RetrogeneDB ID:

retro_amel_676

Retrocopy
location
Organism:Panda (Ailuropoda melanoleuca)
Coordinates:GL192564.1:232230..233445(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSAMEG00000020099
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSAMEG00000011535
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_amel_676
GCCAAGTACCGCCAGGCATCCCTGTATGTGGGTGACCTCAGTGCAGATGTCACCGAGGACCTGCTGTTCAAAAAGTTCAG
CGCTGTGGGGCCTGTGCTGTCCATCCGCATCTGCAGGGACCTGGTCACCCGACGCTCTCTGGGCTATGCCTACGTGAACT
TCCTGAAGCTGGCTGATGCCCAGAAGGCCCTGGACACAATGAACTTTGACATGATAAAAGGCAAACCCATCCGTCTCATG
TGGTCTCAACGTGATGCCTACTTAAGGAAATCTGGCATTGGGAACGTGTTCATCAAGAATCTGGACAAATCTATTGATAA
CAAAACCCTTTACGAACATTTTTCAGCTTTTGGGAAGATCCTGTCCTCCAAGGTGATGAGTGATGATCAAGGCTCTAGGG
GCTATGCGTTTGTGCACTTTCAGAACCAGAACGCGGCCGACAGGGCCATCGAGGAGATGAACGGGGCCCTGCTTAAGGAC
TGCAGGCTGTTTGTTGGCAGATTCAAAAACCGTAAAGATCGGGAAGCCGAGCTCCAAAACAAGGTCAATGAATTCACCAA
TGTTTACGTCAAAAACTTTGGAGACGACATGGATGATGAGAGACTGAAGGAAGTTTTTAGTAAATATGGCAAAACCCTGA
GTGTTAAGGTGATGACAGATTCCGGCGGGAAATCCAAAGGCTTTGGCTTTGTGAGTTTTGATAGCCATGAGGCTGCCAAA
AAGGCTGTGGAAGAAATGAATGGAAAGGACGTAAACGGACAGCTGCTTTTTGTAGGACGGGCTCAAAAGAAATCAGAGCG
ACAGGCTGAGTTAAAGCAAATGTTTGAGCAGCTGAAACAGGAAAGATTTCGGAGATGCCAGGGCATGAAGCTCTATATTA
AGAACCTCGATGATACCATTGATGATGAAAAACTGTGGAGGGAATTTTCTTCATTTGGATCAATTAGCAGAGTCAAGATA
ATGCGGGAAGAAGGGCGAAGCAAAGGGTTCGGCTTGATCTGCTTCTCCTCTCCTGAGGAGGCCACTAAAGCAATGGCTGA
GATGAATGGCCGAATCTTGGGCTCCAAGCCACTCTACATCGCCCTGGCCCAGAGGCCCTAGGAGAGAAAAAACTTCCTGC
ACCAGCCAGTGTTTGCAGCAGGCCTGGGAATGATAGTGATCTCTGCCTGAATTATCCTTAGAAAATTCCGAATCCCAGCT
GATGGCTGCTTAATT

ORF - retro_amel_676 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 69.14 %
Parental protein coverage: 61.36 %
Number of stop codons detected: 2
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalSSYPMASLYVGDLHSDVTEAMLYEKFSPAGPVLSIWVCRDMITRRSLGYAYVNFQQPADAERALDTMNFD
..Y..ASLYVGDL..DVTE..L..KFS..GPVLSI..CRD..TRRSLGYAYVNF...ADA..ALDTMNFD
RetrocopyAKYRQASLYVGDLSADVTEDLLFKKFSAVGPVLSIRICRDLVTRRSLGYAYVNFLKLADAQKALDTMNFD
ParentalVIKGKPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYAFVHF
.IKGKPIR.MWSQRD..LRKSG.GNVFIKNLDKSIDNK.LY..FSAFG.ILS.KV..D..GS.GYAFVHF
RetrocopyMIKGKPIRLMWSQRDAYLRKSGIGNVFIKNLDKSIDNKTLYEHFSAFGKILSSKVMSDDQGSRGYAFVHF
ParentalETQEAADKAIEKMNGMLLNDRKVFVGRFKSRKEREAELGAKAKEFTNVYIKNFGEEVDDESLKELFSQFG
..Q.AAD.AIE.MNG.LL.D...FVGRFK.RK.REAEL..K..EFTNVY.KNFG...DDE.LKE.FS..G
RetrocopyQNQNAADRAIEEMNGALLKDCRLFVGRFKNRKDREAELQNKVNEFTNVYVKNFGDDMDDERLKEVFSKYG
ParentalKTLSVKVMRDPSGKSKGFGFVSYEKHEDANKAVEEMNGKEISGKVIFVGRAQKKVERQAELKRKFEQLKQ
KTLSVKVM.D..GKSKGFGFVS...HE.A.KAVEEMNGK...G...FVGRAQKK.ERQAELK..FEQLKQ
RetrocopyKTLSVKVMTDSGGKSKGFGFVSFDSHEAAKKAVEEMNGKDVNGQLLFVGRAQKKSERQAELKQMFEQLKQ
ParentalERISRYQGVNLYIKNLDDTIDDEKLRKEFSPFGSITSAKVMLEDGRSKGFGFVCFSSPEEATKAVTEMNG
ER..R.QG..LYIKNLDDTIDDEKL..EFS.FGSI...K.M.E.GRSKGFG..CFSSPEEATKA..EMNG
RetrocopyERFRRCQGMKLYIKNLDDTIDDEKLWREFSSFGSISRVKIMREEGRSKGFGLICFSSPEEATKAMAEMNG
ParentalRIVGSKPLYVALAQRKEERKAHLTNQYMQRVAGMRALPANAILNQFQPAAGGYFV
RI.GSKPLY.ALAQR..ERK..L.........GM....A..IL..F...A.G...
RetrocopyRILGSKPLYIALAQRP*ERKNFLHQPVFAAGLGMIVISA*IILRKFRIPADGCLI

