RetrogeneDB ID: retro_lafr_94

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_14:32944609..32946025(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSLAFG00000028496
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSLAFG00000018056
• Aliases: None
• Description: None

Sequence

>retro_lafr_94
ATGTCGGCCTTCGACGACTTTCAGCGGCAGCTCAAGAAGAGTAAACACGGGCGGGAAGAGGAGAACCGGCACCGGAAGCG
CAGCCATAGCCACTCGCGAAACCGGGACCGTAAGCGCCGGAGTCAGAGCCGTGACAGGCGGAACCACGACCAGAGGAACG
ACCCGCGGGACCAGCGGCGGCGAAGCAAACCTTGGAGCAGAGACGCTGAGGAGGAGCGCGGTGGATTGATCCCTTCCGCC
CGCCATGACAGGAAGAGGAAGGTCCACAAGTACTGGGATGTGCCGCCCCCGGGCTTTGAGCATATCACCCCCATGCAGTA
CAAGGCCATGCAAGCTGCAGGTCAGATTCCTGCCACTGCCTTTCTCCCCACCATGACCCCTGACGGCCTGGCCATGATCC
CAACACCAGTGCCCATGGGTGGCAGCCAGATGACCCGAAAGGCTCGGCGCCTCTACGTGGGCAACATCCCCTTCGGCATC
ACTGAGGAGGCCATGATGGACTTCTTCAATATCCAGATGCGCCTGGGGGTGCTGACGCAGGCCCCTGGCAACCCAATCTT
GGCCGTGCAGATCAACCAGGACAAGAATTTTGCCTTTTTGGAGTTCCGCTCAGTGGACGAGACTACCCAGGCCACGGCCT
TGGACGGCATCATCTTCCAGGGCCAGTCCCTGAAGATCCGCAGGCCTCACGACTACCAGCCACTGCCCAGCATGTCGGAG
AACCTGTCTGCCTACATGGCTGGAGTTGCGTCCACTGTGGTCCCCGACTCTGACCACAAGCTCTTCATCGAAGGTTTACC
CACCTACCTGAATGACGACCAGGTAAAGGAGCTGCTGACCTCATTCGGGCCTCTCAAGGCCTTCAGCCTGGTCAAGGACA
GCGCCACGGGGCTCTCTAAGGGCTACGCCGTCTGTGAATACGTGGATATCAACGACACGGACCAGGCCACTGCGGGGCTG
AACGGCATGCAGCTGGGGGACAAGAAACTGCTTGTCCTGCGGGGCAGTGTCGGTGCCAAGAACGGCACACTGAGCACGAT
CAACCAGGTGCCGGTGACCCCGCAAGTGCCAGGGCTTAGGAGTTCCCAGGTGCAGATGGGCGGCCACCCGACCGAGGTGC
TGTGCCTCATGAACATGGTGCTGCCTGAGGAGCTGCTGGATGACGAGGAGTACGAGGAGATCATGGAGGACGTGCGCGAG
GAGTGCAGCAAGTACGGGCTCGTCAAGTCCATGGAGATCCCCCGGCCCGTGGACGGCGTGGAGGTGCCCGGCTGCGGAAA
GATCTTTGTGGAGTTCACCACGGTGTTTGACTGCCAGAAAGCCATGCAGGGCCTGACTGGCCGCAAGTTCGCCAACAGAG
TGGTTGTCACAAAATACTGTGACCTTGACTCTTACCACCACCGGGACTTCTGGTAG

Alignment

ORF - retro_lafr_94 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.35 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSDFDEFERQLNENKQERDKENRHRKRSHSRSRSRDRKRRSRSRDRRNRDQRSASRDRRRRRKRCLRALK
          MS.FD.F.RQL...K..R..ENRHRKRSHS.SR.RDRKRRS.SRDRRN.DQR...RD.RRR.K...R...
Retrocopy MSAFDDFQRQLKKSKHGREEENRHRKRSHSHSRNRDRKRRSQSRDRRNHDQRNDPRDQRRRSKPWSRDAE

Parental  REHGGLIRSPRHEKKKKVRKYWDVPPPGFEHITPMQYKAMQAAGQIPATALLPTMTPDGLAVTPTPVPVV
          .E.GGLI.S.RH..K.KV.KYWDVPPPGFEHITPMQYKAMQAAGQIPATA.LPTMTPDGLA..PTPVP..
Retrocopy EERGGLIPSARHDRKRKVHKYWDVPPPGFEHITPMQYKAMQAAGQIPATAFLPTMTPDGLAMIPTPVPMG

Parental  GSQMTRQARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ
          GSQMTR.ARRLYVGNIPFGITEEAMMDFFN.QMRLG.LTQAPGNP.LAVQINQDKNFAFLEFRSVDETTQ
Retrocopy GSQMTRKARRLYVGNIPFGITEEAMMDFFNIQMRLGVLTQAPGNPILAVQINQDKNFAFLEFRSVDETTQ

Parental  AMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLT
          A.A.DGIIFQGQSLKIRRPHDYQPLP.MSEN.S.Y..GV.STVVPDS.HKLFI.GLP.YLNDDQVKELLT
Retrocopy ATALDGIIFQGQSLKIRRPHDYQPLPSMSENLSAYMAGVASTVVPDSDHKLFIEGLPTYLNDDQVKELLT

Parental  SFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAKNATLSTINQT
          SFGPLKAF.LVKDSATGLSKGYA.CEYVDIN.TDQA.AGLNGMQLGDKKLLV.R.SVGAKN.TLSTINQ.
Retrocopy SFGPLKAFSLVKDSATGLSKGYAVCEYVDINDTDQATAGLNGMQLGDKKLLVLRGSVGAKNGTLSTINQV

Parental  PVTLQVPGLMSSQVQMGGHPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGV
          PVT.QVPGL.SSQVQMGGHPTEVLCLMNMVLPEELLDDEEYEEI.EDVR.ECSKYGLVKS.EIPRPVDGV
Retrocopy PVTPQVPGLRSSQVQMGGHPTEVLCLMNMVLPEELLDDEEYEEIMEDVREECSKYGLVKSMEIPRPVDGV

Parental  EVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCDPDSYHRRDFW
          EVPGCGKIFVEFT.VFDCQKAMQGLTGRKFANRVVVTKYCD.DSYH.RDFW
Retrocopy EVPGCGKIFVEFTTVFDCQKAMQGLTGRKFANRVVVTKYCDLDSYHHRDFW

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_94 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 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000018056	1 retrocopy	retro_lafr_94 ,
Myotis lucifugus	ENSMLUG00000011051	2 retrocopies	retro_mluc_406, retro_mluc_797,
Macaca mulatta	ENSMMUG00000004810	1 retrocopy	retro_mmul_30,
Mus musculus	ENSMUSG00000030435	3 retrocopies	retro_mmus_2251, retro_mmus_3663, retro_mmus_991,
Otolemur garnettii	ENSOGAG00000007206	1 retrocopy	retro_ogar_3304,