RetrogeneDB ID: retro_lafr_119

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_39:15143149..15144913(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSLAFG00000028084
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSLAFG00000023244
• Aliases: None
• Description: None

Sequence

>retro_lafr_119
ATGGAGGTAATTCATGGCAGGTCCTGCTGTTGCAGCGAGCTTGAAGGGGATGATCTGTCAGACACCTTTTGCTCTCAGGA
AGTACACACTCCACTGCAAACACCTGCTCGCCCAACTGCCTCAGATGACAGGTATCAAGAATTAAGGGAGTCATTCCAAC
AACGCAGACTTTCCTGGGGTGCCGATAGGGAATATTGTGGGATGACACCAACCTCACTCCCCGCGGAACACAGGCCAAAA
AGCGAACCTCCTCGTGTCATGGGTAAAGGACACCAGCACTACGGATTTGGTGGAGAAACCTGGCAAAGAAAGCTTCCTGT
TGAACAATTCTATTATTTGACGCAGAACAAAGGAAGTGACATCTATGGAAACGATTCTTTGAGTCCCAAACCACCTAATC
CTACAGTAGAAGAAATCTGCTGCCCGTATCTTGTTGAACACCCCCACAACACCCACATCTCTGGCTGTGCCAAGTTCCCG
ACCTTCACATCACCCAAGGAGCTCTACGCTGGCATTAAAGCACGCAGCCAACAGCCATTTCCCCCAACTGTGCCAACGAA
GGCTTACGATACAACAATTTTGAAGGCAAGAGGTAATCCTTATAGACATGAACTGGTTGATTTTCCCTCCGATTCAAAGA
AGAAAACCTCGACTTGGCCTGGTCAGGGTGTGTATTACAATTTTCCCAAATGTGTTGAGAAAAATAAGCCAGTGTTCTAC
CCGAAACCTCCTAAATCCTTCGCTCCTAACACTTCTTTAAATTCGTGGGATCCTATTAACTCTCTAAAAGAAGCCAACAT
ACAAAGAAATCTTGAGAGGTCCCACTGGATCACTTCGTACACTCATGATTTTACAGGTCTGGGGCCCATGAATCCTCCCG
AACTGGCCAATGACTATGAAAAGGAGGTAGGTGACATAACTGGACAGATAGGATTTGACCCAGAGCCTCAAGAAAAACTC
AGTCCTGTCTTAAAACCTGTCAGACCCTTGGAAGGAAGAATTGCCCGACTGATTCATGACCAAAGTCCTCTGGAGGCTAC
TGTCCAGGAAAAACCACCTTCCTGTCCAGATTGTACCCCTGTAATTTTGTGTACTTTTCACACCTTTATACCCAGTTCTG
AAGAAATGAGGGCACTTAATGATAACACATGGGCCAACGTCACCCATGAAAACCAGGGCATTGAAGAGAAGATTAAGGAA
GAACAAAGCTTGCTATCTAAGTATGCACTTCCATCTCGTTACCCAACAAAAGATTTGACTGACATTTATGACATGAAACC
ATTTCCAAAAGTCACAGATAGTAAAAAGACAGAGGATTTGTACTGGAGACAGCTAGCATTAAAACCCCAACCTATACCTT
ATCCTAAAGCAAACAATTACATTCACTATGAATATTTTAAATCTGACCAGTATACTGTGTGTCAAGATCCTACTCGTCCT
AGTAGGCCTAGTACTTTACAAAATAAACAAGGCACTGAAGCCTTCACTTTAGAACAGTTTTTCGGTAAACCAGAAGAACA
TCAGTTGGCCTTGAACATGGAAAACAATGAAGAAAGAAGACCTGTTCTGGGTTGGATTCCTAGAACTGGAGTGGCCAAAC
CTCAGACCAACCTGCTGGGCCTTAAGAACTCTTCTTCGAAATCCGCTGTACGAAAACGTTTCCATAAATTAATTCTAGAT
GACCATAAAGGCTTCAGGGATAAGGAGCATTCAGGGATGAAACACCAACTCTATGGCCATGATTCCTATTATTTCTACAA
CTGA

