RetrogeneDB ID:

retro_lafr_1220

Retrocopy
location
Organism:Elephant (Loxodonta africana)
Coordinates:scaffold_9:47075930..47076560(+)
Located in intron of:ENSLAFG00000009503
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:ATP6V1E1
Ensembl ID:ENSLAFG00000003802
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_lafr_1220
ATGGCCCTCAGTGATGCTGACATGCAAAAGCAGATTAAGCACATGGTGGCTTTCATTGAACAAGAGGCCAGTAAGGTAGA
AGAAATGGATGCAAAGGCAGAAGAAGGGTTCAACATTGAGAGAGGTCATCTTGTGTAAACCCAAAGACTGAAGATTACAG
AATACTCTGAGAAGAAAGAAAAACAAATTGAGCAGCAGAAGAAAATTCACATGTCCAATTTGATGAATCAAGTAAGACTG
AAAATCCTCAGAACAAGAGACCTTATCACAGACCTACTAAATGAAGCAAAACAGAGACTCAGCAAGGTGGTAAAAGATAC
AGCCAAGTACCAACTGCTGCTGGATGGACTGGTCCTCTAGGGTTTCTGCCAGTCGCTCGAGCCCCAAATGATTGCTCATT
GCAGGAAACAGGATTTCCCTCTGGTAAAGGCTTCAGTGCAAAAAGCAATCCCTACATACAAAATTGCCACCAAAAAAGAT
GTTGAGGCCTGAATTGATCAGGAGACCTAACTGACTGAGGACATAGATGGTGGTGTTGAGATCTATAATGCAGATCATAA
GATAAAGGTTTCCAACACCCTAGAAAGCCAACTGGATCTCATAGCCCAGCAGATGATGCCAGAAGTACAA

ORF - retro_lafr_1220 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 77.21 %
Parental protein coverage: 93.89 %
Number of stop codons detected: 4
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMALSDADVQKQIKHMMAFIEQEANEKAEEIDAKAEEEFNIEKGRLVQTQRLKIMEYYEKKEKQIEQQKKI
MALSDAD.QKQIKHM.AFIEQEA..K.EE.DAKAEE.FNIE.G.LV.TQRLKI.EY.EKKEKQIEQQKKI
RetrocopyMALSDADMQKQIKHMVAFIEQEAS-KVEEMDAKAEEGFNIERGHLV*TQRLKITEYSEKKEKQIEQQKKI
ParentalQMSNLMNQARLKVLRARDDLITDLLNEAKQRLSKVVKDTTRYQVLLDGLVLQGLYQLLEPRMIVRCRKQT
.MSNLMNQ.RLK.LR.RD.LITDLLNEAKQRLSKVVKDT..YQ.LLDGLVL.G..Q.LEP.MI..CRKQ.
RetrocopyHMSNLMNQVRLKILRTRD-LITDLLNEAKQRLSKVVKDTAKYQLLLDGLVL*GFCQSLEPQMIAHCRKQ-
ParentalSHSFLFFQAAVQKAIPMYKIATKRDVDVQIDQEAYLPEDIAGGVEIYNGDRKIKVSNTLESRLDLIAQQM
...F....A.VQKAIP.YKIATK.DV...IDQE..L.EDI.GGVEIYN.D.KIKVSNTLES.LDLIAQQM
Retrocopy--DFPLVKASVQKAIPTYKIATKKDVEA*IDQET*LTEDIDGGVEIYNADHKIKVSNTLESQLDLIAQQM
ParentalMPEVR
MPEV.
RetrocopyMPEVQ

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_1220 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 30 parental genes, and 79 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000174892 retrocopies
retro_amel_116, retro_amel_1502,
Bos taurus ENSBTAG000000142381 retrocopy
retro_btau_244,
Canis familiaris ENSCAFG000000161517 retrocopies
retro_cfam_1050, retro_cfam_1260, retro_cfam_1354, retro_cfam_1379, retro_cfam_1446, retro_cfam_1997, retro_cfam_73,
Callithrix jacchus ENSCJAG000000172771 retrocopy
retro_cjac_1160,
Cavia porcellus ENSCPOG000000245593 retrocopies
retro_cpor_172, retro_cpor_580, retro_cpor_76,
Dasypus novemcinctus ENSDNOG000000145923 retrocopies
retro_dnov_2037, retro_dnov_44, retro_dnov_688,
Equus caballus ENSECAG000000164872 retrocopies
retro_ecab_165, retro_ecab_84,
Echinops telfairi ENSETEG000000192832 retrocopies
retro_etel_1384, retro_etel_6,
Felis catus ENSFCAG000000080814 retrocopies
retro_fcat_153, retro_fcat_602, retro_fcat_61, retro_fcat_654,
Homo sapiens ENSG000001311003 retrocopies
retro_hsap_1126, retro_hsap_145, retro_hsap_21,
Gorilla gorilla ENSGGOG000000150272 retrocopies
retro_ggor_105, retro_ggor_235,
Loxodonta africana ENSLAFG00000003802 4 retrocopies
retro_lafr_1220 , retro_lafr_123, retro_lafr_134, retro_lafr_742,
Microcebus murinus ENSMICG000000106436 retrocopies
retro_mmur_1214, retro_mmur_1234, retro_mmur_813, retro_mmur_886, retro_mmur_971, retro_mmur_978,
Myotis lucifugus ENSMLUG000000148762 retrocopies
retro_mluc_312, retro_mluc_57,
Macaca mulatta ENSMMUG000000214774 retrocopies
retro_mmul_1102, retro_mmul_139, retro_mmul_370, retro_mmul_873,
Monodelphis domestica ENSMODG000000184524 retrocopies
retro_mdom_1456, retro_mdom_1853, retro_mdom_248, retro_mdom_489,
Mustela putorius furoENSMPUG000000181092 retrocopies
retro_mputfur_23, retro_mputfur_4,
Mus musculus ENSMUSG000000192101 retrocopy
retro_mmus_122,
Nomascus leucogenys ENSNLEG000000078391 retrocopy
retro_nleu_18,
Oryctolagus cuniculus ENSOCUG000000069641 retrocopy
retro_ocun_88,
Otolemur garnettii ENSOGAG000000138865 retrocopies
retro_ogar_1255, retro_ogar_1401, retro_ogar_2930, retro_ogar_6, retro_ogar_839,
Ochotona princeps ENSOPRG000000045912 retrocopies
retro_opri_184, retro_opri_539,
Procavia capensis ENSPCAG000000160941 retrocopy
retro_pcap_455,
Pongo abelii ENSPPYG000000115601 retrocopy
retro_pabe_189,
Rattus norvegicus ENSRNOG000000119051 retrocopy
retro_rnor_383,
Sarcophilus harrisii ENSSHAG000000083002 retrocopies
retro_shar_501, retro_shar_780,
Sus scrofa ENSSSCG000000007673 retrocopies
retro_sscr_788, retro_sscr_789, retro_sscr_83,
Ictidomys tridecemlineatus ENSSTOG000000220313 retrocopies
retro_itri_579, retro_itri_630, retro_itri_64,
Tarsius syrichta ENSTSYG000000106795 retrocopies
retro_tsyr_1093, retro_tsyr_1812, retro_tsyr_23, retro_tsyr_532, retro_tsyr_797,
Tursiops truncatus ENSTTRG000000159311 retrocopy
retro_ttru_1,


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