RetrogeneDB ID: retro_lafr_248

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_10:46839805..46840362(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSLAFG00000030132
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SUDS3
• Ensembl ID: ENSLAFG00000001274
• Aliases: None
• Description: None

Sequence

>retro_lafr_248
GACAAGGAAGACTGGATGGCGTGAAGGAACAGATGTTATCAGGACAAACTGGCTCTCTCGAGAGGCAGTTGTAGCAGCTG
CAGGAAGGTACGTTACAGGAATATCAGAAGAGAATGAAAAAACTAGATCAGCAGTACCAACAGAGGATACCAAACCCGCA
ACTCTTCCTCCAGCTGGAAACTGAACAAGTGGAAAGAAATTACTCTGAAGGAAAGAAGGCATTGGTGAAAGAATTTGAAG
GCAACAAGGTTGAGCTGAACGAGAACCTAACTGATGAACTAGAAGAAAAGAAAAAGATGATTGAAAATGAAAACCTCACA
ATGGAACTGACTAGAGATTCTATGGGAGTGAAACTCATCATGACCCGGAAGTTGCGGAGGCAACCAAATGATCCTGTCCC
CATCCCAGACAAGAGGAGGAAACCTGCTCCTGCCCAGCTAAACTATAAACAGATCGGGGAGGATCTGAGGACATTCAATA
AGCTTAAGTCACCTAAGAGACCAGGACCCCCATCCTTTTCTGAACACTTGCCTGCCACACGGGCAGAGTCTCCGGCC

Alignment

ORF - retro_lafr_248 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.04 %
• Parental protein coverage: 58.05 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DEEDYVEMKEQMYQDKLA-SLKRQLQQLQEGTLQEYQKRMKKLDQQYKERIRNAELFLQLETEQVERNYI
          D.ED........YQDKLA.SL.RQL.QLQEGTLQEYQKRMKKLDQQY..RI.N..LFLQLETEQVERNY.
Retrocopy DKEDWMA*RNRCYQDKLA<SLERQL*QLQEGTLQEYQKRMKKLDQQYQQRIPNPQLFLQLETEQVERNYS

Parental  KEKKAAVKEFEDKKIELKENLIAELEEKKKMIENEKLTMELTGDSMEVKPIMTRKLRRRPNDPVPIPDKR
          ..KKA.VKEFE..K.EL.ENL..ELEEKKKMIENE.LTMELT.DSM.VK.IMTRKLRR.PNDPVPIPDKR
Retrocopy EGKKALVKEFEGNKVELNENLTDELEEKKKMIENENLTMELTRDSMGVKLIMTRKLRRQPNDPVPIPDKR

Parental  RKPAPVPQLNYLLTDEQIMEDLRTLNKLKSPKRPASPSSPEHLPATPAESPA
          RKPAP..QLNY.....QI.EDLRT.NKLKSPKRP..PS..EHLPAT.AESPA
Retrocopy RKPAPA-QLNY----KQIGEDLRTFNKLKSPKRPGPPSFSEHLPATRAESPA

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_248 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000111707	1 retrocopy	retro_hsap_3273,
Loxodonta africana	ENSLAFG00000001274	1 retrocopy	retro_lafr_248 ,
Macaca mulatta	ENSMMUG00000020629	1 retrocopy	retro_mmul_1197,