RetrogeneDB ID: retro_lafr_469

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_18:27454643..27456198(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPIL2
• Ensembl ID: ENSLAFG00000016750
• Aliases: None
• Description: None

Sequence

>retro_lafr_469
ATGGGGAAGAGACAGCATCAGAAGGACAAGATGTACATTACCTGTGCTGAATACACTCACTTCTATGGTGGCAAGAAGCC
AGGTATTCCTAAAACAAATTTTCATCCTTTACCTTTTGACCACTTCAGTCTCTCTCTAAAGCCCTTCATTTACCCAGTGT
GCACCTCGGAAGGCATCATTTTTGACTTGCTGAGCATCCTTCCTTGGCTTAAGAAGTACGGGACCAACCCCAGCAATGGA
GAATAACTGGAGGGGAGGTCCCTGATTAAGCTAAATTTTGCAAAGAACAATGGAGATAAATACCACTGCCCGGTGCTGTT
CACAGTGTTCACTAACACCACCCACATTGTGGCCATCAGAACTACTGGCAACGTATATGCCTACGAGGCAGTGGAGAAGC
TGAATACCAAGGCCAAGGACTTCCAGGACCTGCTGACCGATGAGCCCTTTTCCTGGCAGGACATCATCACCCTCCAGTAT
CCCACCAATTTGGACAAATTTAACATCTCCAACTTCTTTCATGTGAAGAACAACATGCAGATGACAGACCCGGATGAAGA
AAAGGCCAAACAGGACCCGTCCTACTATCTGAAAAACACAAATGCAGAGATCCGGGAGACCCTGCAGGAGCTCTACAAGG
AGTTCAAAGGGGACAAGGTTCTGGGGGTCACCATGAGGGCCCCCAAGAAGAAACTGGAGAAACTGAACGCTGCCCACTAC
CCTACTGGGAAGGTCAGCGCTTCCTTCTCCTCCACCACCATGGTTCTGGAGACTACGCACGAAGCAGCTGCCATCGATGA
AGACGTCTCGCACTACCAGTTTGTGAAGAAGGTCTACGTGCTGCTCCACACCAACAAGGGCGACCTCAGCCTGGAGCTAC
ACTGCGACCTGACGCCAAAGACCTGTGAGAACTTCATTAGGCTCTGCAAGAAGCACTACTACAATGGCACCCTCTTCCAC
AGGTCCATCAGGAACTTTGTGATCCAAGGCGGCAACCCCACTGGCACTGCCTTGAGTGGAGAGTCATTCTGGGGAAAGCC
TTTTGAAGATGAGTTCCAGCTGAACCTCTCGCACATGGGCCGGGGCGTCCTCAGCATGGCCAACTCGGGGCCCAACAGCA
ACAAGTCTCAGTTCTTCTTCACCTTCCACTCCTGCGCCTACCTGGACAAGTAGCACATCATCTTTGGACGGGTTATCGGG
GGCTTCGACACACTGACAGCCATGGAGAACGTGGAGAGTGGCCCCCAAAAGTGACTGCCCTAAGAAAGAGATCCGCACTG
AGCCCACAACAGTGTTTGTGGACCCTTATGAGGAGGCTGACGCTCAGATCGCCGAGGAGCGGAAGACGCAGCTGAAAGAG
GAGGCCCTGGAGGCCACGGTGAAGATGAGCCAGCCCCAGCTGGGGAGAGCAGGACCCCAAGCGGACCACCAGGGGGTGGG
CAGGTACATCAGCCCAGCGGCCATGAACCGGGCAGCAGAGCAAGGGACGTCCACCAGCACAGCCGCCCCTGCAGCCAAGA
AGCACAGCCGAGGCTTTGGGGACTTCAGTTTCTGG

Alignment

ORF - retro_lafr_469 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.94 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGKRQHQKDKMYITCAEYTHFYGGKKPDIPKTNFRRLPFDHCSLSLQPFVYPVCTPEGIVFDLLSILPWL
          MGKRQHQKDKMYITCAEYTHFYGGKKP.IPKTNF..LPFDH.SLSL.PF.YPVCT.EGI.FDLLSILPWL
Retrocopy MGKRQHQKDKMYITCAEYTHFYGGKKPGIPKTNFHPLPFDHFSLSLKPFIYPVCTSEGIIFDLLSILPWL

