RetrogeneDB ID: retro_lafr_1022

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_6:11313047..11313953(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAPK3
• Ensembl ID: ENSLAFG00000017904
• Aliases: None
• Description: None

Sequence

>retro_lafr_1022
GGCACAGTCAGCTCAGCTTATGACCACTTGCACAGGACTCGTGTGGTCATCAAGAAGATCAGCCCCTTAGAGCATCACAC
CACTTCCAGCACAAGCTTCCAGAGATCCAGATATTGCTACATTTCTGCCAGAAGAATGTTATCGGTATCCAAGACATTCT
GTAGGCAGCCACCCTGGGAGCCAGGAGGGATGTCTGCATTGTACAGGCCCCAATGGAGACAAACCTGTACAAGTTGCTCA
AAAGCTGACAGCTGGGAAATGACCATGTCCACTATTTCCTCTACCAGATCCTGTGGGGCCTCAAGTATATTTGCTCAGCC
AACATGCTGCTTGGAAACCTAAGGCCCTCCAACTTGCTCATCAACACCACCTGTGACCTTAAAATCTGTGATTTCAGCCT
GGCCCAGATCCCTGATCCTGAACAGGACCACACCGGCTTTTTGACAGAGTACGTAGCTACACACTGGTACTGGGCACCAG
AGATCAAGCTCAACTCCAAGAGCTATACCCAATCTATTGACACCTGATCTGTGGGTTGCATCCTGGCTGAGATGCTCTCC
AACCAGCCCATCTTCCCCGGCAAGCACTACTTGGATCAGCTTAACTAAATTCTGAGTGTTCTGGGCTCCCCATCCTAAGA
GGACCTGAATTGTATCATCAACATGAAGGCTTGAAGCTACCTAGAATCGCTGCCCACCAAGACCAAGGTGGCCTTGGCCA
AGCTCTTTCCCAAGTCAGACCCCAAAGCCCCTAAACAGGATGTTGACCTTTAACTCCAACAAACAGATCACAGTGGAAGA
AGCATTGGCCCACCCCTACCTGGAGCAGTACTATCACCCCATGGATAAGCTGGTGGCTGATGAAACCTTTGCCTTTAACA
TGGAATTAGATGATCTACCAAAGGAA

Alignment

ORF - retro_lafr_1022 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.92 %
• Parental protein coverage: 93.56 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GPLSSAYDHVRKIRVAIKKISPFEHQT-YCQRTLREIQILLRFRHENVIGIRDILRAPTLEAMRDVYIVQ
          G..SSAYDH....RV.IKKISP.EH.T...Q..L.EIQILL.F...NVIGI.DIL.A.TL.A.RDV.IVQ
Retrocopy GTVSSAYDHLHRTRVVIKKISPLEHHT<HFQHKLPEIQILLHFCQKNVIGIQDIL*AATLGARRDVCIVQ

Parental  DLMETDLYKLLKSQQLSNDHVCYFLYQILRGLKYIHSANVLHRDLKPSNLLINTTCDLKICDFGLARIAD
          ..MET.LYKLLKS.QL.NDHV.YFLYQIL.GLKYI.SAN.L...L.PSNLLINTTCDLKICDF.LA.I.D
Retrocopy APMETNLYKLLKS*QLGNDHVHYFLYQILWGLKYICSANMLLGNLRPSNLLINTTCDLKICDFSLAQIPD

Parental  PEHDHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILSILG
          PE.DHTGFLTEYVAT.WY.APEI.LNSK.YT.SID..SVGCILAEMLSN.PIFPGKHYLDQLN.ILS.LG
Retrocopy PEQDHTGFLTEYVATHWYWAPEIKLNSKSYTQSIDT*SVGCILAEMLSNQPIFPGKHYLDQLN*ILSVLG

Parental  SPSQEDLNCIINMKARNYLQSLPAKTKVAWAKLF-PKSDPKALELLDRMLTFNPNKRITVEEALAHPYLE
          SPS.EDLNCIINMKA..YL.SLP.KTKVA.AKLF.P...PK....L.RMLTFN.NK.ITVEEALAHPYLE
Retrocopy SPS*EDLNCIINMKA*SYLESLPTKTKVALAKLF>PSQTPKP---LNRMLTFNSNKQITVEEALAHPYLE

Parental  QYYDPTDEPVAEEPFTFDMELDDLPKE
          QYY.P.D..VA.E.F.F.MELDDLPKE
Retrocopy QYYHPMDKLVADETFAFNMELDDLPKE

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_1022 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000017108	1 retrocopy	retro_cfam_1254,
Dasypus novemcinctus	ENSDNOG00000002191	1 retrocopy	retro_dnov_1241,
Loxodonta africana	ENSLAFG00000017904	1 retrocopy	retro_lafr_1022 ,
Myotis lucifugus	ENSMLUG00000011284	1 retrocopy	retro_mluc_1697,
Mus musculus	ENSMUSG00000063065	1 retrocopy	retro_mmus_2694,
Pongo abelii	ENSPPYG00000007239	1 retrocopy	retro_pabe_1440,
Rattus norvegicus	ENSRNOG00000019601	1 retrocopy	retro_rnor_831,