RetrogeneDB ID: retro_lafr_698

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_300:142835..143796(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSLAFG00000000867
• Aliases: None
• Description: None

Sequence

>retro_lafr_698
AATTGTGATAGTGAAAAAACAGCTGCACTGTGGGCCAAAATCTGTCATCAAGTTGAGTATTGTTTTGGCGACTTTAATTT
GCTATGGGACAAATTTTTAAAGGAACAGATCAAACTGGGTGAAGGTTGGGTACCTTTGGAGATAATGATAAAAATCAACA
GGTTAAACCATCGAACAACAGACTTTAATGTAATAGGAGAAACACTGAATAAGTGAAAGGTGGAACTGATAGAAATAAGT
GAAGATAAAATTAAAGTCAGAAGATCTCTAAGCAAGCCCCTCCCTGAAGTGACAGATGATTATAAAAATGATGTGAAAAA
GAAATCTGTTTATATGAAAGGCTTCTCTACTGATGCAATCCCTGATGATATAAAAGAATGGTTAGAAGACAAAGGTGAAG
TACTAAATATTCAGACGAGAAGAACCTTGCACAAAGCACTCAAAGGATTAATATCTATGTTTGATAGCACTGAATCTGCT
AACAAGGTCATAGAGACCCCTGGCCAGAAGTACAAAGACACAAACCTGCTAATACTTTTCCAAGAAGATTAATTTGCAAA
GAAGAATGACAAAAGAAAGCAAAGTGGAAGCTAAATTACAAACTAAACAAAAGCAAGAATTAAAACAGAAAATAGCAGAA
GACGTTGAACTGAAATCTCTAGAAGGAAAGATTGGCTGCTTGCTAAAATTTTGGAGCGACTTTAGATGATCAAACCTGTA
GAGAAGATTTGCACATCATCTTCTCACATTATGGAGAAATAAAATGAATAAACTTTGTCAGAGGAGTAGAAGAAGGAGTA
ATTCTACTTAAAAAGATAAAGAAGTACTGGATAAAGCCAAATATGTAAGTAATGGTGAACTACAATTAAGGAACAATGAA
GTGACCTGGAAGTACTAGGAGAGGTGAAAAAAGGCAGCACTGAAAAAAAAAAAAAAAAAAAAAAAACGGAAGATCAACAA
G

Alignment

ORF - retro_lafr_698 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.3 %
• Parental protein coverage: 77.01 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  NGDSEKMAALEAKICHQIEYYFGDFNLPRDKFLKEQIKLDEGWVPLEIMIKFNRLNRLTTDFNVIVEALS
          N.DSEK.AAL.AKICHQ.EY.FGDFNL..DKFLKEQIKL.EGWVPLEIMIK.NRLN..TTDFNVI.E.L.
Retrocopy NCDSEKTAALWAKICHQVEYCFGDFNLLWDKFLKEQIKLGEGWVPLEIMIKINRLNHRTTDFNVIGETLN

Parental  KSKVELMEISEDKTKIRRSPSKPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNILMR
          K.KVEL.EISEDK.K.RRS.SKPLPEVTD.YKNDVK..SVY.KGF.TDA..DDIKEWLEDKG.VLNI..R
Retrocopy K*KVELIEISEDKIKVRRSLSKPLPEVTDDYKNDVKKKSVYMKGFSTDAIPDDIKEWLEDKGEVLNIQTR

Parental  RTLHKAFKGSIFVVFDSIESAKKFVETPGQKYKDTDLLILFKEDYFAKKNEERKQN-KLEAKLRAKQEQE
          RTLHKA.KG.....FDS.ESA.K..ETPGQKYKDT.LLILF.ED.FAKKN..RKQ..........KQE..
Retrocopy RTLHKALKG-LISMFDSTESANKVIETPGQKYKDTNLLILFQED*FAKKNDKRKQS>EAKLQTKQKQEL-

Parental  EKQKLAEDAEMKSLEEKMGCLLKFSGD-LDDQTCREDLQDLFSSHGEIKWIDFVRGAKEGVILFKEKAK-
          .KQK.AED.E.KSLE.K.GCLLKF..D.LDDQTCREDL...FS..GEIK.I.FVRG..EGVIL.K.K.K.
Retrocopy -KQKIAEDVELKSLEGKIGCLLKFWSD>LDDQTCREDLHIIFSHYGEIK*INFVRGVEEGVILLK-KIK<

Parental  EALDKAKDASNGNLQLRNKEVTW-EVLEGEV-EKAALKKILEDQQESLNK
          E.LDKAK..SNG.LQLRN.EVTW.EVL.GEV..KAAL...........NK
Retrocopy EVLDKAKYVSNGELQLRNNEVTW<EVL-GEV>KKAALXXXXXXXXRKINK

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_698 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 18 parental genes, and 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007763	5 retrocopies	retro_chof_1125, retro_chof_1292, retro_chof_1380, retro_chof_185, retro_chof_2593,
Dasypus novemcinctus	ENSDNOG00000013450	1 retrocopy	retro_dnov_2038,
Echinops telfairi	ENSETEG00000004614	1 retrocopy	retro_etel_2056,
Homo sapiens	ENSG00000138385	1 retrocopy	retro_hsap_448,
Gorilla gorilla	ENSGGOG00000011507	3 retrocopies	retro_ggor_2914, retro_ggor_434, retro_ggor_791,
Gorilla gorilla	ENSGGOG00000023471	4 retrocopies	retro_ggor_2834, retro_ggor_2915, retro_ggor_433, retro_ggor_792,
Loxodonta africana	ENSLAFG00000000867	3 retrocopies	retro_lafr_698 , retro_lafr_745, retro_lafr_982,
Macropus eugenii	ENSMEUG00000001650	1 retrocopy	retro_meug_1908,
Myotis lucifugus	ENSMLUG00000016316	1 retrocopy	retro_mluc_2493,
Macaca mulatta	ENSMMUG00000023051	2 retrocopies	retro_mmul_1153, retro_mmul_529,
Monodelphis domestica	ENSMODG00000008227	1 retrocopy	retro_mdom_1080,
Nomascus leucogenys	ENSNLEG00000004958	3 retrocopies	retro_nleu_1039, retro_nleu_177, retro_nleu_3011,
Otolemur garnettii	ENSOGAG00000029768	1 retrocopy	retro_ogar_1642,
Pongo abelii	ENSPPYG00000012919	3 retrocopies	retro_pabe_3408, retro_pabe_3641, retro_pabe_424,
Pan troglodytes	ENSPTRG00000012620	1 retrocopy	retro_ptro_2509,
Rattus norvegicus	ENSRNOG00000007998	1 retrocopy	retro_rnor_405,
Tupaia belangeri	ENSTBEG00000009056	4 retrocopies	retro_tbel_1065, retro_tbel_1269, retro_tbel_3318, retro_tbel_4012,
Tursiops truncatus	ENSTTRG00000002152	2 retrocopies	retro_ttru_1926, retro_ttru_466,