Parental  KKYGTNPSNGEKLDGRSLIKLNFAKNNEGKYHCPVLFTVFTNNTHIVAIKTTGNVYAYEAVEQLNIKAKN
          KKYGTNPSNGE.L.GRSLIKLNFAKNN..KYHCPVLFTVFTN.THIVAI.TTGNVYAYEAVE.LN.KAK.
Retrocopy KKYGTNPSNGE*LEGRSLIKLNFAKNNGDKYHCPVLFTVFTNTTHIVAIRTTGNVYAYEAVEKLNTKAKD

Parental  FRDLLTDEPFSRQDIITLQDPTNLDKFNVSNFFHVKNNMKMIDPDEEKAKQDPSYYLKNTNAETRETLQE
          F.DLLTDEPFS.QDIITLQ.PTNLDKFN.SNFFHVKNNM.M.DPDEEKAKQDPSYYLKNTNAE.RETLQE
Retrocopy FQDLLTDEPFSWQDIITLQYPTNLDKFNISNFFHVKNNMQMTDPDEEKAKQDPSYYLKNTNAEIRETLQE

Parental  LYKEFKGDEVLAATMKAPEKKKVDKLNAAHYSTGKVSASFTSTAMAPETTHEAAAIDEDVLRYQFVKKKG
          LYKEFKGD.VL..TM.AP.KKK..KLNAAHY.TGKVSASF.ST.M..ETTHEAAAIDEDV..YQFVKK..
Retrocopy LYKEFKGDKVLGVTMRAP-KKKLEKLNAAHYPTGKVSASFSSTTMVLETTHEAAAIDEDVSHYQFVKKV-

Parental  YVRLHTNRGDLNLELHCDLTPKTCENFIRLCKKHYYDGTIFHRSIRNFVIQGGDPTGTGTGGESFWGKPF
          YV.LHTN.GDL.LELHCDLTPKTCENFIRLCKKHYY.GT.FHRSIRNFVIQGG.PTGT...GESFWGKPF
Retrocopy YVLLHTNKGDLSLELHCDLTPKTCENFIRLCKKHYYNGTLFHRSIRNFVIQGGNPTGTALSGESFWGKPF

Parental  KDEFRPNLSHTGRGILSMANSGPNSNKSQFFITFRSCAYLDKKHTIFGRVVGGFDTLTAMENVESD-PKT
          .DEF..NLSH.GRG.LSMANSGPNSNKSQFF.TF.SCAYLDK.H.IFGRV.GGFDTLTAMENVES..PK.
Retrocopy EDEFQLNLSHMGRGVLSMANSGPNSNKSQFFFTFHSCAYLDK*HIIFGRVIGGFDTLTAMENVESG>PKS

Parental  DRPKEEIRIESTTVFVDPYEEADAQIAEERKKTQLKEEALETTVKTSQPQLGSPGPQAYRQGVGKYISPE
          D.PK.EIR.E.TTVFVDPYEEADAQIAEER.KTQLKEEALE.TVK.SQPQLG..GPQA..QGVG.YISP.
Retrocopy DCPKKEIRTEPTTVFVDPYEEADAQIAEER-KTQLKEEALEATVKMSQPQLGRAGPQADHQGVGRYISPA

Parental  ATKRAAEEEPSTSTAAPTAKKRPSRGFGDFSSW
          A..RAAE...STSTAAP.AKK..SRGFGDFS.W
Retrocopy AMNRAAEQGTSTSTAAPAAKKH-SRGFGDFSFW

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_469 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000016750	1 retrocopy	retro_lafr_469 ,
Loxodonta africana	ENSLAFG00000018698	1 retrocopy	retro_lafr_521,
Loxodonta africana	ENSLAFG00000028161	2 retrocopies	retro_lafr_1187, retro_lafr_435,
Rattus norvegicus	ENSRNOG00000026900	2 retrocopies	retro_rnor_1216, retro_rnor_2392,