RetrogeneDB ID: retro_lafr_625

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_26:33127882..33128188(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SPCS1
• Ensembl ID: ENSLAFG00000016073
• Aliases: None
• Description: None

Sequence

>retro_lafr_625
GTATTAGAGCATCTGGGCTTGCTGCCCACACGAATGAATTACAAGGCCGGAAGCTAGCTAAACAGATGTTTCATGGAATT
ATGCTTTTTTTCTGCAATAGTTGGATTTATCTGTGGGTACGTGGCTGAACAGTTCAGATGCACTGTCTATATCGTTCTAG
CTGGATTTGCTTTTTGGTGTTTGCTGACACTTACTCCCTGGCCCATCTATCGAGAGCACCCCTACAAGTGGTTACCTGTT
CAAGGTTCAGGAGCAGAAGGCAAGAAACCAGGGGATGGTAAAATCAAGAGGCATGCTAAAAATAAT

Alignment

ORF - retro_lafr_625 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75. %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MIETLGSLPTQMDYK-GQKLAEQMFQGIILS-SAIVGFVYGYVAEQFGWTVYIVMAGFAFSCLLTLPPWP
          ..E.LG.LPT.M.YK.G.KLA.QMF.GI.L..SAIVGF..GYVAEQF..TVYIV.AGFAF.CLLTL.PWP
Retrocopy VLEHLGLLPTRMNYK<GRKLAKQMFHGIMLF>SAIVGFICGYVAEQFRCTVYIVLAGFAFWCLLTLTPWP

Parental  IYRRHPLKWLPVQDSGTEDKKPGDRKIKRHAKNN
          IYR.HP.KWLPVQ.SG.E.KKPGD.KIKRHAKNN
Retrocopy IYREHPYKWLPVQGSGAEGKKPGDGKIKRHAKNN

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_625 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.

---

Parental genes homology:

Parental genes homology involve 8 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000012421	3 retrocopies	retro_dnov_2086, retro_dnov_2245, retro_dnov_698,
Dipodomys ordii	ENSDORG00000000678	4 retrocopies	retro_dord_273, retro_dord_274, retro_dord_686, retro_dord_734,
Equus caballus	ENSECAG00000023559	1 retrocopy	retro_ecab_86,
Erinaceus europaeus	ENSEEUG00000007914	1 retrocopy	retro_eeur_25,
Echinops telfairi	ENSETEG00000004020	1 retrocopy	retro_etel_1056,
Loxodonta africana	ENSLAFG00000016073	2 retrocopies	retro_lafr_575, retro_lafr_625 ,
Mus musculus	ENSMUSG00000021917	2 retrocopies	retro_mmus_2758, retro_mmus_2928,
Vicugna pacos	ENSVPAG00000007380	1 retrocopy	retro_vpac_269,