RetrogeneDB ID: retro_lafr_1056

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_63:4036371..4037314(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SPAST
• Ensembl ID: ENSLAFG00000007400
• Aliases: None
• Description: None

Sequence

>retro_lafr_1056
CTGGTTGTGGCCACAGACTGTTTATAACTTCTAGAGAAGCCGCAACCAATTTTGTAATTTTCCAAGTGACAAATGTATAA
TGACAGTACAAATTTGACATGCTGCAGTGAACATCTCCAGTCAGAAAGTGGAGCTGTTCCAAAAAAAGATCCCTTAACAT
ACCCTAGTCATTCACTGCCTTGTTCAAACAAAGTTATGATGACTGAATCCACAGGGTTTTCAGGCCACCATGGTGCACCT
CATTACAGTGGATTATCCATGGTTTCTGGAGGGAGACAAAGGCCTGGTCCTGACTCTGCAACCTATAAGCGTATTCCAAA
AACAAGTAGAACAAATAAGCCTTCTACTCCTCCAACTGCTGCTCAGAAGAATGACTTGAAGAATTTTAGGAATGTGGACC
TTGCTAACCTTATAATGAATGAAATTGTAGACAATCGAGCAGCTGCTAAATTTGATGATATAGCTGGGCAAGAGTTGGCA
AAACAGGCATGACAAGAAATTGTTATTCTTCCTTCTCTGTGGCCTGAGTTGCTCACAGGGCTTAGCGTTCCTGCCAGAGA
ATTGTTACTCTTTGGCTCACCCAGAAGTGGAAAAACAATACTGGCTAAGGCAGTAGCTGCAGAGTCCAATGCAACCTCTT
TAATGTAAGTGCTGCAAATTTAACATCAAAATATTTGGGGAAGGGGAGAAATTGGTGATAGTGCTTCCTGCTGTGGCTTG
AGAACTTCAGCCTTGTAGCATTTTTATAGATGAAGTTGACAGCCTTTTGTGTGAAAGAAGAGAAGGAGAGCATGATGCTA
GTAGGCATCTAAAAACTAAATTTCTAATAGAATTTGATGGTGTACAAACTGTTGGAGATTACAGAGTACTTGTAATGGAT
GCAGCTAACAGACCACAAGAGCTTGATGAGGCTGTTCTCAGGCATTTTATCAAATGTGTCTTT

Alignment

ORF - retro_lafr_1056 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.54 %
• Parental protein coverage: 52.11 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LGMAKDRLQLLEKLQPVLQFSKSQTDVYNDNTNLTCRNGHLQSESGAVPKRKDPLTHPSNSLPRSKTAMK
          L..A.D.L.LLEK.QP.L.FSK.Q...YND.TNLTC...HLQSESGAVPK.KDPLT.PS.SLP.S...M.
Retrocopy LVVATDCL*LLEKPQPIL*FSK*Q--MYNDSTNLTCCSEHLQSESGAVPK-KDPLTYPSHSLPCSNKVMM

Parental  TGSTGLSGHHRAPSCSGLASVSGVRQGPGLATAIHKGTPKTNRTNKPSTPPTAAQKKKDLKNFRNVDSNL
          T.STG.SGHH.AP..SGL..VSG.RQ.PG...A..K..PKT.RTNKPSTPPTAAQK..DLKNFRNVD..L
Retrocopy TESTGFSGHHGAPHYSGLSMVSGGRQRPGPDSATYKRIPKTSRTNKPSTPPTAAQKN-DLKNFRNVD--L

Parental  ANLIMNEIVDNGTAVKFDDIAGQELAKQALQEIVILPSLRPELFTGLRAPARGLLLFGPPGNGKTMLAKA
          ANLIMNEIVDN..A.KFDDIAGQELAKQA.QEIVILPSL.PEL.TGL..PAR.LLLFG.P..GKT.LAKA
Retrocopy ANLIMNEIVDNRAAAKFDDIAGQELAKQA*QEIVILPSLWPELLTGLSVPARELLLFGSPRSGKTILAKA

Parental  VAAESSAT-FFNISAASLTSKYLG-EGEKLVRALFAVARELQPSIIFIDEVDSLLCERREGEHDASRRLK
          VAAES.AT..FN.SAA.LTSKYLG.EGEKLV..L.AVA.ELQP..IFIDEVDSLLCERREGEHDASR.LK
Retrocopy VAAESNAT<LFNVSAANLTSKYLG<EGEKLVIVLPAVA*ELQPCSIFIDEVDSLLCERREGEHDASRHLK

Parental  TEFLIEFDGVQTAGDDRVLVMGATNRPQELDEAVLRRFIKRVY
          T.FLIEFDGVQT.GD.RVLVM.A.NRPQELDEAVLR.FIK.V.
Retrocopy TKFLIEFDGVQTVGDYRVLVMDAANRPQELDEAVLRHFIKCVF

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_1056 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000007400	1 retrocopy	retro_lafr_1056 ,
Myotis lucifugus	ENSMLUG00000015352	1 retrocopy	retro_mluc_1873,
Oryzias latipes	ENSORLG00000012235	1 retrocopy	retro_olat_10,
Takifugu rubripes	ENSTRUG00000000131	1 retrocopy	retro_trub_21,