RetrogeneDB ID: retro_lafr_656

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_29:17959654..17960321(-)
• Located in intron of: ENSLAFG00000000935

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHTOP
• Ensembl ID: ENSLAFG00000002658
• Aliases: None
• Description: None

Sequence

>retro_lafr_656
ACCTATACGCTAAAGAACAAACAGCTGATGCCAGGGAACATTTGGGCTTCGACGCAGCAATGCAGCAGCTGGCCAGTGCT
TGAAAGAGAAGAGCGGCCCAGCAGGGACAGAATAGGCCCCCGTCCATGCAGCATTACAACTAAGCAGAGCTTAAAGCAGT
GCCTGGGTGAGAGTAACATCCAGGCACAGTTTGGCCAACCCATAGGGGCCCCAGCGAGGAGTGATGAGAGGACGAGGCCT
GCCCCTAATCCAGAGAGGCTTTCCCAGAGGAGGACTACATGGGGGACGTGCCAGGAGTACCCTACTTAGGGGTGGGATGT
CACTCCCAGGTCAAAACCTGCGCTGAGGTGGACAAGCCATAGCTCCCTGAACAGGCTTAAGAAGCAGTGGTGTGGAGGTG
GTGGAGGTCCTGGGAGAGGGGTCCCGTGGCATGGAGCTATGCGTCGTGGCAGAATCAGAGGTAGAGGTCAGGGTATGATA
GGTGGGGAAAGAGGGGGCTTTGGGAGCAGAGGCCGAGGCTGTGGATGAGGGAGAGGTGCCCTTTCTCACCCTGTACTGAC
CAAGGAGCAAGTGGACAACCAGGCGGATGTGTTATGTCGAAAACAAAAGGACACCTGGATGCTGAGTTGGATGCTACATG
GAGCAGACAGATTCGGAAACTAATGAT

Alignment

ORF - retro_lafr_656 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.1 %
• Parental protein coverage: 90.76 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  TNMLKNKQPMPVNIRASMQQ-QQQLASARNRRLAQQMENRPS-VQAALKL-KQKSLKQRLGKSNIQAR-L
          T..LKNKQ.MP.NI.AS.QQ..QQLASA..RR.AQQ..NRP..V.AAL.L.KQ.SLKQ.LG.SNIQA..L
Retrocopy TYTLKNKQLMPGNIWASTQQ<MQQLASA*KRRAAQQGQNRPP<VHAALQL<KQ-SLKQCLGESNIQAQ>L

Parental  GRPIGVLARGAIGGRGLPIIQRGLPRGGLRGGRATRTLLRGGMSLRGQNLLRGGRAVAPRMGLRRGGVR-
          ..P.G...RG...GRGLP.IQRG.PRGGL.GGRA..TLLRGGMSL.GQNL..GG.A.AP..GLR..GV..
Retrocopy ANP*GP-QRGVMRGRGLPLIQRGFPRGGLHGGRARSTLLRGGMSLPGQNLR*GGQAIAP*TGLRSSGVE<

Parental  GRGGPGRGGLGRGAMGRGGIGGRGRGMIGRGRGGFGGRGRGRGRGRGALSRPVLTKEQLDNQLD-AYMSK
          G.GGPGRG....GAM.RG.I.GRG.GMIG..RGGFG.RGRG.G.GRGALS.PVLTKEQ.DNQ.D...MSK
Retrocopy GGGGPGRGVPWHGAMRRGRIRGRGQGMIGGERGGFGSRGRGCG*GRGALSHPVLTKEQVDNQAD<CVMSK

Parental  TKGHLDAELDA-YMAQTDPETNE
          TKGHLDAELDA.YM.QTD.ETN.
Retrocopy TKGHLDAELDA<YMEQTDSETND

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_656 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 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013518	1 retrocopy	retro_chof_6,
Dasypus novemcinctus	ENSDNOG00000004834	1 retrocopy	retro_dnov_1054,
Equus caballus	ENSECAG00000020889	1 retrocopy	retro_ecab_729,
Loxodonta africana	ENSLAFG00000002658	3 retrocopies	retro_lafr_131, retro_lafr_282, retro_lafr_656 ,
Myotis lucifugus	ENSMLUG00000016098	2 retrocopies	retro_mluc_201, retro_mluc_247,
Rattus norvegicus	ENSRNOG00000012760	1 retrocopy	retro_rnor_1095,
Vicugna pacos	ENSVPAG00000010259	1 retrocopy	retro_vpac_353,