RetrogeneDB ID: retro_lafr_141

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_0:67671939..67673305(+)
• Located in intron of: ENSLAFG00000005788

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSLAFG00000010393
• Aliases: None
• Description: None

Sequence

>retro_lafr_141
ACCATGTTGCTGTGAGTCACCTGGAGGCTAGCGGCCAGGGCCTTAACTGTGGCTCCTGCACTGAAGTCTGGGGCACCCAT
TCAGGGGTTGCACTTACGTATTATGGATCATACTCCCCAGTTGGCTGTTCCCTCAGATACAGTCCCTGCTCCACAGGTAG
AGTCTGTGCTGCGATCTCTCTATATGGATGTGCAGCTACAACTCCTCTGGACCCTGGTCCTTAATGCCATGCTCCCTTAC
GCAGTCAACTACTATGGGAACCCACACTCCTGGACACATGCTTACGGCTGGGAGAGTGAAGCAGCCATGGAACATGCTCA
CCAGCAAGCAGCATCTCTGATTGGGGCCGACCCTTGTGAGATCATTTTCACCAGTGGTGCTACTGAATTCAACAACACAG
CAATTAAGGGGGTGGCTAGGTTCTGTAAGTCACAGAAAAAGCACTTAATCACCACCCAGACTGAACACAAATTTGTCTTG
GACTCCTGCCATCCACTAGAAGCTGAGGGCTTCTAGGTCACCTACCAGCCAGTGCAGAAGAGTGGGATCATTGACCTAAA
GGAACTAGAGGCTACCATCCAGCCAGATACCAGTCTGGTCTCGGTCGGGACTGTGAACAATGAAACCGGAGTGAAGCAAT
CCATTGTGGAAATAGGGTGAATTTCCAATTCCAGAAAGATATATTTCCACACCGATGCTGCCTAGGTCATTGGAAAAATC
CCACATGACATCAACATGAAAATTGATCTCATGAGCATCAGTGGTCACAAAATCTATGGTCCAAAAAGGGTTGGTGCCAT
CTACATTCACCACTGGCCTCGTGTGCATGTGGAGACCCTGCAGAGTGGAGGGATTAGGAGTGGGGTATGCGGTCTTGGAC
AGAGCCCACACCCTTGGTGGTGGGGCAGGGGCTGTGTGTGAAGTGACACAGCAAGAGATGGAGTATGACCACAAGCAGAT
CTCAAAGTTAGCAGACTAACTGACTCCGAAGATATTGAAGAGCCTTCCAGATGTGGTGATGAATGGGGACCCTGAGCATC
ATTACCCAGGCTGCATCAAGCTCAACTTTGCATACGTGGAAGGGGAGAGTCTGCTGATGGCACTCAAGGATGTCACCTTA
TTCTCAGAGGACACTTGGACCTCTGCTTCCCTGAAGCCCTCTTATGCCCTTAGAGCAACTGGCACTGATGAGCATTTAGC
TCATTCTTCCATCAGGTTTGGCTTTGGCTGCTTCACTGCAGAGGAAGAAGTGGACTACACATTGGAGACGTGCATCCAGC
CTGTGAAGCATCTTCAAGAAATGAGCCCTCTCTGGGAGATGGTGCAGGATGGTGTTGACCTCAAGAGCATCAAGTGGACT
CAACAC

Alignment

ORF - retro_lafr_141 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.26 %
• Parental protein coverage: 98.49 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TMLLRVVWRRVTAALTAAPRSKSGAPIRGLRLRVVDHAPQSAIPSDTVPAPEAEPVLRPLYMDVQATTPL
          TMLL.V.WR....ALT.AP..KSGAPI.GL.LR..DH.PQ.A.PSDTVPAP..E.VLR.LYMDVQ....L
Retrocopy TMLL*VTWRLAARALTVAPALKSGAPIQGLHLRIMDHTPQLAVPSDTVPAPQVESVLRSLYMDVQLQL-L

Parental  DPRVLDAMLPYLVNYYGNPHSRTHAYGWESEAAMEHARQQVASLIGADPREIIFTSGATESNNIAIKGVA
          ...VL.AMLPY.VNYYGNPHS.THAYGWESEAAMEHA.QQ.ASLIGADP.EIIFTSGATE.NN.AIKGVA
Retrocopy WTLVLNAMLPYAVNYYGNPHSWTHAYGWESEAAMEHAHQQAASLIGADPCEIIFTSGATEFNNTAIKGVA

Parental  RFYKSRKKHLITTQTEHKCVLDSCRSLEAEGFQVTYLPVQKSGIINLKELEAAIQPDTSLVSVMTVNNEI
          RF.KS.KKHLITTQTEHK.VLDSC..LEAEGF.VTY.PVQKSGII.LKELEA.IQPDTSLVSV.TVNNE.
Retrocopy RFCKSQKKHLITTQTEHKFVLDSCHPLEAEGF*VTYQPVQKSGIIDLKELEATIQPDTSLVSVGTVNNET

Parental  GVKQPIAEIGRICSSRKVYFHTDAAQAVGKIPLDVNDMKIDLMSISGHKIYGPKGVGAIYIRRRPRVRVE
          GVKQ.I.EIG.I..SRK.YFHTDAA...GKIP.D.N.MKIDLMSISGHKIYGPK.VGAIYI...PRV.VE
Retrocopy GVKQSIVEIG*ISNSRKIYFHTDAA*VIGKIPHDIN-MKIDLMSISGHKIYGPKRVGAIYIHHWPRVHVE

Parental  ALQSGGGQ-ERGMRSGTVPTPLVV-GLGAACEVAQQEMEYDHKRISKLAERLTQKIMKSLPDVVMNGDPE
          .LQSGG...E.GMRS.T.PTPLVV.G.GA.CEV.QQEMEYDHK.ISKLA..LT.KI.KSLPDVVMNGDPE
Retrocopy TLQSGGIR<EWGMRSWTEPTPLVV<GAGAVCEVTQQEMEYDHKQISKLAD*LTPKILKSLPDVVMNGDPE

Parental  HHYPGCINLSFAYVEGESLLMALKDVALSSGSACTSASLEPSYVLRAIGTDEDLAHSSIRFGIGRFTTEE
          HHYPGCI.L.FAYVEGESLLMALKDV.L.S....TSASL.PSY.LRA.GTDE.LAHSSIRFG.G.FT.EE
Retrocopy HHYPGCIKLNFAYVEGESLLMALKDVTLFSEDTWTSASLKPSYALRATGTDEHLAHSSIRFGFGCFTAEE

Parental  EVDYTVEKCIQHVKRLREMSPLWEMVQDGIDLKSIKWTQH
          EVDYT.E.CIQ.VK.L.EMSPLWEMVQDG.DLKSIKWTQH
Retrocopy EVDYTLETCIQPVKHLQEMSPLWEMVQDGVDLKSIKWTQH

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_141 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000010393	1 retrocopy	retro_lafr_141 ,
Oryctolagus cuniculus	ENSOCUG00000017050	1 retrocopy	retro_ocun_1214,
Tarsius syrichta	ENSTSYG00000005561	1 retrocopy	retro_tsyr_412,
Xenopus tropicalis	ENSXETG00000007430	1 retrocopy	retro_xtro_67,