RetrogeneDB ID: retro_lafr_390

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_14:48048610..48049836(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PABPC4
• Ensembl ID: ENSLAFG00000000151
• Aliases: None
• Description: None

Sequence

>retro_lafr_390
ATGAATGTAGCAGCCAAGTACCGCATGGCCTCTCTGTATGTGGGTGACCTACACGCAGATGTCACGGAGGACCTGTTGTT
TAAGAAGTTCAGCACCGTGGGGCCGGTGTTGTCCATCCGCATTTGCAGGGACCTGGTCACGCGCCGCTCCCTGGGCTATG
CCTATGTGAACTTCCTGCACGTGGCTGATGCCCAGAAAGCCCTGGACACCATGAACTTTGACGTGATAAAAGGCAAATCC
ATCCGTCTTATGTGGTCTCAACGTGATGCCTACTTAAGAAAATCTGGAATTGGGAACGTGTTCATCAAGAATCTGGACAA
ATCCATTGACAATAAAACCCTTTATGAACATTTTTCAACTTTTGGGAAGATTCTATCCTCCAAGGTGATGAGTGATGATC
AAGGCTCCAAGGGCTATGCATTTGTGCACTTTCAGAACCAGAGTGCTGCAGACAGGGCCATTGAAGAGATGAATGGGACC
CTGCTCAAGAACTGCAGAGTGTTTGTTAGCCGATTCAAAAGCCGCAAAGATCGAGAATCTGAGCTCAAAAACAAAGCCAG
TGAATTCACCAATGTTTACATCAAAAACTTTGGAGATGACATGGATGATATGAGACTGAAGGAAGTTTTCAGCAAATATG
GTACAACTCTGAGTGTTAAGGTGATGACAGATTCCAGTGGCAAATCCAAAGGCTTTGGCTTTGTGAGTTTTGCTAGCCAT
GAGGCTGCCAAAAATGCTGTGGAAGAAATGAACGGCAAGGACATAAATGGGCAGCTGATATTTGTAGGCCGAGCCCAAAA
GAAGATAGAGCGACAGGCTGAGTTAAAGCAAATGTTTGAGCAGCTGAGACAAGAAAGATTTCGCCGGTGCCGGGGAGTGA
AGCTCTATATTAAGAACCTTGATGACACCATTGATGATGAAAAACTACGGAAGGAATTTGCTTCATTTGGATCAATTAGC
AGAGTTAAGGTAATGCAGGAAGAAGGCCGAAGTAAAGGGTTTGGCTTGATCTGCTTCTCCTCTCATGAGGAAGCTATTAA
AGCAATGACTGAGATGAATGGCCGCATCTTGGGCTCCAAGCCTCTCAACATAGCCCTAGCCCAGAGGAATGAAGAAAGAA
AAACATGCTTTGACAACCAATAGTTGGAAGAGGCGGGGGAATGACAGTCATCCCTGCCTAAATTGTCCTTAGTAAATTTC
AGACCCTGTGTGTTGGCAACTTAGTT

Alignment

ORF - retro_lafr_390 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.8 %
• Parental protein coverage: 66.67 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MNAAASSYPMASLYVGDLHSDVTEAMLYEKFSPAGPVLSIRVCRDMITRRSLGYAYVNFQQPADAERALD
          MN.AA..Y.MASLYVGDLH.DVTE..L..KFS..GPVLSIR.CRD..TRRSLGYAYVNF...ADA..ALD
Retrocopy MNVAAK-YRMASLYVGDLHADVTEDLLFKKFSTVGPVLSIRICRDLVTRRSLGYAYVNFLHVADAQKALD

Parental  TMNFDVIKGKPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGY
          TMNFDVIKGK.IR.MWSQRD..LRKSG.GNVFIKNLDKSIDNK.LY..FS.FG.ILS.KV..D..GSKGY
Retrocopy TMNFDVIKGKSIRLMWSQRDAYLRKSGIGNVFIKNLDKSIDNKTLYEHFSTFGKILSSKVMSDDQGSKGY

