RetrogeneDB ID:

retro_lafr_1218

Retrocopy
location
Organism:Elephant (Loxodonta africana)
Coordinates:scaffold_9:40111296..40113176(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSLAFG00000028852
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:HSPA8
Ensembl ID:ENSLAFG00000030312
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_lafr_1218
GCCCGCGGCCCGGCTATCGGCATCGACCTGGGCACCACCTACTCGTGCGTGGGGGTCTTCCAACATGGCAAGGTCGAGAT
CATCGCCAACGACCAGGGCAACCGCACCACCCCCAGCTACGTAGCCTTCACCGACACCGAGCGCCTGATCGGCGACGCCG
CCAAGAACCAGGTGGGCCATGAACCTCACCAACACCATCTTCGACGCTCAGAGGCTGATCGGGACGCAAGTTCGAGGACG
CCACAGTGCAGTCGGACATGAAACACTGGCCGTTCTGGGTGGTGAGCGAGGGAGGGAAGCCCAAAGTGCAGGTGGAGTAC
AAGGGCGAAATCAAGACCTTCTTCCCGGAGGAGATCTCCTCCATGGTCCTCACGAAGATGAAGGAGATCGCCGAAGCCTA
CCTGGGGGGCAAGGTGCAGAGCGCGGTCATCACCGTGCCGGCCTATTTCAATGACTCGCAGCGCCAGGCCACCAAGGACG
CGGGCACCATCACCGGCCTCAACGTGCTGCGCATCATCAACGAGCCCACGGCGGCGGCCATCGCTTACGGCCTGGACAAG
AAGGGCTGCGCGGGCGGCGAGAAGAACGTGCTCATCTTTGACCTGGGTGGCGGCACCTTCGACGTGTCCATCCTGACCAT
CGAGGACGGCATCTTCGAGGTGAAGTCCACCGCCGGGGACACCCACCTGGGCGGCGAGGACTTCGACAACCGCATGGTGA
GCCACCTGGCGGAGGAGTTCAAGCGCAAGCACAAGAAGGACATTGGGCCCAACAAGCGGGCCGTGCGGCGGCTGCGCACC
GCCTGCGAGCGCGCCAAGCGCACCCTGAGCTCGTCTACGCAGGCCAGCATCGAGATCGACTCGCTCTACGAGGGCGTGGA
CTTCTACACGTCCATCACCCGCGCCCGCTTCGAGGAGCTCAACGCCGACCTCTTCCGCGGGACCCTGGAACCGGTGGAGA
AGGCGCTGCGCGACGCCAAGCTGGACAAGGGCCAAATACAAGAGATCGTCCTGGTGGGCGGCTCCACGCGCATCCCCAAG
ATCCAGAAGCTGCTGCAGGATTTCTTCAATGGCAAGGAGCTGAACAAGAGCATCAACCCCGACGAGGCGGTGGCTTACGG
TGCCGCGGTGCAGGCGGCCATCCTCATCGGGGACAAGTCGGAGAACGTGCAAGACCTGCTGCTGCTCGACGTGACCCCGT
TGTCGCTGGGCATCGAGACGGCTGGCGGCGTCATGACCCCACTCATCAAGAGAAACACCACCATCCCTACCAAGCAGACG
CAGACCTTCACGACCTACTCAGACAACCAGAGCAGCGTGCTGGTGCAGGTGTACGAGGGCGAACGGGCCATGACCAAGGA
CAATAACCTGCTGGGCAAATTCGACCTGACCGGGATTCCCCCCGCGCCCCGCGGCGTCCCCCAGATCGAGGTCACCTTCG
ACATCGACGCCAACGGCATCCTCAACGTCACCGCCGCCGACAAGAGCACCGGTAAGGAAAACAAAATCACCATCACCAAC
GACAAGGGTCGTCTGAGCAAGGATGACATTGACCGGATGGTGCAGGAGGCGGAGCGGTACAAGTCGGAAGATGAGGCCAA
TCGCGACCGGGTCGCCGCCAAAAACGCAGTGGAGTCCTATACCTACAACATCAAGCAGACGGTGGAAGACGAGAAACTGA
GGGGCAAGATTAGCGAGCAGGACAAAAACAAGATCCTCGACAAGTGCCAGGAGGTGATCAGCTGGCTCGACCGAAACCAG
ATGGCAGAGAAAGACGAGTATGAACACAAGCAGAAGGAGCTCGAAAGAGTGTGCAACCCCATCATCAGCAAACTTTACCA
AGGCGGCCCTGGCGGTGGCGGGTCCGGAGCCTCCGGGGGA

