RetrogeneDB ID: retro_lafr_1144

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_77:5710137..5711691(+)
• 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_1144
ATGAACCCCAGCGCCCCCAGCTACCCCACGGCCTCGCTCTGCGTGGGGGACCTGCACCCCGACGTGACCGAGGCGATGCT
CCATGAGCAGTTCAGCCCGGCCGGCCCATCCTCTCCGTCCGGGTCTGCAGGGACGTGACCACCCGCCGCTCTTCGGGCTA
AGCCTCTGTGAACTTCCAGCAGCCGGCGGGCGCGGAGCGTGCTTTGAACGCCGTGAATTTTGACGTTATAAAGGGCAAGC
CGGTACGCATCCTGCGGTCTCAGCGTGATCCATCGCTTGGCAAAAGTGGAGTGGGCAACATATTCACTAAAAATTTGGAC
AAATCCATTGATAATAAAGCGTTGTATGATACATTTTCTGCTTTTGGTAACATCCTCTCATGTAAGGTGGTTTGTGACGA
AAATGGTTCCAAGGGCTGTGGATTTGTACATTTTGAGACGCAAGAAGCAGCTGAAAGAGCTATTGAAAAAATGAATGGAA
TGCTTCTTAATGACCGTTAAGTATTTGTTGGGCGATTTAAGTCTCGTAAAGAACGAGAAGCAGAACTCGGAGCTCGGGCA
AAAGAGTTCACCAATGTTTACATCAAGAATTTTGGAGAAGACATGGATGACGAGCGCCTTAAGGATCTCTTTGGCAAGTT
TGGACCTGCCTTAAGTGTGAAAGGAATGACTGACGAAAGTGGAAAATCCAAAGGTTTTGGATTTGTGAGCTTTGAGAGGC
ATGAAGATGCACAGAAAGCTGTGGATGAGATGAACGGAAAGGAGCTCAGTGGGAAACAAATTTATGTTGGTCGAGCTGAG
AAAAAAGTGGAACGACAGACGGAACTTAAGCGCAAATTCGAACAGGTGAAGCAAGACAGGATCACCAGATACCAGGGTGT
TAACTTGTATGTGAGAAGTCTTGATGCCGGTATTGATGATGAACGTCTCCGCAGAGTGTTCTCCATTGGGTACAATCACT
AGCGCAAACGTTATGATGGAGGGCGGTCGCAGCAAAGGTTTTGGTTTTGTATGTTTCTCCTCCCCAGAAGAAGCCAAGCA
GTTACAGAAATGAATGGTAGAATTGTGGCCACCAAGCCTTGTATGTAGCTTCAGCTCAGCGCAAAGAAGAGCGCCAGGCT
CACCCCACTAACCAGTATATGCAGAGAATGGCAAGTGTGAGAGCTGCGCCCAAGCCCGTAATCGACCCCTACCAGCCAGC
ACCTCCTTCAGGTTACTTCATGGCAGCTTTCCCAAGACTCAGAGCCGTGCTGCATACTATCCTCCTAGCCAAACTGCTCA
ATTAAGACCAAGTCCTCGCTGGACTGCTCAGGGTGCCAGCCCTCATCCATTCCAAAATATGCCCGGTGCTATCCGCCCAG
CTGCTCCTAGACCACCATTTAGTACTATGAGACCAGCTTCTTCACAAGTTCCACGAGTCATGTCAGCACAACGTGTTGCT
AACACATCAACACAGACCATGGGTCCCCGTCCTGCAGCAGCTGCTGCCGCGGCTACTCCTGCTGTCCGCACCGTTCCCCA
ATATGAATACGCTGCAGGAGTTCGCAATCCTCAG

Alignment

ORF - retro_lafr_1144 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.42 %
• Parental protein coverage: 85.04 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MNAAASSYPMASLYVGDLHSDVTEAMLYEKFSPAGP-VLSIRVCRDMITRRSLGYAYVNFQQPADAERAL
          MN..A.SYP.ASL.VGDLH.DVTEAML.E.FSPAGP..LS.RVCRD..TRRS.G.A.VNFQQPA.AERAL
Retrocopy MNPSAPSYPTASLCVGDLHPDVTEAMLHEQFSPAGP<ILSVRVCRDVTTRRSSG*ASVNFQQPAGAERAL

Parental  DTMNFDVIKGKPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKG
          ...NFDVIKGKP.RI..SQRDPSL.KSGVGN.F.KNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKG
Retrocopy NAVNFDVIKGKPVRILRSQRDPSLGKSGVGNIFTKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKG

Parental  YAFVHFETQEAADKAIEKMNGMLLNDRKVFVGRFKSRKEREAELGAKAKEFTNVYIKNFGEEVDDESLKE
          ..FVHFETQEAA..AIEKMNGMLLNDR.VFVGRFKSRKEREAELGA.AKEFTNVYIKNFGE..DDE.LK.
Retrocopy CGFVHFETQEAAERAIEKMNGMLLNDR*VFVGRFKSRKEREAELGARAKEFTNVYIKNFGEDMDDERLKD

Parental  LFSQFGKTLSVKVMRDPSGKSKGFGFVSYEKHEDANKAVEEMNGKEISGKVIFVGRAQKKVERQAELKRK
          LF..FG..LSVK.M.D.SGKSKGFGFVS.E.HEDA.KAV.EMNGKE.SGK.I.VGRA.KKVERQ.ELKRK
Retrocopy LFGKFGPALSVKGMTDESGKSKGFGFVSFERHEDAQKAVDEMNGKELSGKQIYVGRAEKKVERQTELKRK

Parental  FEQLKQERISRYQGVNLYIKNLDDTIDDEK-LRKEFSPFGSITSAKVMLEDGRSKGFGFVCFSSPEEATK
          FEQ.KQ.RI.RYQGVNLY...LD..I.D......E.SP.G.ITSA.VM.E.GRSKGFGFVCF.S..E..K
Retrocopy FEQVKQDRITRYQGVNLYVRSLDAGI-DDE>VSAECSPLGTITSANVMMEGGRSKGFGFVCF-SSPEEAK

Parental  -AVTEMNGRIVGSKP-LYVALAQRKEERKAHLTNQYMQRVAGMRALPANAILNQFQPA-AGGYFVPA-VP
          .AVTEMNGRIV..KP.LYVA.AQRKEER.AH.TNQYMQR.A..RA.P........QPA...GYF..A..P
Retrocopy <AVTEMNGRIVATKP<LYVASAQRKEERQAHPTNQYMQRMASVRAAP-KPVIDPYQPAPPSGYFMAA<FP

Parental  QAQGRPPYYTPNQLAQMRPNPRW-QQGGRPQGFQGMPSAIRQSGPRPALRHLAPTGVPTAVQSLAPRAAV
          ..Q.R..YY.P.Q.AQ.RP.PRW..QG..P..FQ.MP.AIR...PRP......P......V........V
Retrocopy KTQSRAAYYPPSQTAQLRPSPRWTAQGASPHPFQNMPGAIRPAAPRPPFSTMRPAS--SQVPRVMSAQRV

Parental  AAAAPRAVAPYKYASSVRSPHPAMQPLQAPQPAVHVQGQE
          A........P...A.......PA.........A..V....
Retrocopy ANTSTQTMGP-RPAAAAAAATPAVRTVPQYEYAAGVRNPQ

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_1144 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,