RetrogeneDB ID:

retro_amel_1355

Retrocopy
location
Organism:Panda (Ailuropoda melanoleuca)
Coordinates:GL193243.1:678067..678636(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PEBP1
Ensembl ID:ENSAMEG00000016143
Aliases:None
Description:phosphatidylethanolamine binding protein 1 [Source:HGNC Symbol;Acc:8630]


Retrocopy-Parental alignment summary:






>retro_amel_1355
TCCCTGTTATCTGCCCAACTCACCCCCACGATGCTGGTGGACTTCAGCAAGTGGTCCGGGCCTTTGAGCCTGCAGGAAAT
GGACAAGTGGTCACAGCATCTGTGGCAGGTTAGATACACTGGGGCAGAGGTCAGCAAACTGGCAAAGTGCTGATGCCCAC
CCAGGTTAAGAACTGGCCCACCACTATTGCATGGGATGGCCTTGATCCAGGTAAACACTACACCTTGATCATGACAGATC
CAGATGCTCCCAGCAGGAAGGACCCCAAATACAGGGAATGGCACCATTTCCTGATGGTCAACACGAAGGGCCGTGACATC
AGCAAAGGCACTATCCTCTCTAATTACGTAGGCTCTGCGCCTCCCAAGGGCACAGGCCTTCTTCACTACATCTGGTTGGT
TTATGAGCAGAATGGGCCACTGAGGTTTGACGAGTCCATTTTCAGCAACTGATCTGGAGACCACCATGGCAAATTCAAAG
TGGGGTGTTTCCACAAAAAGTACGAGCTCAGGTCCTTGATGGCTGGCATGTGTTATCAGGCTGAGTGGGATGCCTGTGTG
CTCAGACTC

ORF - retro_amel_1355 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 70.68 %
Parental protein coverage: 92.68 %
Number of stop codons detected: 1
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalSSLFPQLGSAMPVDLSKWSGPLSLQEVDERPQHPLQVKYTGTEIDEL-GKVLTPTQVKNRPTSISWDGID
S.L..QL...M.VD.SKWSGPLSLQE.D...QH..QV.YTG.E...L.GKVL.PTQVKN.PT.I.WDG.D
RetrocopySLLSAQLTPTMLVDFSKWSGPLSLQEMDKWSQHLWQVRYTGAEVSKL<GKVLMPTQVKNWPTTIAWDGLD
ParentalPGKLYTLVMTDPDAPSRKDPKYREWHHFLVVNMKGNDVSSGTVLSDYVGSGPPKGTGLHRYVWLVYEQNG
PGK.YTL.MTDPDAPSRKDPKYREWHHFL.VN.KG.D.S.GT.LS.YVGS.PPKGTGL..Y.WLVYEQNG
RetrocopyPGKHYTLIMTDPDAPSRKDPKYREWHHFLMVNTKGRDISKGTILSNYVGSAPPKGTGLLHYIWLVYEQNG
ParentalPLKCDEPILSNRSGDHRGKFKVASFRKKYELGPPVAGTCYQAEWDDYVPKL
PL..DE.I.SN.SGDH.GKFKV..F.KKYEL....AG.CYQAEWD..V..L
RetrocopyPLRFDESIFSN*SGDHHGKFKVGCFHKKYELRSLMAGMCYQAEWDACVLRL

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_1355 retrocopy.

TSS - click to see more details

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab - click to see more details

retro_amel_1355 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 48 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG00000016143 2 retrocopies
retro_amel_1355 , retro_amel_754,
Canis familiaris ENSCAFG000000099101 retrocopy
retro_cfam_526,
Callithrix jacchus ENSCJAG000000093142 retrocopies
retro_cjac_1410, retro_cjac_818,
Felis catus ENSFCAG000000022773 retrocopies
retro_fcat_1317, retro_fcat_1360, retro_fcat_299,
Homo sapiens ENSG000000892203 retrocopies
retro_hsap_1456, retro_hsap_2288, retro_hsap_492,
Gorilla gorilla ENSGGOG000000132813 retrocopies
retro_ggor_1121, retro_ggor_1701, retro_ggor_461,
Myotis lucifugus ENSMLUG000000022597 retrocopies
retro_mluc_103, retro_mluc_1612, retro_mluc_1742, retro_mluc_2357, retro_mluc_2373, retro_mluc_984, retro_mluc_998,
Macaca mulatta ENSMMUG000000050984 retrocopies
retro_mmul_1621, retro_mmul_2272, retro_mmul_328, retro_mmul_442,
Mustela putorius furoENSMPUG000000028613 retrocopies
retro_mputfur_1228, retro_mputfur_1361, retro_mputfur_223,
Mus musculus ENSMUSG000000329594 retrocopies
retro_mmus_138, retro_mmus_1857, retro_mmus_2314, retro_mmus_542,
Nomascus leucogenys ENSNLEG000000003221 retrocopy
retro_nleu_1966,
Oryctolagus cuniculus ENSOCUG000000083952 retrocopies
retro_ocun_1329, retro_ocun_1900,
Otolemur garnettii ENSOGAG000000017401 retrocopy
retro_ogar_2750,
Pongo abelii ENSPPYG000000050112 retrocopies
retro_pabe_1202, retro_pabe_241,
Pan troglodytes ENSPTRG000000055123 retrocopies
retro_ptro_1621, retro_ptro_371, retro_ptro_992,
Rattus norvegicus ENSRNOG000000011363 retrocopies
retro_rnor_1223, retro_rnor_46, retro_rnor_541,
Ictidomys tridecemlineatus ENSSTOG000000040852 retrocopies
retro_itri_1603, retro_itri_961,
Tupaia belangeri ENSTBEG000000001772 retrocopies
retro_tbel_272, retro_tbel_2728,


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