ORF - retro_lafr_1218 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.05 %
Parental protein coverage: 96.46 %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalSKGPAVGIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERLIGDAAKNQV-AMNPTNTVFDA
..GPA.GIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERLIGDAAKNQV.AMN.TNT.FDA
RetrocopyARGPAIGIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERLIGDAAKNQV>AMNLTNTIFDA
ParentalKRLIG-RRFDDAVVQSDMKHWPFVVVNDAGRPKVQVEYKGETKSFYPEEVSSMVLTKMKEIAEAYLGKTV
.RLIG.R.F.DA.VQSDMKHWPF.VV...G.PKVQVEYKGE.K.F.PEE.SSMVLTKMKEIAEAYLG..V
RetrocopyQRLIG>RKFEDATVQSDMKHWPFWVVSEGGKPKVQVEYKGEIKTFFPEEISSMVLTKMKEIAEAYLGGKV
ParentalTNAVVTVPAYFNDSQRQATKDAGTIAGLNVLRIINEPTAAAIAYGLDKK--VGAERNVLIFDLGGGTFDV
..AV.TVPAYFNDSQRQATKDAGTI.GLNVLRIINEPTAAAIAYGLDKK...G.E.NVLIFDLGGGTFDV
RetrocopyQSAVITVPAYFNDSQRQATKDAGTITGLNVLRIINEPTAAAIAYGLDKKGCAGGEKNVLIFDLGGGTFDV
ParentalSILTIEDGIFEVKSTAGDTHLGGEDFDNRMVNHFIAEFKRKHKKDISENKRAVRRLRTACERAKRTLSSS
SILTIEDGIFEVKSTAGDTHLGGEDFDNRMV.H...EFKRKHKKDI..NKRAVRRLRTACERAKRTLSSS
RetrocopySILTIEDGIFEVKSTAGDTHLGGEDFDNRMVSHLAEEFKRKHKKDIGPNKRAVRRLRTACERAKRTLSSS
ParentalTQASIEIDSLYEGIDFYTSITRARFEELNADLFRGTLDPVEKALRDAKLDKSQIHDIVLVGGSTRIPKIQ
TQASIEIDSLYEG.DFYTSITRARFEELNADLFRGTL.PVEKALRDAKLDK.QI..IVLVGGSTRIPKIQ
RetrocopyTQASIEIDSLYEGVDFYTSITRARFEELNADLFRGTLEPVEKALRDAKLDKGQIQEIVLVGGSTRIPKIQ
ParentalKLLQDFFNGKELNKSINPDEAVAYGAAVQAAILSGDKSENVQDLLLLDVTPLSLGIETAGGVMTVLIKRN
KLLQDFFNGKELNKSINPDEAVAYGAAVQAAIL.GDKSENVQDLLLLDVTPLSLGIETAGGVMT.LIKRN
RetrocopyKLLQDFFNGKELNKSINPDEAVAYGAAVQAAILIGDKSENVQDLLLLDVTPLSLGIETAGGVMTPLIKRN
ParentalTTIPTKQTQTFTTYSDNQPGVLIQVYEGERAMTKDNNLLGKFELTGIPPAPRGVPQIEVTFDIDANGILN
TTIPTKQTQTFTTYSDNQ..VL.QVYEGERAMTKDNNLLGKF.LTGIPPAPRGVPQIEVTFDIDANGILN
RetrocopyTTIPTKQTQTFTTYSDNQSSVLVQVYEGERAMTKDNNLLGKFDLTGIPPAPRGVPQIEVTFDIDANGILN
ParentalVSAVDKSTGKENKITITNDKGRLSKEDIERMVQEAEKYKAEDEKQRDKVSSKNSLESYAFNMKATVEDEK
V.A.DKSTGKENKITITNDKGRLSK.DI.RMVQEAE.YK.EDE..RD.V..KN..ESY..N.K.TVEDEK
RetrocopyVTAADKSTGKENKITITNDKGRLSKDDIDRMVQEAERYKSEDEANRDRVAAKNAVESYTYNIKQTVEDEK
ParentalLQGKISDEDKQKILDKCNEIINWLDKNQTAEKEEFEHQQKELEKVCNPIITKLYQSAGGMPGGMPGGMPG
L.GKIS..DK.KILDKC.E.I.WLD.NQ.AEK.E.EH.QKELE.VCNPII.KLYQ...G.PGG...G..G
RetrocopyLRGKISEQDKNKILDKCQEVISWLDRNQMAEKDEYEHKQKELERVCNPIISKLYQ---GGPGGGGSGASG
ParentalG
G
RetrocopyG

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

Loxodonta africana was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Loxodonta africana was not studied using ChIP-Seq data.

EST - click to see more details

Loxodonta africana was not studied using EST data.

TSS - click to see more details

Loxodonta africana was not studied using FANTOM5 data.

Lab - click to see more details

retro_lafr_1218 was not experimentally validated.

