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 symbol: ATP6V1E1
• Ensembl ID: ENSLAFG00000003802
• Aliases: None
• Description: None

Sequence

>retro_lafr_1220
ATGGCCCTCAGTGATGCTGACATGCAAAAGCAGATTAAGCACATGGTGGCTTTCATTGAACAAGAGGCCAGTAAGGTAGA
AGAAATGGATGCAAAGGCAGAAGAAGGGTTCAACATTGAGAGAGGTCATCTTGTGTAAACCCAAAGACTGAAGATTACAG
AATACTCTGAGAAGAAAGAAAAACAAATTGAGCAGCAGAAGAAAATTCACATGTCCAATTTGATGAATCAAGTAAGACTG
AAAATCCTCAGAACAAGAGACCTTATCACAGACCTACTAAATGAAGCAAAACAGAGACTCAGCAAGGTGGTAAAAGATAC
AGCCAAGTACCAACTGCTGCTGGATGGACTGGTCCTCTAGGGTTTCTGCCAGTCGCTCGAGCCCCAAATGATTGCTCATT
GCAGGAAACAGGATTTCCCTCTGGTAAAGGCTTCAGTGCAAAAAGCAATCCCTACATACAAAATTGCCACCAAAAAAGAT
GTTGAGGCCTGAATTGATCAGGAGACCTAACTGACTGAGGACATAGATGGTGGTGTTGAGATCTATAATGCAGATCATAA
GATAAAGGTTTCCAACACCCTAGAAAGCCAACTGGATCTCATAGCCCAGCAGATGATGCCAGAAGTACAA

Alignment

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:

Parental  MALSDADVQKQIKHMMAFIEQEANEKAEEIDAKAEEEFNIEKGRLVQTQRLKIMEYYEKKEKQIEQQKKI
          MALSDAD.QKQIKHM.AFIEQEA..K.EE.DAKAEE.FNIE.G.LV.TQRLKI.EY.EKKEKQIEQQKKI
Retrocopy MALSDADMQKQIKHMVAFIEQEAS-KVEEMDAKAEEGFNIERGHLV*TQRLKITEYSEKKEKQIEQQKKI

Parental  QMSNLMNQARLKVLRARDDLITDLLNEAKQRLSKVVKDTTRYQVLLDGLVLQGLYQLLEPRMIVRCRKQT
          .MSNLMNQ.RLK.LR.RD.LITDLLNEAKQRLSKVVKDT..YQ.LLDGLVL.G..Q.LEP.MI..CRKQ.
Retrocopy HMSNLMNQVRLKILRTRD-LITDLLNEAKQRLSKVVKDTAKYQLLLDGLVL*GFCQSLEPQMIAHCRKQ-

Parental  SHSFLFFQAAVQKAIPMYKIATKRDVDVQIDQEAYLPEDIAGGVEIYNGDRKIKVSNTLESRLDLIAQQM
          ...F....A.VQKAIP.YKIATK.DV...IDQE..L.EDI.GGVEIYN.D.KIKVSNTLES.LDLIAQQM
Retrocopy --DFPLVKASVQKAIPTYKIATKKDVEA*IDQET*LTEDIDGGVEIYNADHKIKVSNTLESQLDLIAQQM

Parental  MPEVR
          MPEV.
Retrocopy MPEVQ

Legend:

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

Expression

RNA-Seq

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

ChIP-Seq

Loxodonta africana was not studied using ChIP-Seq data.

EST

Loxodonta africana was not studied using EST data.

TSS

Loxodonta africana was not studied using FANTOM5 data.

Lab

retro_lafr_1220 was not experimentally validated.

Homology

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.

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Parental genes homology:

Parental genes homology involve 30 parental genes, and 79 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017489	2 retrocopies	retro_amel_116, retro_amel_1502,
Bos taurus	ENSBTAG00000014238	1 retrocopy	retro_btau_244,
Canis familiaris	ENSCAFG00000016151	7 retrocopies	retro_cfam_1050, retro_cfam_1260, retro_cfam_1354, retro_cfam_1379, retro_cfam_1446, retro_cfam_1997, retro_cfam_73,
Callithrix jacchus	ENSCJAG00000017277	1 retrocopy	retro_cjac_1160,
Cavia porcellus	ENSCPOG00000024559	3 retrocopies	retro_cpor_172, retro_cpor_580, retro_cpor_76,
Dasypus novemcinctus	ENSDNOG00000014592	3 retrocopies	retro_dnov_2037, retro_dnov_44, retro_dnov_688,
Equus caballus	ENSECAG00000016487	2 retrocopies	retro_ecab_165, retro_ecab_84,
Echinops telfairi	ENSETEG00000019283	2 retrocopies	retro_etel_1384, retro_etel_6,
Felis catus	ENSFCAG00000008081	4 retrocopies	retro_fcat_153, retro_fcat_602, retro_fcat_61, retro_fcat_654,
Homo sapiens	ENSG00000131100	3 retrocopies	retro_hsap_1126, retro_hsap_145, retro_hsap_21,
Gorilla gorilla	ENSGGOG00000015027	2 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	ENSMICG00000010643	6 retrocopies	retro_mmur_1214, retro_mmur_1234, retro_mmur_813, retro_mmur_886, retro_mmur_971, retro_mmur_978,
Myotis lucifugus	ENSMLUG00000014876	2 retrocopies	retro_mluc_312, retro_mluc_57,
Macaca mulatta	ENSMMUG00000021477	4 retrocopies	retro_mmul_1102, retro_mmul_139, retro_mmul_370, retro_mmul_873,
Monodelphis domestica	ENSMODG00000018452	4 retrocopies	retro_mdom_1456, retro_mdom_1853, retro_mdom_248, retro_mdom_489,
Mustela putorius furo	ENSMPUG00000018109	2 retrocopies	retro_mputfur_23, retro_mputfur_4,
Mus musculus	ENSMUSG00000019210	1 retrocopy	retro_mmus_122,
Nomascus leucogenys	ENSNLEG00000007839	1 retrocopy	retro_nleu_18,
Oryctolagus cuniculus	ENSOCUG00000006964	1 retrocopy	retro_ocun_88,
Otolemur garnettii	ENSOGAG00000013886	5 retrocopies	retro_ogar_1255, retro_ogar_1401, retro_ogar_2930, retro_ogar_6, retro_ogar_839,
Ochotona princeps	ENSOPRG00000004591	2 retrocopies	retro_opri_184, retro_opri_539,
Procavia capensis	ENSPCAG00000016094	1 retrocopy	retro_pcap_455,
Pongo abelii	ENSPPYG00000011560	1 retrocopy	retro_pabe_189,
Rattus norvegicus	ENSRNOG00000011905	1 retrocopy	retro_rnor_383,
Sarcophilus harrisii	ENSSHAG00000008300	2 retrocopies	retro_shar_501, retro_shar_780,
Sus scrofa	ENSSSCG00000000767	3 retrocopies	retro_sscr_788, retro_sscr_789, retro_sscr_83,
Ictidomys tridecemlineatus	ENSSTOG00000022031	3 retrocopies	retro_itri_579, retro_itri_630, retro_itri_64,
Tarsius syrichta	ENSTSYG00000010679	5 retrocopies	retro_tsyr_1093, retro_tsyr_1812, retro_tsyr_23, retro_tsyr_532, retro_tsyr_797,
Tursiops truncatus	ENSTTRG00000015931	1 retrocopy	retro_ttru_1,