RetrogeneDB ID:

retro_lafr_476

Retrocopy
location
Organism:Elephant (Loxodonta africana)
Coordinates:scaffold_18:22411569..22412825(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:HSPD1
Ensembl ID:ENSLAFG00000000053
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_lafr_476
ATGCTCCGATTACCTGCAGTCCTTTGACAGAGGAGGCCAGCATCCAGGGTACCGGCTTCTCATCTCACTCAGGCTTATGC
CAAAGATGTAAAACTTAGTGCAGATGCCCAAGGCTTAATGCTTCAAGGAGTAGATCTTTTAGCTGATGCTGTAGCCATTA
CTATGGGGCCAAAGGAAAGAACCGTGATAACTGAACAGAATTGGGGAAGTCCCAAAGCAACAAAAGATGGTGTGACTGTT
GTAAAGTCCATTGACTTAAAGGATAAATACAAGAATATTGGGGCCAAATTCATTCAGGATGTTGCCAATAACACGAATGA
ACAGGCAGGGGATGGCATCACCATTGCTACTGTCCTGGCACACTCTATTGCTAAGGAATGCTTCGAGAAGATGAGCAAAG
GTGTTAACCCAGTGGAAATCAGGAGAGGTGTAATGTTAGCTGTTGATATAGTAATTGCTGAACTGAAGAAGCAGTCTAAA
CCTGTGACAACTCCTGAAGAAATTGCTCAGGTTGCTATGATTTCTGCAAAGGGAGACAAAGAGATTGGCAACATCATTTC
TGATGCAATGAAAAAGGTTTGAAGAAGGGGTGTCATCACAGCAAAGGATGGAAAAAAATTGAATGATGACTTAGAAATTA
CTGAAGGCATGAAGTTTGAGTGAGGTTATATTTCCCAACACTTTATTAATACATCAAATGGTCAAAAACGTGAATTCCAG
GATGCCTATGTTCTATTGAGTGAAAAGAAAATTTCTAGTGTCCGTCCATTGTACCTGCTCTTGAAATTGCCAGTGCTCAC
CGTAAGCCTTTGGTCATAATTGCTGAAGATGTTGATGGAGAAGCTCTAAGTACCCTTGTTTTGAATAGGCTAAAAGTTGG
TCTTCAGGTCATAGCAGTCAAAGCTCCAGGTTTTGTTGACAACAGAAAGAACCAGCTTAAAGACATGGCTATTGCTACTG
GTAATGCAGTATTTGGAGAAGAAGGATTGACTTTAAATCTTGAAGATGTTCAAGCTCATGATTTAGGAAAAGTTGGAGAG
GTCATTGTGACCAAAGATGATACTATGCTCTTGAAAAGAAAAGGTGATAAGGCTCAAATAGAAAAACATATTCAAGAAAT
CATTCAGCAGTTAGAAATCACAACTAGTGAATATGAGAAGGAAAAGCTCAATGAACGCCTGGCAGAACTTTCCGAGAGAG
TATCTGTGCTAAAAGTTGGTAGGACAAGCAATGCTGAAGTGAATGAAAAGAAAGAC

ORF - retro_lafr_476 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.43 %
Parental protein coverage: 73.12 %
Number of stop codons detected: 3
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMLRLPAVLRQMRPVSRVLASHLTRAYAKDVKFGADARALMLQGVDLLADAVAVTMGPKGRTVIIEQSWGS
MLRLPAVL.Q.RP.SRV.ASHLT.AYAKDVK..ADA..LMLQGVDLLADAVA.TMGPK.RTVI.EQ.WGS
RetrocopyMLRLPAVL*QRRPASRVPASHLTQAYAKDVKLSADAQGLMLQGVDLLADAVAITMGPKERTVITEQNWGS
ParentalPKVTKDGVTVAKSIDLKDKYKNIGAKLVQDVANNTNEEAGDGTTTATVLARSIAKEGFEKISKGANPVEI
PK.TKDGVTV.KSIDLKDKYKNIGAK..QDVANNTNE.AGDG.T.ATVLA.SIAKE.FEK.SKG.NPVEI
RetrocopyPKATKDGVTVVKSIDLKDKYKNIGAKFIQDVANNTNEQAGDGITIATVLAHSIAKECFEKMSKGVNPVEI
ParentalRRGVMLAVDAVIAELKKQSKPVTTPEEIAQVATISANGDKEVGNIISDAMKKVGRKGVITVKDGKTLNDE
RRGVMLAVD.VIAELKKQSKPVTTPEEIAQVA.ISA.GDKE.GNIISDAMKKV.R.GVIT.KDGK.LND.
RetrocopyRRGVMLAVDIVIAELKKQSKPVTTPEEIAQVAMISAKGDKEIGNIISDAMKKV*RRGVITAKDGKKLNDD
ParentalLEIIEGMKFDRGYISPYFINTSKGQKCEFQDAYVLLSEKKISSVQ-SIVPALEIANAHRKPLVIIAEDVD
LEI.EGMKF..GYIS..FINTS.GQK.EFQDAYVLLSEKKISSV..SIVPALEIA.AHRKPLVIIAEDVD
RetrocopyLEITEGMKFE*GYISQHFINTSNGQKREFQDAYVLLSEKKISSVR<SIVPALEIASAHRKPLVIIAEDVD
ParentalGEALSTLVLNRLKVGLQVVAVKAPGFGDNRKNQLKDMAIATGGAVFGEEGLTLNLEDVQAHDLGKVGEVI
GEALSTLVLNRLKVGLQV.AVKAPGF.DNRKNQLKDMAIATG.AVFGEEGLTLNLEDVQAHDLGKVGEVI
RetrocopyGEALSTLVLNRLKVGLQVIAVKAPGFVDNRKNQLKDMAIATGNAVFGEEGLTLNLEDVQAHDLGKVGEVI
ParentalVTKDDAMLLKGKGDKAQIEKRIQEIIEQLEITTSEYEKEKLNERLAKLSDGVAVLKVGGTSDVEVNEKKD
VTKDD.MLLK.KGDKAQIEK.IQEII.QLEITTSEYEKEKLNERLA.LS..V.VLKVG.TS..EVNEKKD
RetrocopyVTKDDTMLLKRKGDKAQIEKHIQEIIQQLEITTSEYEKEKLNERLAELSERVSVLKVGRTSNAEVNEKKD