Retrocopy orthology:
Loxodonta africana 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 35 parental genes, and 119 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000048842 retrocopies
retro_acar_21, retro_acar_6,
Ailuropoda melanoleuca ENSAMEG000000084251 retrocopy
retro_amel_126,
Anas platyrhynchos ENSAPLG000000106671 retrocopy
retro_apla_6,
Bos taurus ENSBTAG000000131621 retrocopy
retro_btau_354,
Canis familiaris ENSCAFG000000116663 retrocopies
retro_cfam_140, retro_cfam_191, retro_cfam_509,
Ciona intestinalis ENSCING000000096651 retrocopy
retro_cint_12,
Callithrix jacchus ENSCJAG000000076485 retrocopies
retro_cjac_2388, retro_cjac_3306, retro_cjac_3898, retro_cjac_4057, retro_cjac_721,
Cavia porcellus ENSCPOG000000041693 retrocopies
retro_cpor_1072, retro_cpor_619, retro_cpor_938,
Ciona savignyi ENSCSAVG000000085881 retrocopy
retro_csav_3,
Dipodomys ordii ENSDORG000000154671 retrocopy
retro_dord_16,
Equus caballus ENSECAG000000135102 retrocopies
retro_ecab_291, retro_ecab_628,
Echinops telfairi ENSETEG000000109961 retrocopy
retro_etel_43,
Ficedula albicollis ENSFALG000000058121 retrocopy
retro_falb_18,
Felis catus ENSFCAG000000011326 retrocopies
retro_fcat_132, retro_fcat_1331, retro_fcat_1571, retro_fcat_1775, retro_fcat_556, retro_fcat_79,
Homo sapiens ENSG000001099718 retrocopies
retro_hsap_2384, retro_hsap_2710, retro_hsap_2758, retro_hsap_340, retro_hsap_3698, retro_hsap_4892, retro_hsap_4896, retro_hsap_68,
Gallus gallus ENSGALG000000065121 retrocopy
retro_ggal_8,
Gorilla gorilla ENSGGOG000000083818 retrocopies
retro_ggor_1053, retro_ggor_1810, retro_ggor_1888, retro_ggor_1918, retro_ggor_2501, retro_ggor_3054, retro_ggor_3057, retro_ggor_360,
Loxodonta africana ENSLAFG00000030312 4 retrocopies
retro_lafr_1218 , retro_lafr_391, retro_lafr_790, retro_lafr_797,
Meleagris gallopavo ENSMGAG000000019291 retrocopy
retro_mgal_9,
Myotis lucifugus ENSMLUG000000048343 retrocopies
retro_mluc_1800, retro_mluc_2300, retro_mluc_777,
Macaca mulatta ENSMMUG000000046967 retrocopies
retro_mmul_1536, retro_mmul_2188, retro_mmul_2628, retro_mmul_2632, retro_mmul_580, retro_mmul_778, retro_mmul_963,
Monodelphis domestica ENSMODG000000129582 retrocopies
retro_mdom_127, retro_mdom_99,
Mustela putorius furoENSMPUG000000058109 retrocopies
retro_mputfur_1048, retro_mputfur_1056, retro_mputfur_1144, retro_mputfur_131, retro_mputfur_188, retro_mputfur_309, retro_mputfur_627, retro_mputfur_694, retro_mputfur_958,
Mus musculus ENSMUSG000000156568 retrocopies
retro_mmus_2244, retro_mmus_2584, retro_mmus_26, retro_mmus_2621, retro_mmus_2840, retro_mmus_316, retro_mmus_351, retro_mmus_620,
Nomascus leucogenys ENSNLEG000000074198 retrocopies
retro_nleu_119, retro_nleu_1258, retro_nleu_1261, retro_nleu_1582, retro_nleu_175, retro_nleu_1781, retro_nleu_370, retro_nleu_64,
Oryctolagus cuniculus ENSOCUG000000155334 retrocopies
retro_ocun_1308, retro_ocun_53, retro_ocun_584, retro_ocun_753,
Oreochromis niloticus ENSONIG000000047591 retrocopy
retro_onil_2,
Pongo abelii ENSPPYG000000039879 retrocopies
retro_pabe_183, retro_pabe_2193, retro_pabe_2254, retro_pabe_2260, retro_pabe_2261, retro_pabe_3153, retro_pabe_355, retro_pabe_3804, retro_pabe_3808,
Pelodiscus sinensis ENSPSIG000000124502 retrocopies
retro_psin_17, retro_psin_5,
Pan troglodytes ENSPTRG000000044045 retrocopies
retro_ptro_1743, retro_ptro_2507, retro_ptro_272, retro_ptro_3259, retro_ptro_3264,
Ictidomys tridecemlineatus ENSSTOG000000037561 retrocopy
retro_itri_51,
Taeniopygia guttata ENSTGUG000000004911 retrocopy
retro_tgut_7,
Takifugu rubripes ENSTRUG000000052651 retrocopy
retro_trub_30,
Tursiops truncatus ENSTTRG000000111396 retrocopies
retro_ttru_1507, retro_ttru_1650, retro_ttru_1696, retro_ttru_35, retro_ttru_741, retro_ttru_808,
Xiphophorus maculatus ENSXMAG000000016021 retrocopy
retro_xmac_20,


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