Alignment

ORF - retro_lafr_119 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.73 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEVMHGRSCCCGELEGDDLLSDTFCSNEVHTPLQTPARPTASEDRYQELRESLQQCRLPWGADREYGGII
          MEV.HGRSCCC.ELEGDDL.SDTFCS.EVHTPLQTPARPTAS.DRYQELRES.QQ.RL.WGADREY.G..
Retrocopy MEVIHGRSCCCSELEGDDL-SDTFCSQEVHTPLQTPARPTASDDRYQELRESFQQRRLSWGADREYCGMT

Parental  PISLPEEHRPKCEPPRVMGKGHQHYGFGGETWQRKLPIEQCYYLTQNKKSNVYGNDSLIPKPPNAMVEEI
          P.SLP.EHRPK.EPPRVMGKGHQHYGFGGETWQRKLP.EQ.YYLTQNK.S..YGNDSL.PKPPN..VEEI
Retrocopy PTSLPAEHRPKSEPPRVMGKGHQHYGFGGETWQRKLPVEQFYYLTQNKGSDIYGNDSLSPKPPNPTVEEI

Parental  CCPYPVEHPYNTHISRCAMFPTFTSPKELYTGIKARSQQPFPPTVPTKAYDTMILKTRGNPYRYELVDFP
          CCPY.VEHP.NTHIS.CA.FPTFTSPKELY.GIKARSQQPFPPTVPTKAYDT.ILK.RGNPYR.ELVDFP
Retrocopy CCPYLVEHPHNTHISGCAKFPTFTSPKELYAGIKARSQQPFPPTVPTKAYDTTILKARGNPYRHELVDFP

Parental  SDSKKKALTWPGQGVYYDFPKCVEKNKPVFYPKPPKTFAPNTSLNSWDPINSLKEANIQRNLERSHWITS
          SDSKKK..TWPGQGVYY.FPKCVEKNKPVFYPKPPK.FAPNTSLNSWDPINSLKEANIQRNLERSHWITS
Retrocopy SDSKKKTSTWPGQGVYYNFPKCVEKNKPVFYPKPPKSFAPNTSLNSWDPINSLKEANIQRNLERSHWITS

Parental  YTHDFTGLGPMNPLELDDYHEKEVADFTGQIGFDPEPQEKFHPVLKPVRPLEGRIARLIHDQRPLEPTVQ
          YTHDFTGLGPMNP.EL....EKEV.D.TGQIGFDPEPQEK..PVLKPVRPLEGRIARLIHDQ.PLE.TVQ
Retrocopy YTHDFTGLGPMNPPELANDYEKEVGDITGQIGFDPEPQEKLSPVLKPVRPLEGRIARLIHDQSPLEATVQ

Parental  EKPPSCPDCTPTVLCAFHTFIPSSEEMRALNDNTRAGVTHKNQDIEEKIKEEQSLLSTYALPPCYPTKDL
          EKPPSCPDCTP..LC.FHTFIPSSEEMRALNDNT.A.VTH.NQ.IEEKIKEEQSLLS.YALP..YPTKDL
Retrocopy EKPPSCPDCTPVILCTFHTFIPSSEEMRALNDNTWANVTHENQGIEEKIKEEQSLLSKYALPSRYPTKDL

Parental  TDIYDMKPFPKITDTKKTEDLYWRQLALKPQPIPYPKANNYIHYEHFKSDQYTMCQDPTSPNKPSILQNK
          TDIYDMKPFPK.TD.KKTEDLYWRQLALKPQPIPYPKANNYIHYE.FKSDQYT.CQDPT.P..PS.LQNK
Retrocopy TDIYDMKPFPKVTDSKKTEDLYWRQLALKPQPIPYPKANNYIHYEYFKSDQYTVCQDPTRPSRPSTLQNK

Parental  QGTETFTLEQFFGKPEEHQLVLNMENNEETKPILGWIPRSGVAKPQTNLLDLKNSFSKSGVRKRFHKSIL
          QGTE.FTLEQFFGKPEEHQL.LNMENNEE..P.LGWIPR.GVAKPQTNLL.LKNS.SKS.VRKRFHK.IL
Retrocopy QGTEAFTLEQFFGKPEEHQLALNMENNEERRPVLGWIPRTGVAKPQTNLLGLKNSSSKSAVRKRFHKLIL

Parental  DDHRDLRDKEHSGMKHQFYGHNSYYFYN
          DDH...RDKEHSGMKHQ.YGH.SYYFYN
Retrocopy DDHKGFRDKEHSGMKHQLYGHDSYYFYN

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_119 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000023244	1 retrocopy	retro_lafr_119 ,