RetrogeneDB ID: retro_lafr_43

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_54:5988533..5989535(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSLAFG00000006170
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: FAM50A
• Ensembl ID: ENSLAFG00000008766
• Aliases: None
• Description: None

Sequence

>retro_lafr_43
ATGGCCCAGTACAAGGGCACCATGCGGGAGGCGGGCCGCGCCATGCACCTGATCCGGAAGCGGGAGAAGCAGAAGGAGCA
GATGGAGGTGCTGAAGCAGCGCATTGCGGAGGAGACCATCACCAAGTCAAAGGTGGACAAGAAGTTCTCGGCACACTACG
ACGCAGTGGAAGCAGAACTGAAGTCGAGCACGGTGGGCCTGGTGACCCTGAACGACATGAAGGCCAAACAGGAGGCCCTG
CTGAAGGAGCGGGAGATGCAGCTGGCCAAGAAGGAGCAGCTGGAGGAGCGCCGGCTGCAGCTGGAGACACTGCGAGAGAA
AGCGCGAAGGCACCAGCAGAAACGCAAGATCTCTAGCCTGTCCTTCTCAGTGGAAGAGACGGAGGAGGAGGAGGGCGCAG
GTGAGCAGGGGCCTGAGAGGGCGGATGTGACCCAGAAGAGGAAGAACCTGGGGAAGAATCCAGACGTGGACACGAGCTTC
CTGCCGGACCGGGACCGTGAAGAGGAAGAGAATCGCCTGCGGGAGGAGCTGCGCAAAGAGTGGGAGGCTCAGCGCGAGAA
GGTCAAGAGCGAGGAGATGGAGGTCACCTTCAGCTACTGGGATGGCTCAGGGCATCGGCGCACTGTGCGTGTGAACAAGG
GCAGCACTGTGCAGCAGTTCCTTAAGAAGGCCCTGCAGGGCCTGCGCAAGGACTTCAAGGAGCTGCGCGCTGCTGGCGTG
GAGCAGCTCATGTACATCAAGGAGGACCTGATCCTGCCCCACTACCACACCTTCTACGACTTCATCGTCACCAAGGCGCG
TGGCAAGAGCGGGCCGCTCTTCAGCTTCGACGTGCACGATGACGTGCGGCTGCTGAGCGACGCCACCATGGAGAAGGATG
AGTCGCACGCGGGGAAGGTGGTGCTGCGCAGCTGGTACGAGAAGAACAAGCACATCTTCCCAGCCAGCCGCTGGGAGCCC
TACGACCCCGAGAAGAGGTGGGATAAGTACACTATCCGGTGA

Alignment

ORF - retro_lafr_43 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.75 %
• Parental protein coverage: 92.03 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAQYKGAASEAGRAMHLMKKREKQREQMEQMKQRIAEENIMKSNIDKKFSAHYDAVEAELKSSTVGLVTL
          MAQYKG...EAGRAMHL..KREKQ.EQME..KQRIAEE.I.KS..DKKFSAHYDAVEAELKSSTVGLVTL
Retrocopy MAQYKGTMREAGRAMHLIRKREKQKEQMEVLKQRIAEETITKSKVDKKFSAHYDAVEAELKSSTVGLVTL

Parental  NDMKAKQEALVKEREKQLAKKEQSKELQLKLEKLREKERKKEAKRKISSLSFTLEEEEEGAEEEEEVAIY
          NDMKAKQEAL.KERE.QLAKKEQ..E..L.LE.LR..E.......K....S.....E....E.EEE....
Retrocopy NDMKAKQEALLKEREMQLAKKEQLEERRLQLETLR--EKARRHQQKRKISSLSFSVE----ETEEEEGAG

Parental  EEELEREEVITKKRKLGKNPDVDTSFLPDRDREEEENRLREELRQEWEAKQEKIKSEEIEITFSYWDGSG
          E...ER..V..K...LGKNPDVDTSFLPDRDREEEENRLREELR.EWEA..EK.KSEE.E.TFSYWDGSG
Retrocopy EQGPERADVTQKRKNLGKNPDVDTSFLPDRDREEEENRLREELRKEWEAQREKVKSEEMEVTFSYWDGSG

Parental  HRRTVKMKKGNTMQQFLQKALEILRKDFSELRSAGVEQLMYIKEDLIIPHHHSFYDFI-PALQGRS---F
          HRRTV...KG.T.QQFL.KAL..LRKDF.ELR.AGVEQLMYIKEDLI.PH.H.FYDFI.....G.S...F
Retrocopy HRRTVRVNKGSTVQQFLKKALQGLRKDFKELRAAGVEQLMYIKEDLILPHYHTFYDFIVTKARGKSGPLF

Parental  NFDVHDDVRLLSDATVEKDESHAGKVVLRSWYEKNKHIFPASRWEPYDPEKKWDKYTVR
          .FDVHDDVRLLSDAT.EKDESHAGKVVLRSWYEKNKHIFPASRWEPYDPEK.WDKYT.R
Retrocopy SFDVHDDVRLLSDATMEKDESHAGKVVLRSWYEKNKHIFPASRWEPYDPEKRWDKYTIR

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_43 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 12 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000273	1 retrocopy	retro_amel_15,
Felis catus	ENSFCAG00000011399	1 retrocopy	retro_fcat_100,
Homo sapiens	ENSG00000071859	1 retrocopy	retro_hsap_94,
Loxodonta africana	ENSLAFG00000008766	1 retrocopy	retro_lafr_43 ,
Myotis lucifugus	ENSMLUG00000022234	1 retrocopy	retro_mluc_7,
Mustela putorius furo	ENSMPUG00000009476	1 retrocopy	retro_mputfur_145,
Mus musculus	ENSMUSG00000001962	1 retrocopy	retro_mmus_103,
Nomascus leucogenys	ENSNLEG00000014266	1 retrocopy	retro_nleu_109,
Rattus norvegicus	ENSRNOG00000045790	1 retrocopy	retro_rnor_214,
Sorex araneus	ENSSARG00000006465	1 retrocopy	retro_sara_554,
Sus scrofa	ENSSSCG00000025303	1 retrocopy	retro_sscr_56,
Ictidomys tridecemlineatus	ENSSTOG00000004448	10 retrocopies	retro_itri_105, retro_itri_1563, retro_itri_1688, retro_itri_1691, retro_itri_1693, retro_itri_1758, retro_itri_1760, retro_itri_1762, retro_itri_1780, retro_itri_184,