RetrogeneDB ID: retro_lafr_565

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_21:44920815..44921211(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SIKE1
• Ensembl ID: ENSLAFG00000010502
• Aliases: None
• Description: None

Sequence

>retro_lafr_565
ATGGCCCGAACCATCGAAAAGATCCTGCCAGACTCCAAGAAGCTGCTGGGGAGAGTGCAAGAAGACCCTGCGGCCACCGA
GCAGCTGGTAGATCAGTCCGCATAGCTGCCCTGGCAAGCTATGCTGGAGGTGGGGTCAACACTTCCAGACCAGTATCAAG
AGGATGCATCCAATATGAAGGGACATGTCCAAATACAAGCCTCACATTCTGCTGTTCCAAGAGAGCACACAGTTTAGACA
CTGCAGCAGGAAAAGAGAGAGCTATGCGTTTCCTTGGAGGAACACCAGGATGCTTTGGAACTCATCATGAGCAAGTACAG
GACACAGATGTTACAGTTGATGGTTACTTAAAAAATAGCAGTGGATGATAAATCAGTCATGAAAGTTCAACAGTCT

Alignment

ORF - retro_lafr_565 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.38 %
• Parental protein coverage: 64.25 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MTCTIEKILTDAKTLLERLREHDAAAESLVDQSAALHRRVAAMREAGAALPDQYQEDASDVK-DVSKYKP
          M..TIEKIL.D.K.LL.R..E..AA.E.LVDQSA.L.....AM.E.G..LPDQYQEDAS..K.D.SKYKP
Retrocopy MARTIEKILPDSKKLLGRVQEDPAATEQLVDQSA*LPWQ--AMLEVGSTLPDQYQEDASNMK>DMSKYKP

Parental  HILLSQENTQIR-DLQQENRELWVSLEEHQDALELIMSKYRKQMLQLMVA-KKAVDAEPVLKAHQS
          HILL.QE.TQ.R..LQQE.REL.VSLEEHQDALELIMSKYR.QMLQLMV..K.AVD...V.K..QS
Retrocopy HILLFQESTQFR<TLQQEKRELCVSLEEHQDALELIMSKYRTQMLQLMVT*KIAVDDKSVMKVQQS

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_565 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 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012958	1 retrocopy	retro_chof_48,
Echinops telfairi	ENSETEG00000007805	1 retrocopy	retro_etel_615,
Loxodonta africana	ENSLAFG00000010502	1 retrocopy	retro_lafr_565 ,
Loxodonta africana	ENSLAFG00000012476	1 retrocopy	retro_lafr_486,
Microcebus murinus	ENSMICG00000015446	1 retrocopy	retro_mmur_738,
Otolemur garnettii	ENSOGAG00000005952	2 retrocopies	retro_ogar_1794, retro_ogar_2028,
Ictidomys tridecemlineatus	ENSSTOG00000001684	1 retrocopy	retro_itri_1447,
Tupaia belangeri	ENSTBEG00000007772	1 retrocopy	retro_tbel_2455,