RetrogeneDB ID: retro_lafr_855

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_40:17902249..17902723(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DNAJC12
• Ensembl ID: ENSLAFG00000009276
• Aliases: None
• Description: None

Sequence

>retro_lafr_855
ATGAATACAATACTGAATTACAGTTTGGAGACTACTAAAGATTACTATAGATTGCTGGGATGTGACGAATTGTCTTCGGT
TGAACAAATCCTGGCAGAATTTAAGATCAGAGCCCCGGAATATCACCCTGACAAGCATCCTGAAAACTCCAGAGCTGTGG
AGACTTTCCAGAAACTACAGAAGGCAAAGGAGTTTCTGGCCAATGAAAAGAGTTTAGCCCGCTATGACCACTGGCGAAGG
AGCCAGATGACAATGGCCTTCCAGCAGTGGGAAGCTTTGAGCGACTCAGTGAAAACGTCAATGCATTGGGCTGTCAGAGG
CCTGAGGCCAGAATAATCTGGTCAGACTCAAGCCAACAAGATTGAGAATAAGGACTGGAACAAGCAAAGAGAAATAAACA
AAGGGGAGATGGGTTCAACCACAGAGAAAATCGAGCAAAAAGAATCCGAGTCCCTGGAAAAGTCATTCTCCCCA

Alignment

ORF - retro_lafr_855 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.26 %
• Parental protein coverage: 81.31 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDAILNYSSENNEDYYTLLGCDELSSVEQILAEFKIRALECHPDKHPENSKAVETFQKLQKAKEVLTNEE
          M..ILNYS.E...DYY.LLGCDELSSVEQILAEFKIRA.E.HPDKHPENS.AVETFQKLQKAKE.L.NE.
Retrocopy MNTILNYSLETTKDYYRLLGCDELSSVEQILAEFKIRAPEYHPDKHPENSRAVETFQKLQKAKEFLANEK

Parental  SRARYDHWRRSQVSMPFQQWEALSDSVKTSMHWAVRGKKDLMLEESDHTHTNKIENEDRNEQREINKEEM
          S.ARYDHWRRSQ..M.FQQWEALSDSVKTSMHWAVRG...L..E.S..T..NKIEN.D.N.QREINK.EM
Retrocopy SLARYDHWRRSQMTMAFQQWEALSDSVKTSMHWAVRG---LRPE*SGQTQANKIENKDWNKQREINKGEM

Parental  GSNTEKTEEKDSESLEKSFSP
          GS.TEK.E.K.SESLEKSFSP
Retrocopy GSTTEKIEQKESESLEKSFSP

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_855 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000009276	1 retrocopy	retro_lafr_855 ,
Oryctolagus cuniculus	ENSOCUG00000008694	1 retrocopy	retro_ocun_1568,