RetrogeneDB ID: retro_lafr_603

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_24:35953049..35954283(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP4R2
• Ensembl ID: ENSLAFG00000000513
• Aliases: None
• Description: None

Sequence

>retro_lafr_603
ATGGACGTTGTGGGGCTACAGGAGGTGCTGAAAGATTTTGAGAAGAGGGAGGAAAAGGAAGTTTGTCCTGTTCTGAATCA
GCTTTTTTGTCATGTAGCCAAACTGGAGAAACAATCATACAATGGTCCCAATTTAAAGGCTATTTTATTTTCAAACTGGA
GAAAGTGATGGATGATTTCAGAACTTCAGCTCCTGAATCAAGAGGCCGTCCCAACCTTAATGTAGAATACATTTCCTTCG
ATAAAATGAATTAAAGACTACTGAAAATTGTCACTGGATTTAATGGTGTCTCTTTTACTATTCAACGATTATGTGAATTG
CTAACAGATCCAAGGAGAAACTACACAGGAACAGACAAATTTCTCAGAGGAGTAGAAAAGAATGTGATGGTTGTAGTCTG
TGTTTATCCTTCTTCAGAGAAAAACAATGCCAATGGTTTTAAATTGAATGAATGGTATCACGTTTCCTGGAAACTCACCA
AGTTATACTGAGAGGTCTAATATAAATGGGCCTGGTACGCTCAGACCGCTTAATTGACCAAAGATTTCTTTGTCAGCCAT
CATGACGACGACTGGTTTGCCTGAGAACACAGAAGAGTCCAACTTACAGCAAAATGAGGACAAAAACAACAGTGACTCCC
TGACACCTGAATCAGAAGGTTCCTTGGTGAGCCCCCCAAAAAGTAAACATCCAAATGAAGATGCTATGGAAGCTGAGGGG
CATGAGGTAAAAAGACGTAGATGTGACAAAGAAGGTGAAGTAAGAGAGACAGCCAGTCAAACAACTTCCACTGAAATTTC
TTCAGTTAAAGTAGAAGAAACAGAAGCGTCATCTTCATCTCAGGGTAAAGATAAAGAAAGTATTGTACCAGACAGCACTG
TACGGAAGAGGATGAAGAGGAGAATGAAGAGGAAGAAGAGTCTTCTATGGCGTAAAAAGAAATGGTCCCAGAAAGAAAAA
ATCAAGAAAAAGAATCTGATGAAACCTTAGCTGTGAATGAAAAGATTTCTGAGGAAAATCATCAAATGGAGGAATCTGAT
CTATCTCAAGCTGAGAAAGGTTTATATTCTGAAGCAGTGAAAATACAACCCCTGTAAGTAGTGGTACTGACTGTCATGAA
ACAGAAGCTTAAAAATTAGTAGGATCCAATTCCAGGAAAACTGGAGAGATTCTCTTAGAGTCATTCACTGAAAATGACAA
AGCCCCAGAAGTTACAGATGAGCCTGTGAACAAG

Alignment

ORF - retro_lafr_603 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.57 %
• Parental protein coverage: 99.76 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MDVERLQEALKDFEKRGKKEVCPVLDQFLCHVAK-TGETMIQWSQFKGYFIFKLEKVMDDFRTSAPEPRG
          MDV..LQE.LKDFEKR..KEVCPVL.Q..CHVAK.TGET.IQWSQFKGYFIFKLEKVMDDFRTSAPE.RG
Retrocopy MDVVGLQEVLKDFEKREEKEVCPVLNQLFCHVAK<TGETIIQWSQFKGYFIFKLEKVMDDFRTSAPESRG

Parental  PPNPNVEYIPFDEMKERILKIVTGFNGIPFTIQRLCELLTDPRRNYTGTDKFLRGVEKNVMVVSCVYPSS
          .PN.NVEYI.FD.M..R.LKIVTGFNG..FTIQRLCELLTDPRRNYTGTDKFLRGVEKNVMVV.CVYPSS
Retrocopy RPNLNVEYISFDKMN*RLLKIVTGFNGVSFTIQRLCELLTDPRRNYTGTDKFLRGVEKNVMVVVCVYPSS

Parental  EKNNSNS-LNRMNGVMFPGNSPSYTERSNINGPGTPRPLNRPKVPLSAPMTTNGLPENTDSKESNLQQNE
          EKNN.N..LN.MNG..FPGNSPSYTERSNINGPGT.RPLN.PK..LSA.MTT.GLPENT...ESNLQQNE
Retrocopy EKNNANG>LN*MNGITFPGNSPSYTERSNINGPGTLRPLN*PKISLSAIMTTTGLPENTE--ESNLQQNE

Parental  DKNHSDSPTSESEGSSVSPIKNKHPDEDAVEAEGREVKRLRFDKEGEGRETASQTASGEVSSVRVEETET
          DKN.SDS.T.ESEGS.VSP.K.KHP.EDA.EAEG.EVKR.R.DKEGE.RETASQT.S.E.SSV.VEETE.
Retrocopy DKNNSDSLTPESEGSLVSPPKSKHPNEDAMEAEGHEVKRRRCDKEGEVRETASQTTSTEISSVKVEETEA

Parental  SPSSQDKDKES-SRARQHCTEEDEDEDEEEEEESFMTSREMVPERKNQEKESDDALTVNEETSEENNQME
          S.SSQ.KDKES....RQHCTEEDE.E.EEEEE.S.M...EMVPERKNQEKESD..L.VNE..SEEN.QME
Retrocopy SSSSQGKDKES<YCTRQHCTEEDEEENEEEEESS-MA*KEMVPERKNQEKESDETLAVNEKISEENHQME

Parental  ESDLSQAEKDLHSE-GSGNTGPVSSGSDCHETG--PLVGSSSSKTGEVLSESFMENEEATEVTDEPMEQ
          ESDLSQAEK.L.SE..S.NT.PVSSG.DCHET....LVGS.S.KTGE.L.ESF.EN..A.EVTDEP...
Retrocopy ESDLSQAEKGLYSE<SSENTTPVSSGTDCHETEA*KLVGSNSRKTGEILLESFTENDKAPEVTDEPVNK

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_603 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 8 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007954	3 retrocopies	retro_chof_1347, retro_chof_1914, retro_chof_2285,
Echinops telfairi	ENSETEG00000019946	2 retrocopies	retro_etel_1238, retro_etel_148,
Homo sapiens	ENSG00000163605	6 retrocopies	retro_hsap_2744, retro_hsap_2745, retro_hsap_2746, retro_hsap_2904, retro_hsap_3138, retro_hsap_3283,
Loxodonta africana	ENSLAFG00000000513	1 retrocopy	retro_lafr_603 ,
Macaca mulatta	ENSMMUG00000016959	1 retrocopy	retro_mmul_1224,
Mus musculus	ENSMUSG00000052144	3 retrocopies	retro_mmus_1068, retro_mmus_1157, retro_mmus_3474,
Oryctolagus cuniculus	ENSOCUG00000006235	1 retrocopy	retro_ocun_292,
Pan troglodytes	ENSPTRG00000015108	5 retrocopies	retro_ptro_1855, retro_ptro_1856, retro_ptro_2121, retro_ptro_2220, retro_ptro_2974,