RetrogeneDB ID: retro_lafr_633

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_27:34159821..34160659(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAPKAPK5
• Ensembl ID: ENSLAFG00000017919
• Aliases: None
• Description: None

Sequence

>retro_lafr_633
ATTTTAGAAGATATTAGTAAAGCTCAGAAGAGATACTACTTCCTTAAAAATAATAATGTTAGACCATACACTTATAACAA
GAGCTGTGACTTGTGGTCCCTAGGGTGATTATGTATGGGTTACTGTGTGGATACCCTCCTTTTCACTCCAAATACTGCAG
CCAGACATCCCAAAGGATATGTGGAAAAAAGATCCTGACAGGCAGTTTTGAGTTCCCAGAGGAAGAGTGGAGCCAGATCT
CAGATATGGCCAAAGATGTTGTGGTAAAGTTTCTGAAGATCAAACCAGAAGAGAGACTCACCATCGAGGGAGTGTTGGAC
CCTTCCTGGCTCAGCAGTACTGAGGCCCTGAATACTGTACTGCCCTCCGCTCAACTGATGATGGGTAAGGAAGTGGTGGG
AGGAACCCAGCAGTCTCATGCAGAGCAATTGGACAACATGTGAATCCAGGATCTGAACATCGGCCTCAAACCTTTGCATT
CTGTGACCAACCCCATTGTGAGTAAGAGGAAGTTACTTGGCACCAAACCAAAAGATGGTGCTTATATCCACAACCCTGAG
AATGGGGCTGAGGATTCAATGTTGCCTTGGAAAAGCTCTGAGATATGATTACTCAGTGTATTCTCCCCAGGGCTAGTAAA
GGAGGAAATGAAGATGAGAAGCTGAATGAAGTAATGCAGGAGGTTTGGAAGCATAACCGGGAATGCAAACTCCTAAGAGA
CACTCTGCTGAAGTTTCAGCATTAATAGTTATGGATTCACAGATAGAGTAGACGGACAAAACCAGCAGAAATTGTGAAGC
AAGTGATTGAAATGCAAACCATGTCCCATGAATCTCAA

Alignment

ORF - retro_lafr_633 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.08 %
• Parental protein coverage: 59.45 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  VLEAQRRHQKEKSGIIPTSPTPYTYNKSCDLWSLG-VIIYVMLCGYPPFYSKHHSRT-IPKDM-RRKIMT
          .LE.....QK...........PYTYNKSCDLWSLG.VI.Y..LCGYPPF.SK..S.T.IPKDM...KI.T
Retrocopy ILEDISKAQKRYYFLKNNNVRPYTYNKSCDLWSLG<VIMYGLLCGYPPFHSKYCSQT<IPKDM>GKKILT

Parental  GSFEFPEEEWSQISEMAKDVVRKLLKVKPEERLTIEGVLDHPWLNSTEALDNVLPSAQLMMDKAVVAGIQ
          GSFEFPEEEWSQIS.MAKDVV.K.LK.KPEERLTIEGVLD..WL.STEAL..VLPSAQLMM.K.VV.G.Q
Retrocopy GSFEFPEEEWSQISDMAKDVVVKFLKIKPEERLTIEGVLDPSWLSSTEALNTVLPSAQLMMGKEVVGGTQ

Parental  QAHAEQLANMRIQDLKVSLKPLHSVNNPILRKRKLLGTKPKDVVYIHDRENGAEDS-NVALEKLRDVIAQ
          Q.HAEQL.NM.IQDL...LKPLHSV.NPI..KRKLLGTKPKD..YIH..ENGAEDS.NVALEKL.D.I.Q
Retrocopy QSHAEQLDNM*IQDLNIGLKPLHSVTNPIVSKRKLLGTKPKDGAYIHNPENGAEDS<NVALEKL*DMITQ

Parental  CILPQAAIGENEDEKLNEVMQEAWKYNRECKLLRETLQ-SFSWNGRGFTDKVD-RLKLAEIVKQVIEEQT
          CILP.A..G.NEDEKLNEVMQE.WK.NRECKLLR.TL..SFS.N..GFTD.VD.R.K.AEIVKQVIE.QT
Retrocopy CILPRASKGGNEDEKLNEVMQEVWKHNRECKLLRDTLL>SFSINSYGFTDRVD<RTKPAEIVKQVIEMQT

Parental  MSHESQ
          MSHESQ
Retrocopy MSHESQ

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_633 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000017919	1 retrocopy	retro_lafr_633 ,
Microcebus murinus	ENSMICG00000010509	1 retrocopy	retro_mmur_1443,