RetrogeneDB ID: retro_lafr_1099

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_7:63846804..63847146(+)
• Located in intron of: ENSLAFG00000012804

Retrocopy information

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

Parental gene information

• Parental gene symbol: COMMD4
• Ensembl ID: ENSLAFG00000006259
• Aliases: None
• Description: None

Sequence

>retro_lafr_1099
AGGTTCCAGTTCTGTAATGATCTGGACTGTCCCAACTGGGTCCTGGCAGAGATCAGCACACTGGCTAAGATTTCCTCTGT
GAAGCTACAGTTGCTGTGCAGCCAGGTGCTGAAGGAGCTTCTGGGATAGGGGATTGACTATGAGAAGATCCTGAAGCTCT
CAGCTGATGGCAAGTTTGAGACAGGTGATGTGAAGGCCCTGGTGGCGATGTTGAGTTTTATCGTCTCCAGTGCAGCCAAG
CATAGCGTGGATGGCGAGTCCTTGTCCAGTGAACTGCTGCAGCCAGGGCTGCCCAAAGAGCGTGCTGCCATCCTACGCTG
TTGCTACAAGGAGAAGCAAAGC

Alignment

ORF - retro_lafr_1099 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.46 %
• Parental protein coverage: 57.29 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RFRFCGDLDCPDWVLAEISTLAKIVDVKLRLLCSQVLKELLGQGIDYEKILKLTADAKFESGDVKATVAV
          RF.FC.DLDCP.WVLAEISTLAKI..VKL.LLCSQVLKELLG.GIDYEKILKL.AD.KFE.GDVKA.VA.
Retrocopy RFQFCNDLDCPNWVLAEISTLAKISSVKLQLLCSQVLKELLG*GIDYEKILKLSADGKFETGDVKALVAM

Parental  LSFILSSAAKHSVDGESLSSELQQLGLPKEHAASLCRCYEEKQS
          LSFI.SSAAKHSVDGESLSSEL.Q.GLPKE.AA.L..CY.EKQS
Retrocopy LSFIVSSAAKHSVDGESLSSELLQPGLPKERAAILRCCYKEKQS

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_1099 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
Callithrix jacchus	ENSCJAG00000010909	1 retrocopy	retro_cjac_2080,
Dasypus novemcinctus	ENSDNOG00000013425	1 retrocopy	retro_dnov_1860,
Loxodonta africana	ENSLAFG00000006259	1 retrocopy	retro_lafr_1099 ,