RetrogeneDB ID: retro_lafr_72

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_22:22868227..22869190(+)
• Located in intron of: ENSLAFG00000015147

Retrocopy information

• Ensembl ID: ENSLAFG00000029265
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSLAFG00000002110
• Aliases: None
• Description: Pyrroline-5-carboxylate reductase [Source:UniProtKB/TrEMBL;Acc:G3SPV0]

Sequence

>retro_lafr_72
ATGAGCGTGGGCTTCATCGGCGCTGGCCAGCCGGCCTGTGCGCTGGCGCGCGGCTTCACGGCCGTAGGCATCTTGTCCGC
TCACAAGATAATAGCCAGCTCCCCCGAAATGGATCTGCCCACGGTGTCGGCGCTCAGGAAGCTGGGTGTGCATCTGACCC
GCAGCAACAAGGAGACGGTGCTCAACAGTGATGTCCTGTTCCTGGCGGTGAAGCCACACATCATCGCCTTCATCCTGGAT
GAGATCGGAGCCGATGTCAAGGACAGGCACATCGTGGTCTCTTGTGCGGCCGGTGTCACCATCAACTCCATGGAGAAGAA
GCTGATGGCTTTCCAGCTGGCCCCCAAGGTGATTGGGTGCATGACCAACACGCCTGTGGTGGTGCGGGAGGGTGCCACCG
TGTACGCCACGGGCACCCATGCCCTGGTGGAGGACGGGCGCCTCCTGGAGCAGCTCATGAGCAGCGTGGGCTTCTGCACC
GAGGTGGAGGAGGACCTGATGGACGCCGTCACGGGGCTCAGCGGCAGTGGTCCTGCCTATGCTTTCATGGCCCTGGATGC
ATTGGCTGATGGAGGGGTGAAGATGGGCCTCCCGCAGCGACTGGCAGTCCGACTAGGGGCCCAGGCCTTGCTGGGAGCTG
CCAAGATGCTGCTGGATTCAGAGGAGCACCCAGGCCAGCTCAAGGACAATGTTTGCTCCCCTGGGGGTGCCACCATCCAC
GCCTTGCACTTCTTGGAGAGTGGGGGCTTCCGGTCCCTGCTCATCAATGCCGTTGAGGCCTCCTGCATCCGCACACGGGA
GCTACAGTCCATGGCTGACCAAGAAAAGATCTCCCCAGCTGCCCTCAAGAAGACCCTCCTGGACAGAGTGAAGCAGGAAT
CGTCCACAGTGTCCACGATGACCCCCTCCAACCCAAGGACGCTCCTCACAAGAAGCCCAGCCCTGGGAGGCAAGAAGGGC
TAA

Alignment

ORF - retro_lafr_72 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.88 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSVGFIGAGQLACALARGFTAAGILSAHKIIASSPEMDLPTVSALRKLGVHLTRSNKETVLNSDVLFLAV
          MSVGFIGAGQ.ACALARGFTA.GILSAHKIIASSPEMDLPTVSALRKLGVHLTRSNKETVLNSDVLFLAV
Retrocopy MSVGFIGAGQPACALARGFTAVGILSAHKIIASSPEMDLPTVSALRKLGVHLTRSNKETVLNSDVLFLAV

Parental  KPHIIPFILDEIGADVKDRHIVVSCAAGVTINSVEKKLMAFQPAPKVIRCMTNTPVVVREGATVYATGTH
          KPHII.FILDEIGADVKDRHIVVSCAAGVTINS.EKKLMAFQ.APKVI.CMTNTPVVVREGATVYATGTH
Retrocopy KPHIIAFILDEIGADVKDRHIVVSCAAGVTINSMEKKLMAFQLAPKVIGCMTNTPVVVREGATVYATGTH

Parental  ALVEDGHLLEQLMSSVGFCTEVEEDLIDAVTGLSGSGPAYAFMALDALADGGVKMGLPRRLAVRLGAQAL
          ALVEDG.LLEQLMSSVGFCTEVEEDL.DAVTGLSGSGPAYAFMALDALADGGVKMGLP.RLAVRLGAQAL
Retrocopy ALVEDGRLLEQLMSSVGFCTEVEEDLMDAVTGLSGSGPAYAFMALDALADGGVKMGLPQRLAVRLGAQAL

Parental  LGAAKMLLDSEEHPGQLKDNVCSPGGATIHALHFLESGGFRSLLINAVEASCIRTRELQSMADQEKISPA
          LGAAKMLLDSEEHPGQLKDNVCSPGGATIHALHFLESGGFRSLLINAVEASCIRTRELQSMADQEKISPA
Retrocopy LGAAKMLLDSEEHPGQLKDNVCSPGGATIHALHFLESGGFRSLLINAVEASCIRTRELQSMADQEKISPA

Parental  ALKKTLLDRVKQESSTVSTLTPSNPRTLLTRSPALGGKKG
          ALKKTLLDRVKQESSTVST.TPSNPRTLLTRSPALGGKKG
Retrocopy ALKKTLLDRVKQESSTVSTMTPSNPRTLLTRSPALGGKKG

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_72 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000002110	1 retrocopy	retro_lafr_72 ,
Macaca mulatta	ENSMMUG00000011434	1 retrocopy	retro_mmul_258,
Otolemur garnettii	ENSOGAG00000024897	2 retrocopies	retro_ogar_1366, retro_ogar_1521,