RetrogeneDB ID:

retro_amel_1316

Retrocopy
location
Organism:Panda (Ailuropoda melanoleuca)
Coordinates:GL193192.1:225629..226606(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSAMEG00000009005
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSAMEG00000016175
Aliases:None
Description:L-lactate dehydrogenase [Source:UniProtKB/TrEMBL;Acc:D2I1F1]


Retrocopy-Parental alignment summary:






>retro_amel_1316
CAACTGTTAAGGAAAAACGCAGAAGAAGAGGCAATCATCTCAAACCATAAGATCACGGTAGTGGGCATTGGACAAGTTGG
TATGGCCTGTGCCATCAGCATTCTAGGAAAGTCTCCAGCTGATGAATTTGCCCTTGTGGATGCTTTGGAAGATAAACTCA
AAGGAGAAATGATGGATCTGCAACATGGGAGCTTATTTCTTCAGACGCCTAAAATTGTGGCAGAAAAAGATGACTCTGTG
ACCGCCAATTCTAAGATTATAGTGGTAACTGCAGGAGTCCGCCAGCAGGAGGGAGAGAGCCGTCTCAATCTGGTGCAGAA
GAATGTTAATGTCTTCAAATTCATTATTCCTCAGATAGTCAAGTACAGTCCTGATTGTATCATACTTGTGGTTTCCAACC
CAGTGGATATTCTCACATATGTTACCTGGAAACTAAGTGGGCTACCCAAGCACCGTGTGTTTGGAATTGGGTGTAATCTG
GATTCTGCTAGATTTCACTACCTTATGTCTGAAAAACTTGGCATTCATCTCAGCAGCTGCCACGGATGGATTTGGGGAGA
ACATGGTGACTCAAGTGTGACTGCGTGGAGTGGAGTGAATGTGGCAGACGTTTCTCTCAGGAACTGAATCCAGAAATGGA
AACAGGCAATGACAGTGAAAATTGGAAGGAAGTGCATAAGATGGTGGTTGGAAGTGCCTCTGACGTCATGAAGCTGAAAG
GATGTACCAACTGGGCTGTTGGATTGAGTGTGGCTGATCTCATTGAATCCGTGTTGGAAAATCTATCCAGGATTCACCCA
GTGTCAACGATGATGAAGGGAATATACAGCATGGAGAATCAAGTCTTCCCAAGCCTTCCACGTTCCCTGTAGGCTCAGGG
ATTAATCAGTGTGATCAACCAGAAGCTGAAGGATGACGAAGTTGCATAGCTCCAGAAAAGTGCACCTACCTTGTGGGACG
TCCAGAAAGACCTAAAA

ORF - retro_amel_1316 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 83.49 %
Parental protein coverage: 97.6 %
Number of stop codons detected: 2
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalKLIAPVAEEEAAIPNNKITVVGVGQVGMACAISILGKSLADELALVDVLEDKLKGEMMDLQHGSLFLQTP
.L....AEEEA.I.N.KITVVG.GQVGMACAISILGKS.ADE.ALVD.LEDKLKGEMMDLQHGSLFLQTP
RetrocopyQLLRKNAEEEAIISNHKITVVGIGQVGMACAISILGKSPADEFALVDALEDKLKGEMMDLQHGSLFLQTP
ParentalKIVADKDYSVTANSKIVVVTAGVRQQEGESRLNLVQRNVNVFKFIIPQIVKYSPDCIIIVVSNPVDILTY
KIVA.KD.SVTANSKI.VVTAGVRQQEGESRLNLVQ.NVNVFKFIIPQIVKYSPDCII.VVSNPVDILTY
RetrocopyKIVAEKDDSVTANSKIIVVTAGVRQQEGESRLNLVQKNVNVFKFIIPQIVKYSPDCIILVVSNPVDILTY
ParentalVTWKLSALPKHRVIGSGCNLDSARFRYLMAEKLGVHPSSCHGWILGEHGDSSVAVWSGVNVAGVSL-QEL
VTWKLS.LPKHRV.G.GCNLDSARF.YLM.EKLG.H.SSCHGWI.GEHGDSSV..WSGVNVA.VSL.QEL
RetrocopyVTWKLSGLPKHRVFGIGCNLDSARFHYLMSEKLGIHLSSCHGWIWGEHGDSSVTAWSGVNVADVSL<QEL
ParentalNPEMGTDNDSENWKEVHKMVVESAYEVIKLKGYTNWAIGLSVADLIESMLKNLSRIHPVSTMVKGMYGIE
NPEM.T.NDSENWKEVHKMVV.SA..V.KLKG.TNWA.GLSVADLIES.L.NLSRIHPVSTM.KG.Y..E
RetrocopyNPEMETGNDSENWKEVHKMVVGSASDVMKLKGCTNWAVGLSVADLIESVLENLSRIHPVSTMMKGIYSME
ParentalNEVFLSLPCILNARGLTSVINQKLKDDEVAQLKKSADTLWDIQKDLK
N.VF.SLP..L.A.GL.SVINQKLKDDEVA.L.KSA.TLWD.QKDLK
RetrocopyNQVFPSLPRSL*AQGLISVINQKLKDDEVA*LQKSAPTLWDVQKDLK

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_1316 retrocopy.

