RetrogeneDB ID: retro_lafr_1027

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_6:33463062..33463445(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LRRC57
• Ensembl ID: ENSLAFG00000005465
• Aliases: None
• Description: None

Sequence

>retro_lafr_1027
AAGAACCTGAACCTCTCTGGAAACCAACTCTGAGCACTGCCACCCCAACTTTGTAGCCTACGGCACCTGGATGTGATGGA
TCTTGCTAAGAACCAGATTCGGAGTATGCCTGACATAGTGGAGGAGCTGCAGGTCACTGAACTCAACCTCAACCAGAACC
AGATATCTCAAATCTCAGTGAAGATATCTTGCTGTCCTTGTCTCAAAGTTCGTCATCTGGAGAGAACTGTCTTGAGCTCA
GCATACTTCCGCAGGGCATCCTTAGTGATTCCCAGGCATGTCTGCTTGCTGTGGAAGGCAATCTTTTTGAGATAAAGAAA
CTTCTAGAACTGGAAGGCTATGATAAGCACATGGAGAGGTTCATGGCCACCAAGAAGAAGTTT

Alignment

ORF - retro_lafr_1027 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.72 %
• Parental protein coverage: 51.61 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KTLSLSGNRLRTLPPQLCSLRHLDVMDLSKNQIRSIPDTVGDLQVIELNLNQNQISQISVKISCCPRLKV
          K.L.LSGN.L..LPPQLCSLRHLDVMDL.KNQIRS.PD.V..LQV.ELNLNQNQISQISVKISCCP.LKV
Retrocopy KNLNLSGNQL*ALPPQLCSLRHLDVMDLAKNQIRSMPDIVEELQVTELNLNQNQISQISVKISCCPCLKV

Parental  LRLE-ENCLELSMLPQSILSDSQICLLAVEGNLFEIKKLRELEGYDKYMERFTATKKKF
          ..LE.ENCLELS.LPQ.ILSDSQ.CLLAVEGNLFEIKKL.ELEGYDK.MERF.ATKKKF
Retrocopy RHLE<ENCLELSILPQGILSDSQACLLAVEGNLFEIKKLLELEGYDKHMERFMATKKKF

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_1027 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 11 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006482	1 retrocopy	retro_chof_2306,
Callithrix jacchus	ENSCJAG00000002991	1 retrocopy	retro_cjac_2819,
Homo sapiens	ENSG00000180979	1 retrocopy	retro_hsap_2163,
Gorilla gorilla	ENSGGOG00000009597	1 retrocopy	retro_ggor_1718,
Loxodonta africana	ENSLAFG00000005465	2 retrocopies	retro_lafr_1027 , retro_lafr_767,
Macaca mulatta	ENSMMUG00000001544	1 retrocopy	retro_mmul_901,
Nomascus leucogenys	ENSNLEG00000004485	1 retrocopy	retro_nleu_1812,
Otolemur garnettii	ENSOGAG00000007751	1 retrocopy	retro_ogar_3437,
Pan troglodytes	ENSPTRG00000006976	2 retrocopies	retro_ptro_1649, retro_ptro_1650,
Rattus norvegicus	ENSRNOG00000009143	1 retrocopy	retro_rnor_796,
Rattus norvegicus	ENSRNOG00000048310	1 retrocopy	retro_rnor_1732,