RetrogeneDB ID: retro_lafr_167

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_0:88229173..88229611(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP5S
• Ensembl ID: ENSLAFG00000013773
• Aliases: None
• Description: None

Sequence

>retro_lafr_167
TGGCTGCTGCGCCATGGGGCTGTGGTGTGATACTACATACAGGAGAGGTGGCAGAAGGACTACAACTCCCTCCCAACAGG
CCCTCTGGTCAAATACAAGATTCAAAAAATCGACACCATGGATTCTTGTATCATGAATGTTGGATTTGATCACATGGAAG
GCCTACAGCATGTTGAAAAAATAAAATTATGCAAGTGTCATTATGTCGAGGATGACTGTTTAGAGAGACTTGGTCAGATT
GAAAATTTACAAAAAAGCATCTTGGAAATGGAAATAATTTTTTGTGGGAATGTCATAGGCAGAGGCATCATTGCTTTGTA
TCACTTAAGAAACCTCCAGTATTTGTTATGTGGTCTTCCTGGAGTAAGAGAAAAAGAAAAGATTATTCAAGCCTTTCAGA
TATCACTGCCTTCTCTGAAGTTAAAATTAGACTTGAAG

Alignment

ORF - retro_lafr_167 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.31 %
• Parental protein coverage: 73.5 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  WLLRCGAMVRYHGQERWQKDYNHLPTGPLDKYKIQAIDATNSCIMEIGFDHMEGLQHVEKIKLCKCHYIQ
          WLLR.GA.V.Y..QERWQKDYN.LPTGPL.KYKIQ.ID...SCIM..GFDHMEGLQHVEKIKLCKCHY..
Retrocopy WLLRHGAVV*YYIQERWQKDYNSLPTGPLVKYKIQKIDTMDSCIMNVGFDHMEGLQHVEKIKLCKCHYVE

Parental  DGCLKRLGQIENLQKSILEMEIISCGNVTDKGIIALHPLRNLKYLLLCDLPGVREKEKIIQAFQISLPSL
          D.CL.RLGQIENLQKSILEMEII.CGNV...GIIAL..LRNL.Y.LLC.LPGVREKEKIIQAFQISLPSL
Retrocopy DDCLERLGQIENLQKSILEMEIIFCGNVIGRGIIALYHLRNLQY-LLCGLPGVREKEKIIQAFQISLPSL

Parental  KLKLDLK
          KLKLDLK
Retrocopy KLKLDLK

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_167 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 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009828	1 retrocopy	retro_amel_377,
Canis familiaris	ENSCAFG00000014285	1 retrocopy	retro_cfam_267,
Cavia porcellus	ENSCPOG00000014471	1 retrocopy	retro_cpor_740,
Felis catus	ENSFCAG00000029962	1 retrocopy	retro_fcat_72,
Loxodonta africana	ENSLAFG00000013773	1 retrocopy	retro_lafr_167 ,
Pteropus vampyrus	ENSPVAG00000006173	1 retrocopy	retro_pvam_539,
Sorex araneus	ENSSARG00000007707	1 retrocopy	retro_sara_694,