TSS - click to see more details

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab - click to see more details

retro_amel_1316 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 80 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG00000016175 4 retrocopies
retro_amel_1316 , retro_amel_814, retro_amel_882, retro_amel_977,
Ailuropoda melanoleuca ENSAMEG000000178542 retrocopies
retro_amel_389, retro_amel_462,
Bos taurus ENSBTAG000000196034 retrocopies
retro_btau_1589, retro_btau_303, retro_btau_451, retro_btau_647,
Canis familiaris ENSCAFG000000121959 retrocopies
retro_cfam_1068, retro_cfam_111, retro_cfam_1674, retro_cfam_17, retro_cfam_1700, retro_cfam_174, retro_cfam_1836, retro_cfam_701, retro_cfam_93,
Choloepus hoffmanni ENSCHOG000000076581 retrocopy
retro_chof_1145,
Cavia porcellus ENSCPOG000000071381 retrocopy
retro_cpor_762,
Dasypus novemcinctus ENSDNOG000000136204 retrocopies
retro_dnov_1161, retro_dnov_1511, retro_dnov_1570, retro_dnov_529,
Echinops telfairi ENSETEG000000199551 retrocopy
retro_etel_850,
Felis catus ENSFCAG000000126391 retrocopy
retro_fcat_462,
Homo sapiens ENSG000001117161 retrocopy
retro_hsap_4863,
Gorilla gorilla ENSGGOG000000157581 retrocopy
retro_ggor_3033,
Loxodonta africana ENSLAFG000000009722 retrocopies
retro_lafr_197, retro_lafr_315,
Macropus eugenii ENSMEUG000000048251 retrocopy
retro_meug_311,
Microcebus murinus ENSMICG000000171832 retrocopies
retro_mmur_275, retro_mmur_300,
Myotis lucifugus ENSMLUG000000121551 retrocopy
retro_mluc_202,
Macaca mulatta ENSMMUG000000026794 retrocopies
retro_mmul_212, retro_mmul_303, retro_mmul_308, retro_mmul_315,
Monodelphis domestica ENSMODG000000177861 retrocopy
retro_mdom_1484,
Mustela putorius furoENSMPUG000000001725 retrocopies
retro_mputfur_1300, retro_mputfur_1561, retro_mputfur_492, retro_mputfur_539, retro_mputfur_549,
Mus musculus ENSMUSG000000302464 retrocopies
retro_mmus_1817, retro_mmus_2035, retro_mmus_2509, retro_mmus_335,
Oryctolagus cuniculus ENSOCUG000000220151 retrocopy
retro_ocun_805,
Otolemur garnettii ENSOGAG000000047639 retrocopies
retro_ogar_1469, retro_ogar_2093, retro_ogar_2344, retro_ogar_2459, retro_ogar_3288, retro_ogar_3342, retro_ogar_3383, retro_ogar_689, retro_ogar_721,
Pongo abelii ENSPPYG000000043563 retrocopies
retro_pabe_1738, retro_pabe_1744, retro_pabe_3780,
Pan troglodytes ENSPTRG000000047621 retrocopy
retro_ptro_3237,
Pteropus vampyrus ENSPVAG000000024623 retrocopies
retro_pvam_1487, retro_pvam_320, retro_pvam_673,
Rattus norvegicus ENSRNOG000000130003 retrocopies
retro_rnor_2697, retro_rnor_2749, retro_rnor_2834,
Sorex araneus ENSSARG000000025651 retrocopy
retro_sara_713,
Sus scrofa ENSSSCG000000005761 retrocopy
retro_sscr_37,
Ictidomys tridecemlineatus ENSSTOG000000220582 retrocopies
retro_itri_501, retro_itri_648,
Tarsius syrichta ENSTSYG000000137597 retrocopies
retro_tsyr_1130, retro_tsyr_1532, retro_tsyr_1860, retro_tsyr_2051, retro_tsyr_334, retro_tsyr_64, retro_tsyr_986,


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