Y..GGN....GNY.G
RetrocopyNFGGNYGGGGNYNDFGNYSG

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_557 retrocopy.

TSS - click to see more details

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab - click to see more details

retro_amel_557 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 50 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000007173 retrocopies
retro_amel_1726, retro_amel_547, retro_amel_925,
Ailuropoda melanoleuca ENSAMEG00000011920 4 retrocopies
retro_amel_1407, retro_amel_557 , retro_amel_715, retro_amel_765,
Cavia porcellus ENSCPOG000000042513 retrocopies
retro_cpor_1516, retro_cpor_1543, retro_cpor_65,
Ficedula albicollis ENSFALG000000032151 retrocopy
retro_falb_15,
Gallus gallus ENSGALG000000092501 retrocopy
retro_ggal_10,
Monodelphis domestica ENSMODG000000198031 retrocopy
retro_mdom_1590,
Mustela putorius furoENSMPUG000000141036 retrocopies
retro_mputfur_1141, retro_mputfur_1336, retro_mputfur_1545, retro_mputfur_603, retro_mputfur_674, retro_mputfur_779,
Oryctolagus cuniculus ENSOCUG000000027432 retrocopies
retro_ocun_994, retro_ocun_995,
Otolemur garnettii ENSOGAG000000259483 retrocopies
retro_ogar_1685, retro_ogar_3010, retro_ogar_3175,
Pongo abelii ENSPPYG000000129671 retrocopy
retro_pabe_450,
Pelodiscus sinensis ENSPSIG000000030111 retrocopy
retro_psin_16,
Pan troglodytes ENSPTRG000000126765 retrocopies
retro_ptro_1059, retro_ptro_2430, retro_ptro_2966, retro_ptro_683, retro_ptro_872,
Rattus norvegicus ENSRNOG0000000155611 retrocopies
retro_rnor_1510, retro_rnor_1665, retro_rnor_1869, retro_rnor_2053, retro_rnor_2659, retro_rnor_2669, retro_rnor_2713, retro_rnor_2776, retro_rnor_2809, retro_rnor_348, retro_rnor_959,
Sarcophilus harrisii ENSSHAG000000182551 retrocopy
retro_shar_518,
Tarsius syrichta ENSTSYG000000129492 retrocopies
retro_tsyr_1480, retro_tsyr_2122,
Tursiops truncatus ENSTTRG000000142253 retrocopies
retro_ttru_1459, retro_ttru_675, retro_ttru_9,
Xenopus tropicalis ENSXETG000000018061 retrocopy
retro_xtro_11,
Xiphophorus maculatus ENSXMAG000000004391 retrocopy
retro_xmac_2,


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