RetrogeneDB ID: retro_lafr_131

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_0:2726884..2727613(+)
• Located in intron of: None

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_131
GTGGCTACGCAATCAGCTCTGAAAGCTGCGCTGAAAAGCACCACCAAGATGTCTCTAAATGAGCACTCTGCTAATATGCT
GAAGAAGAAACAGCCGATGCCAGGGAATATTCAAGCTTCGATGCAGCAACGACAGCAGCCAGCCAGTGCCAGAAGGAGAA
CACTGGCCCAGCAGACAGAGAACAGACCCTCTGCCCAGGCAGCATGAAAATTTAAGCAGAGCTTAAAGCAGCACCTAGGT
AGGAGTAACATCCTTACTGGTTAGGCAGACCCACAGGGGCCCTGGCCAGGAGAGCATTCGGAGCATGAGGCCTGCCCATA
ATCCAGAGAGGCTTGCCCAGAGGAGGACTATGTGGGGACATGCCACAAGAACCCTACTTAGGGGCAGGATGTCGCTCCAA
GGTCAAAACCTGCCCCCAGGTGGATGAACCATCGCTCCCTGAATGGGCTTAAGAAGAAGTGGTGTTTGAGGTGGGAAGGG
GGGCCTAGGGTGTGGAGCTATGAGTCGGGGTGGATTCGGTGGTAGAGGACGGGGTATGATAGGTTGGGGAAGATGGGGCT
TTGGAGGCAGAGGCCGAGGTTGTGGACGAGGGAGAGGTGTGCTTTCTTGCCCTGTACTGACCAAGGGGCAGCTGGACAAC
CAGTTGTGTACATACATGTCGAAAAGAAAAGGACGGCTGGATCCTGAGCTGGATGCCACATGGCGCAGACAGACCCTGAA
ACCAATGAT

Alignment

ORF - retro_lafr_131 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.41 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAAQSAPKVVLKSTTKMSLNERFTNMLKNKQPMPVNIRASMQQQQQLASARNRRLAQQMENRPSVQAALK
          .A.QSA.K..LKSTTKMSLNE...NMLK.KQPMP.NI.ASMQQ.QQ.ASAR.R.LAQQ.ENRPS.QAA.K
Retrocopy VATQSALKAALKSTTKMSLNEHSANMLKKKQPMPGNIQASMQQRQQPASARRRTLAQQTENRPSAQAA*K

Parental  LKQKSLKQRLGKSNIQAR-LGRPIGVLARGAIGGRGLPIIQRGLPRGGLRG-GRATRTLLRGGMSLRGQN
          .KQ.SLKQ.LG.SNI....LGRP.G.LAR.A.G..GLPIIQRGLPRGGL.G.G.ATRTLLRG.MSL.GQN
Retrocopy FKQ-SLKQHLGRSNILTG<LGRPTGALARRAFGA*GLPIIQRGLPRGGLCG<GHATRTLLRGRMSLQGQN

Parental  LLRGGRAVAPRMGLRRGGVRGRGGPGRGGLGRGAMGRGGIGGRGRGMIGRGRGGFGGRGRGRGRGRGALS
          L..GG...AP.MGLRR.GV.G....G.GGLG.GAM.RGG.GGRGRGMIG.GR.GFGGRGRG.GRGRG.LS
Retrocopy LPPGG*TIAP*MGLRRSGV*G----GKGGLGCGAMSRGGFGGRGRGMIGWGRWGFGGRGRGCGRGRGVLS

Parental  RPVLTKEQLDNQLDAYMSKTKGHLDAELDA-YMAQTDPETNE
          .PVLTK.QLDNQL..YMSK.KG.LD.ELDA..MAQTDPETN.
Retrocopy CPVLTKGQLDNQLCTYMSKRKGRLDPELDA<HMAQTDPETND

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_131 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,