RetrogeneDB ID: retro_lafr_597

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_24:3303178..3304274(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSLAFG00000010739
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_lafr_597
TACCTCAAAGCTGCCCTGTACGTGGGTGACTTGGACCCAGACGTCACCGAGGACATGCTATATAAGAAGTTCAGGCCTGC
TGGTCCTCTGCGCTTCACACGAATCTGTCGTGACCCAGTGACCCGCAGTCCCCTGGGCTATGGCTATGTTAACTTTCGTT
TTCCTGCGGATGCTGAGTGGGCACTCAACACCATGAATTTTGATTTAATTAATGGCAAACCATTTCGCCTCATGTGGTCT
CAGCCAGATGACCGCTTAAGAAAGTCTGGAGTTGGAAACATCTTCATCAAAAACCTGGACAAATCCATAGACAATAGGGC
CCTTTTTTACTTATTTTCTGCTTTTGGGAACATTCTCTCCTGCAAAGTAGTCTGCGATGACAACGGCTCTAAAGGCTATG
CCTACGTACACTTCGACAGCCTGGCCGCTGCCAACAGGGCGATCTGGCACATGAATGGAGTGCGGCTCAACAACCGCCAG
GTGTATGTTGGCCGGTTCAAATTCCCGGAAGAGCGGGCCGCTGAAGTCAGAACCCGGGATAGAGCAACTTTCACCAATGT
GTTCGTTAAAAATTTTGGGGACGACATGGATGACGAAAAACTGAAGGGACTTTTCAGTGAATATGGGCCAACTGAGAGTG
TTAAAGTGATAAGAGATGTCAGTGGGAAATCCAAAGGCTTTGGATTTGTGAGATATGAGACACACGAGGCTGCCCAAAAA
AGCTGTGCTAGACCTTCATGGAAAGTCAATTGATGGGAAAGCGCTGTATGTAGGACGAGCACAGAAGAAAATTGAACGCC
TGGCTGAGTTAAGGCGGAGATTTGAACGGCTGAGATTAAAGGAAAAAAGTCGGCCTCCAGGGGTGCCTATCTATATTAAG
AACCTAGATGAGACCATTGATGATGAAAAACTGAAGGAAGAGTTTTCTTCCTTTGGATCAGTTAGCCGGGCCAAGGTGAT
GATGGAAGTGGGGCAAGGCAAAGGGTTTGGTGTTGTATGCTTCTCCTCTTTTGAAGAGGCTACCAAAGCAGTGGATGAGA
TGAATGGTCGCGTAGTGGGCTCCAAGCCCCTGCATGTCACCTTGGGCCAGGCCAGA

Alignment

ORF - retro_lafr_597 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.84 %
• Parental protein coverage: 55.15 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  YPMASLYVGDLHSDVTEAMLYEKFSPAGPVLSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVI
          Y..A.LYVGDL..DVTE.MLY.KF.PAGP....R.CRD..TR..LGY.YVNF..PADAE.AL.TMNFD.I
Retrocopy YLKAALYVGDLDPDVTEDMLYKKFRPAGPLRFTRICRDPVTRSPLGYGYVNFRFPADAEWALNTMNFDLI

Parental  KGKPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYAFVHFET
          .GKP.R.MWSQ.D..LRKSGVGN.FIKNLDKSIDN.AL...FSAFGNILSCKVVCD.NGSKGYA.VHF..
Retrocopy NGKPFRLMWSQPDDRLRKSGVGNIFIKNLDKSIDNRALFYLFSAFGNILSCKVVCDDNGSKGYAYVHFDS

Parental  QEAADKAIEKMNGMLLNDRKVFVGRFKSRKEREAELGAKAK-EFTNVYIKNFGEEVDDESLKELFSQFGK
          ..AA..AI..MNG..LN.R.V.VGRFK...ER.AE........FTNV..KNFG...DDE.LK.LFS..G.
Retrocopy LAAANRAIWHMNGVRLNNRQVYVGRFKFPEERAAEVRTRDRATFTNVFVKNFGDDMDDEKLKGLFSEYGP

Parental  TLSVKVMRDPSGKSKGFGFVSYEKHEDA-NKAVEEMNGKEISGKVIFVGRAQKKVERQAELKRKFEQLKQ
          T.SVKV.RD.SGKSKGFGFV.YE.HE.A..KAV....GK.I.GK...VGRAQKK.ER.AEL.R.FE.L..
Retrocopy TESVKVIRDVSGKSKGFGFVRYETHEAA>KKAVLDLHGKSIDGKALYVGRAQKKIERLAELRRRFERLRL

Parental  ERISRYQGVNLYIKNLDDTIDDEKLRKEFSPFGSITSAKVMLEDGRSKGFGFVCFSSPEEATKAVTEMNG
          ...SR..GV..YIKNLD.TIDDEKL..EFS.FGS...AKVM.E.G..KGFG.VC................
Retrocopy KEKSRPPGVPIYIKNLDETIDDEKLKEEFSSFGSVSRAKVMMEVGQGKGFGVVCXXXXXXXXXXXXXXXX

Parental  RIVGSKPLYVALAQRK
          R.VGSKPL.V.L.Q..
Retrocopy RVVGSKPLHVTLGQAR

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_597 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,