RetrogeneDB ID: retro_lafr_1181

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_82:1614601..1615795(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNF168
• Ensembl ID: ENSLAFG00000010864
• Aliases: None
• Description: None

Sequence

>retro_lafr_1181
AGGGCTGAACAACTGTCAGGAAAACTAAGCGTTAATGTTTACAGACTCTGTGAGGGAAGTTACTGGGCTTCTCCCTCGAA
TTCCAGAAAAGCTGATTCGATCATAATCGAGTCACGAAAGAAAAGTAAGAGCTATCAAAGAAACACTGGAGTTATTCACA
AGTGTTTGTCACCGAAATATCAGTTTGGGTCAGCATCAGGATCTGAAGTGGTACAAGAAGACAGAAAAAGCCCCACGCCC
AAGGCAACCGACATTATAGACTTGAGAAACCGTATGGGGCAAAACACAGAAATTGAAGAAGATATGCCAGCACTTTCTCC
GCAAATATGCCTTCGCATTGAAGAACTGGGTGCAACGTCTTCAGTAGAGACTCCAATGCCTCAATTAAGCACCTGTCATT
CAGAACAGTGCCTTGAAGGAGGAGTCAAAACAAGACCAAACAATCGTGATAAAGAATTATGTGCTGTAAATCACAAGGAA
CCTAAAACCAGAGCTCCTTACTCTAGAGAAGCTGCAGTTAAGCCTTGTGGCAACACAGAGAGTGGGCCCAGTATATCTGG
TATGACACAGGTAATTGGAAACAGCACAATGGAGAGAGAAAATGAAGAAATTAACCTGTTGGTCAGAACTAACAGTATTT
TCAAAATAAAAACACCAGGAATTTACCTCCAAAGCAGTCAAGTATCCATGCCTCCTCCAAAAAGAAGGGAACTATTCCCC
AGAGCTTCCTCAGACAAAGGGGAAAAAGAAATCAGCTTTACCCAGAAACTGATGGAATTGGAGCATCTGTATTCTGAGAG
GCATAAACAAGAACAACAGGACAGGTTATTAGCAATGAAACTTCAGAAAAAAATGGACAAAGAAATGAAGCCAAACCGGC
AAAAAGGAACCCCAAATGCATATCAGTTACGTTCTGCACCGTTTTCTCCAGACAATTTACAAAAAGGACAGAAGAAGAAT
TCCAAAGATGGGACCTTCAAGAGACAAACTCATAGGGAACATTCAAAATCTTGGAGAAGCTCAAGAAATGAAAACCAGCA
ATGTTCTTTTAAGACGAAATGTTCAGCTAATATTAATGGAAGAAGGATGCCAAATTCTGCTAGAGATCACTGTAATGTAT
CTGAAAGTATCCATTCCCCACAGTCTAGTAATTCATAGAAAAATATTGTTCAAATGTTTCAGAGATACAAGAAG

Alignment

ORF - retro_lafr_1181 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.78 %
• Parental protein coverage: 69.57 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KEETLGLSLPVLRNNFCERSISVSPLNSKKSDSVTIKSQKQNKN-QRNAGDIQKYLSPRSQFGSASQSEV
          ..E.L...L.V.....CE.S...SP.NS.K.DS..I.S.K..K..QRN.G.I.K.LSP..QFGSAS.SEV
Retrocopy RAEQLSGKLSVNVYRLCEGSYWASPSNSRKADSIIIESRKKSKSYQRNTGVIHKCLSPKYQFGSASGSEV

Parental  VQEDRKGTMSTEIDTIDLTSPVWQDTEVEEDMPTLSPQICLEIEEWGAKSSVESPMPQLSACDSEWCLEG
          VQEDRK.......D.IDL.....Q.TE.EEDMP.LSPQICL.IEE.GA.SSVE.PMPQLS.C.SE.CLEG
Retrocopy VQEDRKSPTPKATDIIDLRNRMGQNTEIEEDMPALSPQICLRIEELGATSSVETPMPQLSTCHSEQCLEG

Parental  EVKTRPNNHEKKLCMVNHEEPTTRVPYSREVAVKPGGKTESGLSVSDMTEITGNSTVETKNEETSLLTSS
          .VKTRPNN..K.LC.VNH.EP.TR.PYSRE.AVKP.G.TESG.S.S.MT...GNST.E..NEE..LL...
Retrocopy GVKTRPNNRDKELCAVNHKEPKTRAPYSREAAVKPCGNTESGPSISGMTQVIGNSTMERENEEINLLVRT

Parental  NDI-SKRKNQESSSEAVKDPCF-SAKRRKIFPQTSLDQEETETNFTQKLIELEHLLFERHKQEEQDRLLA
          N.I.SK.K.QE..S.AVK.PC....KRR..FP..S.D..E.E..FTQKL.ELEHL..ERHKQE.QDRLLA
Retrocopy NSI>SK*KHQEFTSKAVKYPCL<PPKRRELFPRASSDKGEKEISFTQKLMELEHLYSERHKQEQQDRLLA

Parental  LELQKEVDKEQMKLNRQKGSPDEYQLRATSFSPDKLLKGQKKNSKDRNFKRQTDTEHSKSWRGSGDENWQ
          ..LQK..DKE.MK.NRQKG.P..YQLR...FSPD.L.KGQKKNSKD..FKRQT..EHSKSWR.S..EN.Q
Retrocopy MKLQKKMDKE-MKPNRQKGTPNAYQLRSAPFSPDNLQKGQKKNSKDGTFKRQTHREHSKSWRSSRNENQQ

Parental  PSFKIQLKHSVTVNGKRMPNSTGDRCNVSKSAHSLQPSNSQKSIFQMFQRYRK
          .SFK...K.S...NG.RMPNS..D.CNVS.S.HS.Q.SNS.K.I.QMFQRY.K
Retrocopy CSFK--TKCSANINGRRMPNSARDHCNVSESIHSPQSSNS*KNIVQMFQRYKK

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_1181 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013317	1 retrocopy	retro_btau_1816,
Felis catus	ENSFCAG00000022131	1 retrocopy	retro_fcat_1967,
Loxodonta africana	ENSLAFG00000010864	1 retrocopy	retro_lafr_1181 ,
Myotis lucifugus	ENSMLUG00000012066	1 retrocopy	retro_mluc_1315,
Ictidomys tridecemlineatus	ENSSTOG00000021829	1 retrocopy	retro_itri_683,