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_476 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 25 parental genes, and 94 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000137701 retrocopy
retro_amel_771,
Bos taurus ENSBTAG000000125861 retrocopy
retro_btau_988,
Canis familiaris ENSCAFG000000108654 retrocopies
retro_cfam_1185, retro_cfam_1620, retro_cfam_2165, retro_cfam_614,
Choloepus hoffmanni ENSCHOG000000074015 retrocopies
retro_chof_1105, retro_chof_1300, retro_chof_1822, retro_chof_2000, retro_chof_2397,
Callithrix jacchus ENSCJAG000000039906 retrocopies
retro_cjac_1516, retro_cjac_1534, retro_cjac_1975, retro_cjac_3172, retro_cjac_3400, retro_cjac_4096,
Dasypus novemcinctus ENSDNOG000000132263 retrocopies
retro_dnov_1990, retro_dnov_2113, retro_dnov_2512,
Echinops telfairi ENSETEG000000091844 retrocopies
retro_etel_1440, retro_etel_426, retro_etel_885, retro_etel_925,
Homo sapiens ENSG000001443817 retrocopies
retro_hsap_1006, retro_hsap_2770, retro_hsap_2987, retro_hsap_3151, retro_hsap_3494, retro_hsap_3930, retro_hsap_4018,
Gorilla gorilla ENSGGOG000000082676 retrocopies
retro_ggor_1927, retro_ggor_2069, retro_ggor_2361, retro_ggor_2698, retro_ggor_800, retro_ggor_985,
Loxodonta africana ENSLAFG00000000053 1 retrocopy
retro_lafr_476 ,
Macropus eugenii ENSMEUG000000119872 retrocopies
retro_meug_1688, retro_meug_224,
Myotis lucifugus ENSMLUG000000008714 retrocopies
retro_mluc_1458, retro_mluc_2280, retro_mluc_2348, retro_mluc_601,
Macaca mulatta ENSMMUG000000104891 retrocopy
retro_mmul_83,
Monodelphis domestica ENSMODG000000122893 retrocopies
retro_mdom_427, retro_mdom_493, retro_mdom_756,
Mustela putorius furoENSMPUG000000078183 retrocopies
retro_mputfur_1118, retro_mputfur_245, retro_mputfur_434,
Mus musculus ENSMUSG000000259805 retrocopies
retro_mmus_1225, retro_mmus_2494, retro_mmus_3206, retro_mmus_439, retro_mmus_706,
Nomascus leucogenys ENSNLEG000000068747 retrocopies
retro_nleu_1349, retro_nleu_2238, retro_nleu_229, retro_nleu_657, retro_nleu_675, retro_nleu_691, retro_nleu_787,
Otolemur garnettii ENSOGAG000000340535 retrocopies
retro_ogar_2335, retro_ogar_2420, retro_ogar_2740, retro_ogar_3221, retro_ogar_3497,
Pongo abelii ENSPPYG000000130465 retrocopies
retro_pabe_2040, retro_pabe_2244, retro_pabe_2476, retro_pabe_2887, retro_pabe_848,
Pteropus vampyrus ENSPVAG000000083061 retrocopy
retro_pvam_250,
Rattus norvegicus ENSRNOG000000145259 retrocopies
retro_rnor_1000, retro_rnor_1006, retro_rnor_1308, retro_rnor_1578, retro_rnor_1585, retro_rnor_2812, retro_rnor_2835, retro_rnor_596, retro_rnor_905,
Ictidomys tridecemlineatus ENSSTOG000000284701 retrocopy
retro_itri_224,
Tarsius syrichta ENSTSYG000000005136 retrocopies
retro_tsyr_1091, retro_tsyr_1181, retro_tsyr_1445, retro_tsyr_2082, retro_tsyr_395, retro_tsyr_804,
Tursiops truncatus ENSTTRG000000034173 retrocopies
retro_ttru_1661, retro_ttru_1798, retro_ttru_951,
Xenopus tropicalis ENSXETG000000075091 retrocopy
retro_xtro_63,




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