RetrogeneDB ID: retro_lafr_1184

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_84:406040..406288(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SRP9
• Ensembl ID: ENSLAFG00000004081
• Aliases: None
• Description: Signal recognition particle 9 kDa protein [Source:UniProtKB/TrEMBL;Acc:G3STL4]

Sequence

>retro_lafr_1184
ATGCCGCTGTACCGGACCTGGGAGGAGGTCAGCCATGGGCAGAGAAGCTCTACCTCCCAAGCCTATGAAGGCTTATGTGG
TTCTCAGATATTCTGATGGGTGTCTGTGTATTAAAGTAACTGACTACTTAGTTTCTTTGGTGTAAAGAGCAGACAGGAAT
CAGGATCAAATGAAGAGTGAGAAATTTCGGTGTTAACTAATATGGTTTTGGTATCCAAGGAGCCCCAAATGTTGCCATGA
AAATAGAC

Alignment

ORF - retro_lafr_1184 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.56 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MPQFQTWEEFSRA-AEKLYLAD-PMKARVVLKYRHTDGSLCIKVTDDLVCLVYRTDQAQDVKKIEKFHSQ
          MP...TWEE.S...AEKLYL...PMKA.VVL.Y...DG.LCIKVTD.LV.LV.R.D..QD..K.EKF...
Retrocopy MPLYRTWEEVSHG<AEKLYLPS<PMKAYVVLRY--SDGCLCIKVTDYLVSLV*RADRNQDQMKSEKFRC*

Parental  LM-RLMVAKESR-SVAMETD
          L.....V.KE....VAM..D
Retrocopy LI<MVLVSKEPQ<NVAMKID

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_1184 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 5 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000016162	2 retrocopies	retro_cfam_1034, retro_cfam_1527,
Dasypus novemcinctus	ENSDNOG00000013412	3 retrocopies	retro_dnov_1947, retro_dnov_2181, retro_dnov_742,
Echinops telfairi	ENSETEG00000012291	1 retrocopy	retro_etel_272,
Loxodonta africana	ENSLAFG00000004081	3 retrocopies	retro_lafr_1184 , retro_lafr_377, retro_lafr_648,
Otolemur garnettii	ENSOGAG00000001752	1 retrocopy	retro_ogar_230,