RetrogeneDB ID: retro_lafr_316

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_12:58529869..58530383(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RHOQ
• Ensembl ID: ENSLAFG00000004327
• Aliases: None
• Description: None

Sequence

>retro_lafr_316
ATGGCTCACAGGCCAGGCCTGCTGATGCTCAGATGCACGGTGGTCGGTGATGGGGCACTGGGCAAGACATGGCTACTTAT
GAACCATGCCAACGATACCTTCCCAGAGGAGTACGTGTGTACCATCTCCGGCCACGGCACAGTCAGTGTCACCGTGAGGG
CAAGCAGTACCTTATGGGACTCTAGGATGTGGCTAGACAGGAAAACTACAATCTTTTGAGGCCTTTGTCTTATCCTTTGA
CTGACGTCTTCCTTATATGCTTCTCTGTGGTAAATCCAGCTTCATTCAAAAATGTGAAAGAGGAGTGGGTATCAGAGCTT
AAGGAATATACACCAAATGTGACCTTTTTATTAACAGAAACTCTGACTGATCTCTGGGATGGCCCCAAAACTTTAGCAAG
ACTGGTATGAAAGAAAAACCTGTATGTGTGGAACAAGGACAGAAACTAGCAAAAGAGACAGGAGCGTGCTGCTATGTGGA
ATGCTCAGCATTAACCCAGAAGGGAGCGAAGACC

Alignment

ORF - retro_lafr_316 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.14 %
• Parental protein coverage: 84.39 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAHGPGALMLKCVVVGDGAVGKTCLLMSYANDAFPEEYVPTVFDHYAVSVTVG-GKQYLLGLYDTAGQED
          MAH.PG.LML.C.VVGDGA.GKT.LLM..AND.FPEEYV.T...H..VSVTV..GKQYL.GL.D.A.QE.
Retrocopy MAHRPGLLMLRCTVVGDGALGKTWLLMNHANDTFPEEYVCTISGHGTVSVTVR<GKQYLMGL*DVARQEN

Parental  YDRLRPLSYPMTDVFLICFSVVNPASFQNVKEEWVPELKEYAPNVPFLLIGTQIDLRDD-PKTLARLNDM
          Y..LRPLSYP.TDVFLICFSVVNPASF.NVKEEWV.ELKEY.PNV.FLL..T..DL.D..P........M
Retrocopy YNLLRPLSYPLTDVFLICFSVVNPASFKNVKEEWVSELKEYTPNVTFLLTETLTDLWDG<PQNFSKTG-M

Parental  KEKPICVEQGQKLAKEIGACCYVECSALTQKGLKT
          KEKP.CVEQGQKLAKE.GACCYVECSALTQKG.KT
Retrocopy KEKPVCVEQGQKLAKETGACCYVECSALTQKGAKT

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_316 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 14 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000549	3 retrocopies	retro_chof_2030, retro_chof_457, retro_chof_914,
Callithrix jacchus	ENSCJAG00000000685	1 retrocopy	retro_cjac_2403,
Erinaceus europaeus	ENSEEUG00000015226	1 retrocopy	retro_eeur_129,
Homo sapiens	ENSG00000119729	3 retrocopies	retro_hsap_1333, retro_hsap_2158, retro_hsap_2316,
Loxodonta africana	ENSLAFG00000004327	1 retrocopy	retro_lafr_316 ,
Loxodonta africana	ENSLAFG00000012844	1 retrocopy	retro_lafr_818,
Loxodonta africana	ENSLAFG00000013012	1 retrocopy	retro_lafr_117,
Microcebus murinus	ENSMICG00000009124	1 retrocopy	retro_mmur_29,
Otolemur garnettii	ENSOGAG00000033272	1 retrocopy	retro_ogar_742,
Pongo abelii	ENSPPYG00000012439	2 retrocopies	retro_pabe_1107, retro_pabe_2195,
Pteropus vampyrus	ENSPVAG00000013691	1 retrocopy	retro_pvam_611,
Rattus norvegicus	ENSRNOG00000015415	1 retrocopy	retro_rnor_473,
Sus scrofa	ENSSSCG00000008439	1 retrocopy	retro_sscr_102,
Tarsius syrichta	ENSTSYG00000002837	1 retrocopy	retro_tsyr_1609,