RetrogeneDB ID:

retro_amel_400

Retrocopy
location
Organism:Panda (Ailuropoda melanoleuca)
Coordinates:GL192424.1:1955534..1956682(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSAMEG00000006096
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:PDHA1
Ensembl ID:ENSAMEG00000016730
Aliases:None
Description:pyruvate dehydrogenase (lipoamide) alpha 1 [Source:HGNC Symbol;Acc:8806]


Retrocopy-Parental alignment summary:






>retro_amel_400
GTCTCCCGCGTGTTGTCCAGGGTCGCCCGGAAGCCCGCTAGCAGAGTGCTGGCGGCTTCCTGTAACTCTTCAGATGATGC
TATGTTTGAAATTAAGAAATGTGGCCTTTATCGATTAGAAGAGGGTCCCCCTGTCACAACAGTGCTCACCCGGGAGGATG
GGCTCAAATACTACAGGATGATGCAGACCATTCGCCGAATGGAATTGAAGGCAGATCAGCGTATAAACAAAAATTCATTC
GTGGGTTCTGTCACTTGTGCGATGGGCAGGAAGCTTGTTGTGTGGGCCTGGAGGCCGGGATAAATCCCACCGATCACGTC
ATCACATCCTATCGGGCTCACGGCTTGTGCTATACTCGTGGACTTTCTGTCCCATCGATCCTTGCGGAGCTGACGGGACG
AAGGGGAGGGTGCGCTAAATGCAAAGGCGGATCTATGCACATGTATGCGAAGAACTTCTATGGTGGCAACGGCATTGTTG
GTGCCCAGGCACCTCTGGGAGCCGGCATCGCCCTGGCCTGTAAATATAAGGGCAACAAGGAGGTCTGTTTGACTGTATAT
GGGGATGGTGCTGCGAATCAGGGTCAGATAGCGGAAGCTTTCAATATGGCTGCTTTGTGGAAATTACCTTGTGTTTTCAT
CTGTGAGAATAACCTCGATGGCATGGGCACGGCTGCTGAGAGAGCAGCAGCGAGCACTGATTACTACAAGAGAGGCCATT
TTATCCCTGGACTAAGGGTGGATGGAATGGATGTTCTATGTGTTCGGGAGGCAACGAAGTTTGCCACTGACTACTGTAGA
TCTGAAAAGGGGCCCATAGTGATGGAGCTGCAGACCTACCGTTATCATGGACACAGCATGAGTGACCCTGGAATAAGTTA
TCGTACCCGACAAGAAATTCAGAATGTAAGAAGCAAAAGTGATCCCATAATGCTTCTCAAAGATAGAATGGTAAACAGTA
AGCTTGCCACTATTGAAGAGTTCAAGGAAATTGATGTGGAAGTGAGGAAAGAAATTGACAATGCAGCCCACTTTGCTATA
ACTGACCCTGAACCACCTTTGGAGGAATTAGGTCATCACATCTACTGCGATAATGAACCTTTTGAAGTTCGTGGTTCAAG
TCAGTGGATCAAGTTTAAGTCCCTCAGT

