RetrogeneDB ID: retro_lafr_158

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_0:42604472..42604751(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C4ORF34
• Ensembl ID: ENSLAFG00000002601
• Aliases: None
• Description: None

Sequence

>retro_lafr_158
ATGGCAGAAGGTGGATTCAATCCATGTGAATGTGTTTGCTGTCATGAATGTGCGATAAGAAGGCTAATCAATTCATTGAG
GCAGTCCCAGTCCTACTGCACAGACACAGAATATCCTCAGGAATTACCAGGACTGTCTGGTGATAATGGTATAGTATTAC
CATGATCTTGATGGCCTGGAAGATTATTGCAGTGATCTTGTTCTTACTGAGACCTCCTAATCTAAGAGGATCCAAAATTA
CCTGGAGAACCAACCAGTCCTCATAATGGACAAGATCCT

Alignment

ORF - retro_lafr_158 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.16 %
• Parental protein coverage: 93.94 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAEGGFDPCECVCSHEHAMRRLINLLRQSQSYCTDTECLQELPGPSGDNGI-SITMILMAWMVIAVILFL
          MAEGGF.PCECVC.HE.A.RRLIN.LRQSQSYCTDTE..QELPG.SGDNGI.SITMILMAW..IAVILFL
Retrocopy MAEGGFNPCECVCCHECAIRRLINSLRQSQSYCTDTEYPQELPGLSGDNGI<SITMILMAWKIIAVILFL

Parental  LRPSNLRGS-SLPGKPASPHNGQDP
          LRP.NLRGS..LPG.P.SPHNGQDP
Retrocopy LRPPNLRGS>KLPGEPTSPHNGQDP

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_158 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 7 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000023287	1 retrocopy	retro_cfam_2156,
Dipodomys ordii	ENSDORG00000001693	2 retrocopies	retro_dord_468, retro_dord_570,
Homo sapiens	ENSG00000163683	1 retrocopy	retro_hsap_3836,
Loxodonta africana	ENSLAFG00000002601	2 retrocopies	retro_lafr_1038, retro_lafr_158 ,
Mustela putorius furo	ENSMPUG00000006076	1 retrocopy	retro_mputfur_641,
Nomascus leucogenys	ENSNLEG00000017113	1 retrocopy	retro_nleu_2132,
Otolemur garnettii	ENSOGAG00000007152	4 retrocopies	retro_ogar_1971, retro_ogar_3123, retro_ogar_3370, retro_ogar_740,