RetrogeneDB ID: retro_lafr_304

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_12:8509818..8510951(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZDHHC6
• Ensembl ID: ENSLAFG00000008129
• Aliases: None
• Description: None

Sequence

>retro_lafr_304
GTGGGTACATTCTGCTTGGTTATAAAGTTTGAAAATCTCCAAAAATTAAAGAGACCGTGTCACTGGGGTCCCATCATAGC
CCTTCATGTTACAACAATGTGTTCTATGGTGGCCATGATTGACTCAGTAGTGTGATGTTGGCCCTTAGATACAACTGGAG
GAAGTGTGAATTTTGTCATGGTGTTAAATTGAACAATCATGATTCTTTATAATTACTTCAGTGCCATGTTTGTGGGGCCT
GGCTTTGTCCCTTTGAACTAGAAACTGAAAATTCTCAAGATAGCATGTATCCCCAGTATTGTAAAGTCTGCCAAGTACAC
AAGGTGCCCCATTCATATCACTGAAGAAAGTGCAACAGATGGGTGATGAAGATGGACCATGACTGTCCTTGGATCAACAA
CTTTTGTGGCAGCCAAAATCATGCTTCATCCTCACTGTTTCTCCTTTTAGCACCACTGGGTTATATTCATGCTCCTTTTA
TTTTCGTTACGACTGTGTACACACAGCTTTATAATTGGCTCTCCTCCGGGTGGAACATGGTAAAGACTGACATGAGTGCA
GCCCAGAGAGGGCCTCTTCCAGTTGTTCTTTTTGGATTGGCTGCATTTGCTGCCACCTTATCTGCCTTGGGATTAGCTAT
AGGAAGAACTGTAGCTGTTGGGATGTTGTTTTTTACTCAGAGGAAAATAATTCTCGGAAACAAAACTCCATTAATCATGG
ATTGAAGAGAAGGCAAAAGGTGTCCAATTCACTATTACCAACTAGATGAAGTCTTTGTTTTTCCTTATGATTTGGGAAGT
AGCTGGAAGAACTTTAAACAAGTGTTTACGTGGTCAGGGCTTCCTGAAGGAGGTGGATTACATTAGCCAGTAAGAGAAGG
CTGTCACCAGTGCACCTTCACAATAGAACAGTTGAAACAAAAAGCAGATGAGAGAGTCAGAAGTGTTCTCAATAAAGTAA
TAGAAGATTATAGTGGAGCCTGCTGTCCTTTAAATAAAGGAATCAAGACCTTCTTTACAAGCCCCTGCACTGAAGAACCT
CGAATAAGGTTACAGAAAGGGGAGTTCATTTTAGCCACAAGAGGCTTCCGATACTGGCTGTATGGAGACAAACTTCTTGA
CGATCGATTCCTT

Alignment

ORF - retro_lafr_304 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.57 %
• Parental protein coverage: 91.53 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGTFCSVIKFENLQELKRLCHWGPIIALGVIAICSTMAMIDSVLWYWPLHTTGGSVNFIMLINWTIMILY
          .GTFC.VIKFENLQ.LKR.CHWGPIIAL.V...CS..AMIDSV...WPL.TTGGSVNF.M..N.TIMILY
Retrocopy VGTFCLVIKFENLQKLKRPCHWGPIIALHVTTMCSMVAMIDSVV*CWPLDTTGGSVNFVMVLN*TIMILY

Parental  NYFNAVFVGPGFVPLGWK-PENSQDSMYLQYCKVCQAYKAPRSHHCRKCNRCVMKMDHHCPWINNCCGYQ
          NYF.A.FVGPGFVPL..K..ENSQDSMY.QYCKVCQ..K.P.S.H.RKCNR.VMKMDH.CPWINN.CG.Q
Retrocopy NYFSAMFVGPGFVPLN*K<TENSQDSMYPQYCKVCQVHKVPHSYH*RKCNRWVMKMDHDCPWINNFCGSQ

Parental  NHASFTLFLLLAPLGCIHAAFIFIMTMYTQLYNRLSFGWNTVRIDMSAARRDPLPLVPFGLAAFAATLFA
          NHAS..LFLLLAPLG.IHA.FIF..T.YTQLYN.LS.GWN.V..DMSAA.R.PLP.V.FGLAAFAATL.A
Retrocopy NHASSSLFLLLAPLGYIHAPFIFVTTVYTQLYNWLSSGWNMVKTDMSAAQRGPLPVVLFGLAAFAATLSA

Parental  LGLAIGTTIAVGMLFFIQMKIVLRNKTSIESWIEEKAKDRIQYYQLDEVFVFPYDLGSRWKNFKQVFTWS
          LGLAIG.T.AVGMLFF.Q.KI.L.NKT.......E.....I.YYQLDEVFVFPYDLGS.WKNFKQVFTWS
Retrocopy LGLAIGRTVAVGMLFFTQRKIILGNKTPLIMD*REGKRCPIHYYQLDEVFVFPYDLGSSWKNFKQVFTWS

Parental  GVPEGDGLEWPIREGCHQYTLTIEQLKQKADKRVRSVRYKVIEDYSGACCPLNKGIKTFFTSPCTEEPRI
          G.PEG.GL..P.REGCHQ.T.TIEQLKQKAD.RVRSV..KVIEDYSGACCPLNKGIKTFFTSPCTEEPRI
Retrocopy GLPEGGGLH*PVREGCHQCTFTIEQLKQKADERVRSVLNKVIEDYSGACCPLNKGIKTFFTSPCTEEPRI

Parental  RLQKGEFILATRGLRYWLYGDKLLDDSFI
          RLQKGEFILATRG.RYWLYGDKLLDD.F.
Retrocopy RLQKGEFILATRGFRYWLYGDKLLDDRFL

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_304 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.

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015401	1 retrocopy	retro_amel_1120,
Canis familiaris	ENSCAFG00000010960	1 retrocopy	retro_cfam_2178,
Choloepus hoffmanni	ENSCHOG00000012828	1 retrocopy	retro_chof_1480,
Felis catus	ENSFCAG00000030784	1 retrocopy	retro_fcat_1193,
Loxodonta africana	ENSLAFG00000008129	1 retrocopy	retro_lafr_304 ,
Mustela putorius furo	ENSMPUG00000002043	1 retrocopy	retro_mputfur_668,
Mus musculus	ENSMUSG00000024982	1 retrocopy	retro_mmus_1740,
Otolemur garnettii	ENSOGAG00000030535	1 retrocopy	retro_ogar_1652,
Ictidomys tridecemlineatus	ENSSTOG00000013840	1 retrocopy	retro_itri_308,
Tarsius syrichta	ENSTSYG00000009673	2 retrocopies	retro_tsyr_1653, retro_tsyr_1771,