RetrogeneDB ID: retro_lafr_1097

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_7:35895860..35896206(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LIN52
• Ensembl ID: ENSLAFG00000002534
• Aliases: None
• Description: None

Sequence

>retro_lafr_1097
ATGGGTTGGAGGATGGCGTCTTCCACAGACAGGACAGATCTGGAAGCACCTTGGCCTAGTTTTGAAAAACGTGACCGTGG
CTCACCAGACCTTTGGCCCGAACGAATACCAGGTGTTGCTGAATTTGCAGCTTCCTTCAAAAAGTCCTATTTCTAGCTCT
CCACCTATTTCTGGCTGAAATAGAATGTGATGGTATTGACATGTTGAAAGAGCTGGGCATCTCACCACAGCTAATTTAAT
GGAGAAGGTATGAGGCCCTCAGAATCTGGCCTTCGAGCTGGGTCTGGATGAGTCCAGAGAAATGACAGGAGGGAAATTCC
TCAACATTCTAGAGAAGCCCAAGGAG

Alignment

ORF - retro_lafr_1097 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.31 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MGWKMASPTDGTDLEASLLSFEKLDRASPDLWPEQLPGVAEFAASFK-SPITSSPPK-WMAEIERDDIDM
          MGW.MAS.TD.TDLEA...SFEK.DR.SPDLWPE..PGVAEFAASFK.SPI.SS.P....AEIE.D.IDM
Retrocopy MGWRMASSTDRTDLEAPWPSFEKRDRGSPDLWPERIPGVAEFAASFK>SPI-SSSPP>FLAEIECDGIDM

Parental  LKELG-SLTTANLMEKVRGLQNLAYQLGLDESREMTRGKFLNILEKPKK
          LKELG..LTTANLMEKV.G.QNLA..LGLDESREMT.GKFLNILEKPK.
Retrocopy LKELG<HLTTANLMEKV*GPQNLAFELGLDESREMTGGKFLNILEKPKE

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_1097 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
Loxodonta africana	ENSLAFG00000002534	1 retrocopy	retro_lafr_1097 ,
Macropus eugenii	ENSMEUG00000007891	1 retrocopy	retro_meug_286,
Mus musculus	ENSMUSG00000085793	1 retrocopy	retro_mmus_750,
Oryctolagus cuniculus	ENSOCUG00000017491	1 retrocopy	retro_ocun_294,
Otolemur garnettii	ENSOGAG00000003009	1 retrocopy	retro_ogar_2580,
Ictidomys tridecemlineatus	ENSSTOG00000008100	1 retrocopy	retro_itri_686,
Tupaia belangeri	ENSTBEG00000005405	1 retrocopy	retro_tbel_388,