RetrogeneDB ID:

retro_amel_48

Retrocopy
location
Organism:Panda (Ailuropoda melanoleuca)
Coordinates:GL193482.1:393875..396224(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSAMEG00000019938
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:SMEK2
Ensembl ID:ENSAMEG00000003843
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_amel_48
ATGGCTGACAAGCAGTATCGTGTAAAAGTCTACTCACTGAACGAGGACCACCAATGGGATGATCTCGGCCCTGGGCACAT
CTCTTCCAGCTACGTGAAGCACCTCCAGGGCATGTGCCTGCTCGTGCGGTCGGATTCCCATGACTCACTAATCTTGGAAT
CAAAGATAAATTCAAATACGCCTTATCAGAAACAACAGGAAACTCTGATTGTCTGGTCTGAAGCAGAGAGCCATGGCATG
GCGTTACGTTTCCAGGACGCTGAGGGTTGTCATAAGATCTGGGAAGACATTTGCCGGGTTCAAGGAAAAGACCCATCCGT
CGTAATCACACAGGACCTCTTGGAGGAACCCATAGATAAACAACTGGATGAAGTACTGGAAACCAATAATGTGTTTGAAC
TGCCTAACTGTGAACTCAGTAAACTTGAGGAGATTTCCGACTTCATTACCTCAGTTCTCGCTTCACCGATCCATAAGGAG
AGACTGGCTCTGATCTTAGAAAATGAGGACTATATTAAAAATTTGCTGCAGCTGTTCCACACTTGTGAGGACCTACGGGA
CACTACAGGCTTACACCATTTGTATGAAATTATTAAAGGCATCTTATTCCTTAACAAGACAGCTCTCCTTGAGATCCTGT
TTTCTGCTGAGTGTATCATGGATGTGGTGGGATGCCTCGAGTATGACCCTGCTTTGGCTCAGCCAAAAAGGCATAGGGAA
TTCTTGACCCAAAATGCGAGGTTCAAGGAAGTTGTACCAATAACAGACCGTGAACTTCGGCAAAAAATACATCAGACATA
CAGGGTACAGTACATCCACGACATCCTTCTGCCTGCACCATCCATGTATGAAGAGAATTTTCTTTCTACTCTTAACACTT
TTATTTTCCTCAACAAGGTTGAGATAGTCAGCATGATGCAGGATCATGCCAACTTTTTGTCTGAAGTGTTTGCACAGTTA
AGGGATGAGACTACAGATGACGATAGACGGCGCGAATTGCTATTTTTCTTCAAGGAATTCTGCGCGTTTTCTCAGACATT
ACAGCGTTCAAGAAAGGATGCACTGTTCAAAACGTTGACAGAATTGGGGATTCTTCCTGTTCTTAAAATCGTCATGAGCA
TGGAGGATTTGCAGATAAGGTCAGCTGCTACTGATATATTTACTTATCTAGTGGAATATAGTCCATCCATGATTCGAGAA
TTTATCATGGAAGAAGCCCAAGAGAGTGAAGACGGTAACCTTTTCATTAATTTAGTCATTGAGCAAATGATGTGTGATAC
TGATCCTGAGCTGGGAGGTGCTGTTCATTTAATGGGACTTCTTCGTACTCTACTTAATCCAGAAAACATGCTAGCAACAT
CTAGTAAATGTGAAAGAAGTGAATTTCTAAATTTCTTCTATCATCATTGTATTCATAACTTCATAGCACCACTTTTTGTC
ACCACTTCAGAAGATATATGTGAAGGAGATAATGTAGTTGGATCCGACAAAAACAACACAAATTGCCTCAATAATTATCA
AAGAGCACAGCTGCTTTCTTTAATTGTAGAGCTGCTCACATTTTGTGTGCAACATCACACATACTACATAAAAAACTATA
TTTTGAGCAAAGACTTGCTAAGAAGAGTCTTGATCTTGTTGAATTCAAAGCACACTTTCCTGATCTTGTGTGCTCTCCGC
TTTATGAGAAGAATGATTGGCCTTAAAGATGAACTTTATAATTGTTACATCATCAAGGGAAATCTTTTTGAGCCAGTTGT
CAATGCTTTTCTGGGTAACGGAACTCGGTACAATATGTTGAATTCAGCTGTTATTGAGCTGTTTGAATATATAAGAGTGG
AAAATATCAAATCTCTTGTTGAACATATAGTTGAAAAGTTTTATAAAACACTTGAATCGATTGAATATGTTCAGACATTC
AAAGGATTGAAGATTAAATATGAACAAGAGAAAGACCGGCAGAGTCAAATACGGAGGAATTTACATTCTATACTGTATAG
TAAAATACTTTTCAGGAGTATCAGCATCGTGGAGAAGAAAGAAGAAAAGCGTTTTAAAGGAAATTCAGAGGAAGGCGAAG
CAATTATACCGCCACTGGAAAATGATTTTCAAGATCGTTATAAATTTATGGAGACGAAAAAAACAAAAGAAAATGAAAAC
AAGGTAGATCCTCCTAAAGGAGAGTCTTCGGGGGCCTCCAAATTCGCTTCATCCCATGCTGCTGCTGCTAATGGAGCACG
TAGCCTGCATGGTAGCAGCACCGTTGGCTTAATGAATCGTCCCAATGACGAAGAAAAAGATAAGGAAGATGAAACACCCC
CCAGGAAGAGATCACATCTTAGCTCATAA

