RetrogeneDB ID: retro_lafr_1094

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_7:3648866..3649172(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VAMP3
• Ensembl ID: ENSLAFG00000000277
• Aliases: None
• Description: None

Sequence

>retro_lafr_1094
TCTACAGGTGTGCCTGCAGGTTCAAGCGCTGCCTCTGGCAGTAATCGAAGACTGCAGCAGACACAAAACCAAGTGGATGA
GGTGGTGGACATCATGCGTGTCAACGTGGACAAGGTATTGGAAAGAGATCAAAAGCTTTCTGAGCTAGACGATCGTGCAG
ACACGCTGCAGGCAGGAGCATCCCAGTTTGAAACAAGTGCTGCCAAGTTGAAGAGGAAATATTGATGGAAGAATTGCACG
ATGTGGGCAATTGGGATTACCATTGTGGTTATCTTCTTCATCATCATCATCGTGTGGAGTCTTTCT

Alignment

ORF - retro_lafr_1094 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.08 %
• Parental protein coverage: 99.03 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  STGVPAGSSAASGSNRRLQQTQNQVDEVVDIMRVNVDKVLERDQKLSELDDRADALQAGASQFETSAAKL
          STGVPAGSSAASGSNRRLQQTQNQVDEVVDIMRVNVDKVLERDQKLSELDDRAD.LQAGASQFETSAAKL
Retrocopy STGVPAGSSAASGSNRRLQQTQNQVDEVVDIMRVNVDKVLERDQKLSELDDRADTLQAGASQFETSAAKL

Parental  KRKYWWKNCKMWAIGITIVVIFIIIIIVWSLS
          KRKY.WKNC.MWAIGITIVVIF.IIIIVWSLS
Retrocopy KRKY*WKNCTMWAIGITIVVIFFIIIIVWSLS

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_1094 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 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000000277	2 retrocopies	retro_lafr_1094 , retro_lafr_463,
Monodelphis domestica	ENSMODG00000005770	1 retrocopy	retro_mdom_273,
Tarsius syrichta	ENSTSYG00000007733	6 retrocopies	retro_tsyr_1027, retro_tsyr_1435, retro_tsyr_1634, retro_tsyr_1757, retro_tsyr_524, retro_tsyr_968,