RetrogeneDB ID: retro_lafr_1194

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_87:2163711..2164103(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COMMD7
• Ensembl ID: ENSLAFG00000008789
• Aliases: None
• Description: None

Sequence

>retro_lafr_1194
CGGATCATTCTGAAAAGCCTCCTGTTGGTCCCCAATGGTGCCTTGAAGAAGAGTCTCACAGCATTGCAGGTCCTGCCGAT
TTCATAACTCTGGGTCTTAGTGAGGACAAAGCCACTTACGTTTCTGAAAAGTGGAAGCAGAATTCCCCAGCCCTTGCTCT
GTGGGTCATGGGTCAGGTTCTGATGTTTAACCAGTTCAGAGATACGGAATGGCAATTTGGAGTGACATCTGGGAGCAGTG
AATTGGAGAAAGTGGGAAGTAGTGTTTTACAATTAAAGTTGGTGGTTAAAAAAGGAAACCAAACTGAAAATTTGTAGGTA
GAGTTAACTTTGTCTCAGTTCTGAAGCCTCCTGAACCAGATGGAGCGAGTCAGAGCCAGCATGGAGTGTTTC

Alignment

ORF - retro_lafr_1194 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.55 %
• Parental protein coverage: 65.83 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RSTVKSLLLVPNGALKKSLTAEQVR-ADFITLGLSEDKATYFSEKWKQKSPTLARWAIGQTLMVNQLIDM
          R...KSLLLVPNGALKKSLTA.QV..ADFITLGLSEDKATY.SEKWKQ.SP.LA.W..GQ.LM.NQ..D.
Retrocopy RIILKSLLLVPNGALKKSLTALQVL<ADFITLGLSEDKATYVSEKWKQNSPALALWVMGQVLMFNQFRDT

Parental  EWKFGVTSGSSELEKVGSIFLQLKLVVKKGNQTENLYIELTLPQFYSFLHEMERVRASMECF
          EW.FGVTSGSSELEKVGS..LQLKLVVKKGNQTENL..ELTL.QF.S.L..MERVRASMECF
Retrocopy EWQFGVTSGSSELEKVGSSVLQLKLVVKKGNQTENL*VELTLSQF*SLLNQMERVRASMECF

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_1194 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 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008561	2 retrocopies	retro_chof_1254, retro_chof_345,
Loxodonta africana	ENSLAFG00000008789	1 retrocopy	retro_lafr_1194 ,
Macropus eugenii	ENSMEUG00000010627	1 retrocopy	retro_meug_1062,
Monodelphis domestica	ENSMODG00000019450	3 retrocopies	retro_mdom_1047, retro_mdom_313, retro_mdom_890,
Sarcophilus harrisii	ENSSHAG00000006762	1 retrocopy	retro_shar_142,
Ictidomys tridecemlineatus	ENSSTOG00000006640	1 retrocopy	retro_itri_311,