Parental  AFVHFETQEAADKAIEKMNGMLLNDRKVFVGRFKSRKEREAELGAKAKEFTNVYIKNFGEEVDDESLKEL
          AFVHF..Q.AAD.AIE.MNG.LL....VFV.RFKSRK.RE.EL..KA.EFTNVYIKNFG...DD..LKE.
Retrocopy AFVHFQNQSAADRAIEEMNGTLLKNCRVFVSRFKSRKDRESELKNKASEFTNVYIKNFGDDMDDMRLKEV

Parental  FSQFGKTLSVKVMRDPSGKSKGFGFVSYEKHEDANKAVEEMNGKEISGKVIFVGRAQKKVERQAELKRKF
          FS..G.TLSVKVM.D.SGKSKGFGFVS...HE.A..AVEEMNGK.I.G..IFVGRAQKK.ERQAELK..F
Retrocopy FSKYGTTLSVKVMTDSSGKSKGFGFVSFASHEAAKNAVEEMNGKDINGQLIFVGRAQKKIERQAELKQMF

Parental  EQLKQERISRYQGVNLYIKNLDDTIDDEKLRKEFSPFGSITSAKVMLEDGRSKGFGFVCFSSPEEATKAV
          EQL.QER..R..GV.LYIKNLDDTIDDEKLRKEF..FGSI...KVM.E.GRSKGFG..CFSS.EEA.KA.
Retrocopy EQLRQERFRRCRGVKLYIKNLDDTIDDEKLRKEFASFGSISRVKVMQEEGRSKGFGLICFSSHEEAIKAM

Parental  TEMNGRIVGSKPLYVALAQRKEERKAHLTNQYMQ-RVAGMRALPANAILNQFQPAAGGYFV
          TEMNGRI.GSKPL..ALAQR.EERK....NQ....R..GM...PA...L..FQ....G..V
Retrocopy TEMNGRILGSKPLNIALAQRNEERKTCFDNQ*LE<RGGGMTVIPA*IVLSKFQTLCVGNLV

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_390 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 16 parental genes, and 39 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011535	2 retrocopies	retro_amel_107, retro_amel_676,
Bos taurus	ENSBTAG00000017125	3 retrocopies	retro_btau_1492, retro_btau_28, retro_btau_656,
Canis familiaris	ENSCAFG00000003081	2 retrocopies	retro_cfam_45, retro_cfam_837,
Choloepus hoffmanni	ENSCHOG00000005327	3 retrocopies	retro_chof_1150, retro_chof_1182, retro_chof_1274,
Equus caballus	ENSECAG00000009396	2 retrocopies	retro_ecab_2, retro_ecab_502,
Felis catus	ENSFCAG00000015254	2 retrocopies	retro_fcat_116, retro_fcat_545,
Loxodonta africana	ENSLAFG00000000151	3 retrocopies	retro_lafr_1144, retro_lafr_390 , retro_lafr_597,
Microcebus murinus	ENSMICG00000016633	1 retrocopy	retro_mmur_675,
Myotis lucifugus	ENSMLUG00000012068	2 retrocopies	retro_mluc_228, retro_mluc_397,
Monodelphis domestica	ENSMODG00000017657	2 retrocopies	retro_mdom_1090, retro_mdom_1805,
Mustela putorius furo	ENSMPUG00000014414	2 retrocopies	retro_mputfur_152, retro_mputfur_546,
Mus musculus	ENSMUSG00000011257	7 retrocopies	retro_mmus_2006, retro_mmus_2326, retro_mmus_2327, retro_mmus_798, retro_mmus_801, retro_mmus_803, retro_mmus_805,
Rattus norvegicus	ENSRNOG00000015642	2 retrocopies	retro_rnor_175, retro_rnor_92,
Sarcophilus harrisii	ENSSHAG00000018139	1 retrocopy	retro_shar_823,
Sus scrofa	ENSSSCG00000003660	3 retrocopies	retro_sscr_1210, retro_sscr_974, retro_sscr_975,
Tursiops truncatus	ENSTTRG00000014340	2 retrocopies	retro_ttru_1117, retro_ttru_246,