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_676 retrocopy.

TSS - click to see more details

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab - click to see more details

retro_amel_676 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 29 parental genes, and 63 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000003481 retrocopy
retro_amel_1650,
Ailuropoda melanoleuca ENSAMEG000000040541 retrocopy
retro_amel_454,
Ailuropoda melanoleuca ENSAMEG00000011535 2 retrocopies
retro_amel_107, retro_amel_676 ,
Bos taurus ENSBTAG000000171253 retrocopies
retro_btau_1492, retro_btau_28, retro_btau_656,
Canis familiaris ENSCAFG000000030812 retrocopies
retro_cfam_45, retro_cfam_837,
Choloepus hoffmanni ENSCHOG000000053273 retrocopies
retro_chof_1150, retro_chof_1182, retro_chof_1274,
Callithrix jacchus ENSCJAG000000025123 retrocopies
retro_cjac_214, retro_cjac_2722, retro_cjac_284,
Cavia porcellus ENSCPOG000000095522 retrocopies
retro_cpor_1330, retro_cpor_77,
Equus caballus ENSECAG000000093962 retrocopies
retro_ecab_2, retro_ecab_502,
Felis catus ENSFCAG000000152542 retrocopies
retro_fcat_116, retro_fcat_545,
Homo sapiens ENSG000000906212 retrocopies
retro_hsap_109, retro_hsap_74,
Gorilla gorilla ENSGGOG000000040023 retrocopies
retro_ggor_2127, retro_ggor_87, retro_ggor_916,
Loxodonta africana ENSLAFG000000001513 retrocopies
retro_lafr_1144, retro_lafr_390, retro_lafr_597,
Microcebus murinus ENSMICG000000166331 retrocopy
retro_mmur_675,
Myotis lucifugus ENSMLUG000000120682 retrocopies
retro_mluc_228, retro_mluc_397,
Macaca mulatta ENSMMUG000000074971 retrocopy
retro_mmul_178,
Monodelphis domestica ENSMODG000000176572 retrocopies
retro_mdom_1090, retro_mdom_1805,
Mustela putorius furoENSMPUG000000144142 retrocopies
retro_mputfur_152, retro_mputfur_546,
Mus musculus ENSMUSG000000112577 retrocopies
retro_mmus_2006, retro_mmus_2326, retro_mmus_2327, retro_mmus_798, retro_mmus_801, retro_mmus_803, retro_mmus_805,
Nomascus leucogenys ENSNLEG000000119282 retrocopies
retro_nleu_1517, retro_nleu_62,
Oryctolagus cuniculus ENSOCUG000000005622 retrocopies
retro_ocun_153, retro_ocun_792,
Otolemur garnettii ENSOGAG000000040671 retrocopy
retro_ogar_71,
Ochotona princeps ENSOPRG000000119841 retrocopy
retro_opri_1133,
Pongo abelii ENSPPYG000000015062 retrocopies
retro_pabe_190, retro_pabe_2563,
Pan troglodytes ENSPTRG000000005733 retrocopies
retro_ptro_101, retro_ptro_2093, retro_ptro_8,
Rattus norvegicus ENSRNOG000000156422 retrocopies
retro_rnor_175, retro_rnor_92,
Sarcophilus harrisii ENSSHAG000000181391 retrocopy
retro_shar_823,
Sus scrofa ENSSSCG000000036603 retrocopies
retro_sscr_1210, retro_sscr_974, retro_sscr_975,
Tursiops truncatus ENSTTRG000000143402 retrocopies
retro_ttru_1117, retro_ttru_246,


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