ORF - retro_amel_400 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 81.77 %
Parental protein coverage: 98.21 %
Number of stop codons detected: 0
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalLSRMKSCARSRTASRVLVASRNFANDATFEIKKCDLHRLEEGPPVTTVLTREDGLRYYRMMQTVRRMELK
.SR..S......ASRVL.AS.N...DA.FEIKKC.L.RLEEGPPVTTVLTREDGL.YYRMMQT.RRMELK
RetrocopyVSRVLSRVARKPASRVLAASCNSSDDAMFEIKKCGLYRLEEGPPVTTVLTREDGLKYYRMMQTIRRMELK
ParentalADQ-LYKQKIIRGFCHLCDGQEACCVGLEAGINPTDHLITAYRAHGFTFTRGLSVREILAELTGRRGGCA
ADQ..YKQK.IRGFCHLCDGQEACCVGLEAGINPTDH.IT.YRAHG...TRGLSV..ILAELTGRRGGCA
RetrocopyADQ<AYKQKFIRGFCHLCDGQEACCVGLEAGINPTDHVITSYRAHGLCYTRGLSVPSILAELTGRRGGCA
ParentalKGKGGSMHMYAKNFYGGNGIVGAQVPLGAGIALACKYNGKDEVCLTLYGDGAANQGQIFEAYNMAALWKL
K.KGGSMHMYAKNFYGGNGIVGAQ.PLGAGIALACKY.G..EVCLT.YGDGAANQGQI.EA.NMAALWKL
RetrocopyKCKGGSMHMYAKNFYGGNGIVGAQAPLGAGIALACKYKGNKEVCLTVYGDGAANQGQIAEAFNMAALWKL
ParentalPCIFICENNRYGMGTSVERAAASTDYYKRGDFIPGLRVDGMDILCVREATRFAAAHCRSGKGPILMELQT
PC.FICENN..GMGT..ERAAASTDYYKRG.FIPGLRVDGMD.LCVREAT.FA...CRS.KGPI.MELQT
RetrocopyPCVFICENNLDGMGTAAERAAASTDYYKRGHFIPGLRVDGMDVLCVREATKFATDYCRSEKGPIVMELQT
ParentalYRYHGHSMSDPGVSYRTREEIQEVRSKSDPIMLLKDRMVNSNLASVEELKEIDVEVRKEIEDAAQFATAD
YRYHGHSMSDPG.SYRTR.EIQ.VRSKSDPIMLLKDRMVNS.LA..EE.KEIDVEVRKEI..AA.FA..D
RetrocopyYRYHGHSMSDPGISYRTRQEIQNVRSKSDPIMLLKDRMVNSKLATIEEFKEIDVEVRKEIDNAAHFAITD
ParentalPEPPLEELGYHIYSSDPPFEVRGANQWIKFKSIS
PEPPLEELG.HIY....PFEVRG..QWIKFKS.S
RetrocopyPEPPLEELGHHIYCDNEPFEVRGSSQWIKFKSLS

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_400 retrocopy.

TSS - click to see more details

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab - click to see more details

retro_amel_400 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 22 parental genes, and 27 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG00000016730 1 retrocopy
retro_amel_400 ,
Bos taurus ENSBTAG000000198522 retrocopies
retro_btau_100, retro_btau_1807,
Callithrix jacchus ENSCJAG000000054962 retrocopies
retro_cjac_2414, retro_cjac_27,
Dipodomys ordii ENSDORG000000118481 retrocopy
retro_dord_35,
Equus caballus ENSECAG000000019641 retrocopy
retro_ecab_21,
Erinaceus europaeus ENSEEUG000000054851 retrocopy
retro_eeur_580,
Homo sapiens ENSG000001318281 retrocopy
retro_hsap_41,
Gorilla gorilla ENSGGOG000000135741 retrocopy
retro_ggor_59,
Myotis lucifugus ENSMLUG000000129322 retrocopies
retro_mluc_2363, retro_mluc_323,
Macaca mulatta ENSMMUG000000173361 retrocopy
retro_mmul_123,
Mustela putorius furoENSMPUG000000032691 retrocopy
retro_mputfur_812,
Mus musculus ENSMUSG000000312992 retrocopies
retro_mmus_63, retro_mmus_631,
Nomascus leucogenys ENSNLEG000000098051 retrocopy
retro_nleu_74,
Oryctolagus cuniculus ENSOCUG000000147481 retrocopy
retro_ocun_264,
Pongo abelii ENSPPYG000000201711 retrocopy
retro_pabe_129,
Pan troglodytes ENSPTRG000000217171 retrocopy
retro_ptro_79,
Pteropus vampyrus ENSPVAG000000054201 retrocopy
retro_pvam_1306,
Sarcophilus harrisii ENSSHAG000000153751 retrocopy
retro_shar_84,
Sus scrofa ENSSSCG000000236432 retrocopies
retro_sscr_1015, retro_sscr_281,
Ictidomys tridecemlineatus ENSSTOG000000154331 retrocopy
retro_itri_1529,
Tupaia belangeri ENSTBEG000000143131 retrocopy
retro_tbel_3327,
Tursiops truncatus ENSTTRG000000006601 retrocopy
retro_ttru_1427,


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