RetrogeneDB ID: retro_lafr_220

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_1:106981286..106982093(-)
• Located in intron of: ENSLAFG00000014532

Retrocopy information

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

Parental gene information

• Parental gene symbol: GMCL1
• Ensembl ID: ENSLAFG00000002565
• Aliases: None
• Description: None

Sequence

>retro_lafr_220
AATGTGAAAACTGTACTTGGCTATTGCATATCGGTAGCGACCTATGGATTAGATTCTGTAAAAAGAAAGTGCCTTGAATG
GCTTCCAAACAACTTGATGAGTCACCAGAATCTTGAACTTTTTAAAGAACTCAGTATAAACACCATGAAACAGCTCATGA
GTTCCTCTAACTTATTTGGGATACAAGTGGAAATGGATGTATACACAGGTCTTAGAAAGCGGATGTTCCTTCAACTTGTG
CCTTCTTGGAATGGGTCTTTAAAACAGCTTTTGACTGAGACAGATGTGTGGTTTTCTAAGCGGAGAAACGATTTTCAAGG
TATGGCCTTCCTTGAAACTGAGCAAGGGAAACCGTTTGTGTCAGTGTTCAGACATTTAAGGTTACAGTGTATTACTAGTG
ATCTGGCCTCTGCAAGAATTATTGAACAAGATTCTCTAGTACCTTCAGAACGGCTGTCTTCTGTGTATAAACAGCAATGG
TTTGCAATGCTCCGGACAGAGCAAGACAGTGAGGTGGAGCCTCAAGAAATCAATAAGGAAGAACTAGAGGGACATAGCAT
GAGGTGTCTAAGAAAGCTTGCCAAAGATGGTGCATACTGCTGGCAGTGGACAGGTTTTAACTTCAGCTTTGACCTGCTTG
TAACTTAAACCAATCAATACCTCATTTTCAAGCTCAATACACTGAATGAGCCATCTAGCATATCTGTCAGTTTACAGCCT
TGAAGGAGCATAGCATTTAGATTACGTTTGGCCTTTTTTGATAGTAGTGGAAAACTAATATGTAGTAGAACAACTGGATA
TCAAATA

Alignment

ORF - retro_lafr_220 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.39 %
• Parental protein coverage: 51.04 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NVKTVCGYYTSAGTYGLDSVKKKCLEWLLNNLMTHQNVELLRELSINVMKQLIGSSNLFVMQVEMDVYTA
          NVKTV.GY..S..TYGLDSVK.KCLEWL.NNLM.HQN.EL..ELSIN.MKQL..SSNLF..QVEMDVYT.
Retrocopy NVKTVLGYCISVATYGLDSVKRKCLEWLPNNLMSHQNLELFKELSINTMKQLMSSSNLFGIQVEMDVYTG

Parental  LKKWMFLQLVPSWNGSLKQLLTETDVWLSKRRKDFEGIAFLETEQGKPFVSVFRHLRLQYIISDLASARI
          L.K.MFLQLVPSWNGSLKQLLTETDVW.SKRR.DF.G.AFLETEQGKPFVSVFRHLRLQ.I.SDLASARI
Retrocopy LRKRMFLQLVPSWNGSLKQLLTETDVWFSKRRNDFQGMAFLETEQGKPFVSVFRHLRLQCITSDLASARI

Parental  IEQDALVPSEWLSSVYKQQWFAMLRAEQDSEVGPQEINKEELEGHSMRCGRKLAKDGEYCWRWTGFNFGF
          IEQD.LVPSE.LSSVYKQQWFAMLR.EQDSEV.PQEINKEELEGHSMRC.RKLAKDG.YCW.WTGFNF.F
Retrocopy IEQDSLVPSERLSSVYKQQWFAMLRTEQDSEVEPQEINKEELEGHSMRCLRKLAKDGAYCWQWTGFNFSF

Parental  DLLVTYTNRYIIFKRNTLNQPCSGSVSLQPRRSIAFRLRLASFDSSGKLICSRTTGYQI
          DLLVT.TN.Y.IFK.NTLN.P.S.SVSLQP.RSIAFRLRLA.FDSSGKLICSRTTGYQI
Retrocopy DLLVT*TNQYLIFKLNTLNEPSSISVSLQP*RSIAFRLRLAFFDSSGKLICSRTTGYQI

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_220 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 19 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016116	1 retrocopy	retro_amel_1915,
Choloepus hoffmanni	ENSCHOG00000012306	2 retrocopies	retro_chof_1562, retro_chof_802,
Equus caballus	ENSECAG00000016813	2 retrocopies	retro_ecab_1109, retro_ecab_899,
Homo sapiens	ENSG00000087338	1 retrocopy	retro_hsap_3407,
Loxodonta africana	ENSLAFG00000002565	3 retrocopies	retro_lafr_220 , retro_lafr_592, retro_lafr_98,
Myotis lucifugus	ENSMLUG00000009183	2 retrocopies	retro_mluc_1521, retro_mluc_31,
Macaca mulatta	ENSMMUG00000000858	1 retrocopy	retro_mmul_98,
Mus musculus	ENSMUSG00000001157	1 retrocopy	retro_mmus_3665,
Nomascus leucogenys	ENSNLEG00000010132	1 retrocopy	retro_nleu_2993,
Oryctolagus cuniculus	ENSOCUG00000015808	2 retrocopies	retro_ocun_112, retro_ocun_160,
Otolemur garnettii	ENSOGAG00000008408	1 retrocopy	retro_ogar_151,
Pongo abelii	ENSPPYG00000012334	1 retrocopy	retro_pabe_209,
Pan troglodytes	ENSPTRG00000012021	1 retrocopy	retro_ptro_2314,
Pteropus vampyrus	ENSPVAG00000001242	3 retrocopies	retro_pvam_1259, retro_pvam_370, retro_pvam_816,
Sorex araneus	ENSSARG00000004651	1 retrocopy	retro_sara_425,
Sus scrofa	ENSSSCG00000008335	1 retrocopy	retro_sscr_62,
Ictidomys tridecemlineatus	ENSSTOG00000000714	1 retrocopy	retro_itri_59,
Tursiops truncatus	ENSTTRG00000007493	3 retrocopies	retro_ttru_1039, retro_ttru_1647, retro_ttru_1648,
Vicugna pacos	ENSVPAG00000001756	1 retrocopy	retro_vpac_617,