RetrogeneDB ID: retro_lafr_252

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_10:65171849..65173069(-)
• Located in intron of: ENSLAFG00000012188

Retrocopy information

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

Parental gene information

• Parental gene symbol: FUCA1
• Ensembl ID: ENSLAFG00000015305
• Aliases: None
• Description: None

Sequence

>retro_lafr_252
GTGTTTGTTCACTGGAGCATGTACTCAGTGCTGGCCTGGGGCAGTGAGTGGTTCTGGTGGCAGTGGAAGGGTGAGGGACA
GCCCCAATATGAGTTCTTCAAGATGAACAACTACCCTCCCAGCTTCAGCTGTGCTAACTTCAGGCTGCAGTTCACAGCCG
CCTTCTTCCAGCCAGACCACTGGACCAACCTCATCTAGTGGTGGGGGCCAGGTATGTAGTTCTGACCACAAAGCATCATG
AGGTCCTCACAACTGGCCAAGTCCTGTGTCTTGGAACTGGAACACTTAGGACTTAAGACCCCATCGTGATTTGTTGGGGA
GCTGGGAACAGCTCTGCCAAAGAGGGACATATGCTATGGACTTTATCATTCACTCTTAGAGTGGTCCCGTCCACTCTACC
TACTTGATGCGAAAAATGGCTTCAAGACACAGTAGTTTGTGAGTTCAAAAGCAATGCCAGAACTATATGATCTCGTTAAT
AGGTATAAGTCTAACCCAATTTGGTCTGATGGAGAGTGAGAATGTCCTGATACTTACTGGAACTCTACAGATTTTCTTGC
TTGGGTCTACAATGATAGCGATATCAAGGATCAAGTGGTAATAAATGACCAGTAGGGTCAGAACTGCTTCTGTCACCATG
GAGGATTCTACAACTGTCCAGATAAATACATGCTAGGGAGCTTGCCAGATCACAAGTGGGAGATGTGCATCCTCCAAGGA
CAAGTCATCCTGGGGCTATCGTTGCAACATGGTGATGGTAAGCCTTGCAAGTGAAGAGGAAAATCATTTCAGAGCTGGTT
CAGGCAGTAAGTGTGAGAGGCAACTCTCTTCTCCACAATGGGCCAACTAAAGATGGGGTGATTTTTCCCATCTTCCAAGA
AAGGCTTCTTGCTGTTGGGAAGCAGCTGACCATCAGCAGGGAGGCTATTTATGCCTCTAAGCTATGGAGGCTACAGTCAG
ATAAGAACATGACATCTCTCTGCTACTCTTCAACAGGACCAGATGTTTATGGCATTTTACTGCACTGGCCAAAAAATGGA
GTCCTATACCTTGCATCCCCTAAAACTACCTTGACTGCAAAGGTTATTATGCTGGAACTCGAAGGGGGTCTGAAATGGTT
CCAATATCCAGTTCAAGGCCTCCTCATTTCCCTGCCTTGGTTACTACCCTCTGCTCTCTCTGTTAGTTTTGCTTGGACTC
TAAAGCTGACAAGAGTGGAG

Alignment

ORF - retro_lafr_252 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.97 %
• Parental protein coverage: 88.67 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  VFVHWGVYSVPAWGSEWFWWHWKGEGQRQYELFMKKNYPPGFSYADFGPQFTATFFEPDDWADLF-RAAG
          VFVHW..YSV.AWGSEWFWW.WKGEGQ.QYE.F...NYPP.FS.A.F..QFTA.FF.PD.W..L.....G
Retrocopy VFVHWSMYSVLAWGSEWFWWQWKGEGQPQYEFFKMNNYPPSFSCANFRLQFTAAFFQPDHWTNLI<LVVG

Parental  ARYVVLTAKHHEGFT-NWPSPVSWNWNSQDLGPHRDL-VGELGTALRKRNIRYGLYHSLLEWFHPLYLLD
          ARYVVLT.KHHE..T.NWPSPVSWNWN..DL.PHRDL.VGELGTAL.KR.I.YGLYHSLLEW..PLYLLD
Retrocopy ARYVVLTTKHHEVLT<NWPSPVSWNWNT*DLRPHRDL<VGELGTALPKRDICYGLYHSLLEWSRPLYLLD

Parental  KKNGFKTQYFVSSKTMPELYDLVNRYKPDLIWSDGEWECPDTYWNSTDFLAWLYNDSPVKDQVVVNDRWG
          .KNGFKTQ.FVSSK.MPELYDLVNRYK...IWSDGE.ECPDTYWNSTDFLAW.YNDS..KDQVV.ND..G
Retrocopy AKNGFKTQ*FVSSKAMPELYDLVNRYKSNPIWSDGE*ECPDTYWNSTDFLAWVYNDSDIKDQVVINDQ*G

Parental  QNCSCHHGGFYNCQDKYMPKSLPAHKWEMC-TSVDKSSWGYRRNMVMAGIASEEE-IISELVQAVSLGGN
          QNC.CHHGGFYNC.DKYM..SLP.HKWEMC..S.DKSSWGYR.NMVM...ASEEE.IISELVQAVS..GN
Retrocopy QNCFCHHGGFYNCPDKYMLGSLPDHKWEMC>SSKDKSSWGYRCNMVMVSLASEEE>IISELVQAVSVRGN

Parental  YLLNVGPTKDGVIVPIFQERLLAVGKWLSISGEAIYASQPWRVQSDRNTTSVWYTSKVPDVYAILLQWPK
          .LL..GPTKDGVI.PIFQERLLAVGK.L.IS.EAIYAS..WR.QSD.N.TS..Y.S..PDVY.ILL.WPK
Retrocopy SLLHNGPTKDGVIFPIFQERLLAVGKQLTISREAIYASKLWRLQSDKNMTSLCYSSTGPDVYGILLHWPK

Parental  NGVLYLASPKTTSATKVTMLGLEGDLKWSQDPGQGLFISLPQLPPSALPVKFAWTLKLTGVE
          NGVLYLASPKTT...KV.ML.LEG.LKW.Q.P.QGL.ISLP.L.PSAL.V.FAWTLKLT.VE
Retrocopy NGVLYLASPKTTLTAKVIMLELEGGLKWFQYPVQGLLISLPWLLPSALSVSFAWTLKLTRVE

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_252 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012304	2 retrocopies	retro_chof_1090, retro_chof_542,
Equus caballus	ENSECAG00000024652	1 retrocopy	retro_ecab_450,
Loxodonta africana	ENSLAFG00000015305	1 retrocopy	retro_lafr_252 ,
Microcebus murinus	ENSMICG00000007213	1 retrocopy	retro_mmur_542,
Tupaia belangeri	ENSTBEG00000013160	1 retrocopy	retro_tbel_3390,