ORF - retro_amel_48 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 71.69 %
Parental protein coverage: 56.94 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalRVKVYTLNEDRQWDDRGTGHVSSTYVEELKGMSLLVRAESDGSLLLESKINPNTAYQKQQDTLIVWSEAE
RVKVY.LNED.QWDD.G.GH.SS.YV..L.GM.LLVR..S..SL.LESKIN.NT.YQKQQ.TLIVWSEAE
RetrocopyRVKVYSLNEDHQWDDLGPGHISSSYVKHLQGMCLLVRSDSHDSLILESKINSNTPYQKQQETLIVWSEAE
ParentalNYDLALSFQEKAGCDEIWEKICQVQGKDPSVEVTQDLIDESEEERFEEMPETSHLIDLPTCELNKLEEIA
....AL.FQ...GC..IWE.IC.VQGKDPSV..TQDL..E.......E..ET.....LP.CEL.KLEEI.
RetrocopySHGMALRFQDAEGCHKIWEDICRVQGKDPSVVITQDLLEEPIDKQLDEVLETNNVFELPNCELSKLEEIS
ParentalDLVTSVLSSPIRREKLALALENEGYIKKLLQLFQACENLENTEGLHHLYEIIRGILFLNKATLFEVMFSD
D..TSVL.SPI..E.LAL.LENE.YIK.LLQLF..CE.L..T.GLHHLYEII.GILFLNK..L.E..FS.
RetrocopyDFITSVLASPIHKERLALILENEDYIKNLLQLFHTCEDLRDTTGLHHLYEIIKGILFLNKTALLEILFSA
ParentalECIMDVVGCLEYDPALAQPKRHREFLTKTAKFKEVIPITDSELRQKIHQTYRVQYIQDIILPTPSVFEEN
ECIMDVVGCLEYDPALAQPKRHREFLT..A.FKEV.PITD.ELRQKIHQTYRVQYI.DI.LP.PS..EEN
RetrocopyECIMDVVGCLEYDPALAQPKRHREFLTQNARFKEVVPITDRELRQKIHQTYRVQYIHDILLPAPSMYEEN
ParentalFLSTLTSFIFFNKVEIVSMLQEDEKFLSEVFAQLTDEATDDDKRRELVNFFKEFCAFSQTLQPQNRDAFF
FLSTL..FIF.NKVEIVSM.Q....FLSEVFAQL.DE.TDDD.RREL..FFKEFCAFSQTLQ....DA.F
RetrocopyFLSTLNTFIFLNKVEIVSMMQDHANFLSEVFAQLRDETTDDDRRRELLFFFKEFCAFSQTLQRSRKDALF
ParentalKTLAKLGILPALEIVMGMDDLQVRSAATDIFSYLVEFSPSMVREFVMQEAQQSDDDILLINVVIEQMICD
KTL..LGILP.L.IVM.M.DLQ.RSAATDIF.YLVE.SPSM.REF.M.EAQ.S.D..L.IN.VIEQM.CD
RetrocopyKTLTELGILPVLKIVMSMEDLQIRSAATDIFTYLVEYSPSMIREFIMEEAQESEDGNLFINLVIEQMMCD
ParentalTDPELGGAVQLMGLLRTLIDPENMLATTNKTEKSEFLNFFYNHCMHVLTAPLLTNTSEDKCEKD
TDPELGGAV.LMGLLRTL..PENMLAT..K.E.SEFLNFFY.HC.H...APL...TSED.CE.D
RetrocopyTDPELGGAVHLMGLLRTLLNPENMLATSSKCERSEFLNFFYHHCIHNFIAPLFVTTSEDICEGD

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_48 retrocopy.

TSS - click to see more details

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab - click to see more details

retro_amel_48 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 18 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG00000003843 1 retrocopy
retro_amel_48 ,
Bos taurus ENSBTAG000000005451 retrocopy
retro_btau_232,
Canis familiaris ENSCAFG000000028601 retrocopy
retro_cfam_226,
Equus caballus ENSECAG000000138191 retrocopy
retro_ecab_23,
Echinops telfairi ENSETEG000000024201 retrocopy
retro_etel_1699,
Felis catus ENSFCAG000000264571 retrocopy
retro_fcat_13,
Homo sapiens ENSG000001380411 retrocopy
retro_hsap_4799,
Loxodonta africana ENSLAFG000000178251 retrocopy
retro_lafr_791,
Myotis lucifugus ENSMLUG000000038751 retrocopy
retro_mluc_994,
Macaca mulatta ENSMMUG000000070011 retrocopy
retro_mmul_238,
Mustela putorius furoENSMPUG000000024351 retrocopy
retro_mputfur_92,
Nomascus leucogenys ENSNLEG000000093381 retrocopy
retro_nleu_1112,
Oryctolagus cuniculus ENSOCUG000000068801 retrocopy
retro_ocun_9,
Otolemur garnettii ENSOGAG000000098371 retrocopy
retro_ogar_140,
Pan troglodytes ENSPTRG000000119331 retrocopy
retro_ptro_3191,
Sus scrofa ENSSSCG000000083981 retrocopy
retro_sscr_1187,
Ictidomys tridecemlineatus ENSSTOG000000062761 retrocopy
retro_itri_63,
Tursiops truncatus ENSTTRG000000000271 retrocopy
retro_ttru_1397,


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