RetrogeneDB ID: retro_lafr_1062

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_63:10465166..10465438(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HBXIP
• Ensembl ID: ENSLAFG00000012907
• Aliases: None
• Description: None

Sequence

>retro_lafr_1062
TTGGACACAACCTTGAAGCAGCACTTGGGGGACACAATGAAGAATTCTTCCATTGTTGGAGTCCTGTGCGCAGATTCACA
AGGACTCAATCTGGGCTGCTGTGGAACCCTGTCAGATAGCATGCTGGGGTGATATATGTTCTAGCCTGGCAAACAGCTAA
GCTGACCTCTGACCCCACTGCTATTCCTGTGGTGCGTCTAGAATCAGGTAACAGGAACATTAGGATCCAGGAACCCAATA
ACCCCACAGTGGCAGTGCACAAAATGGCCTCT

Alignment

ORF - retro_lafr_1062 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.91 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  METTLEQHLEDTMKNPSIVGVLCTDSQGLNLGCRGTLSDE-HAGVISVLAQQAAKLTSDPTDIPVVCLES
          ..TTL.QHL.DTMKN.SIVGVLC.DSQGLNLGC.GTLSD..HAGVI.VLA.Q.AKLTSDPT.IPVV.LES
Retrocopy LDTTLKQHLGDTMKNSSIVGVLCADSQGLNLGCCGTLSDS<HAGVIYVLAWQTAKLTSDPTAIPVVRLES

Parental  DSGNVMIQKHDGITVAVHKMAS
          ...N..IQ.....TVAVHKMAS
Retrocopy GNRNIRIQEPNNPTVAVHKMAS

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_1062 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 6 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011504	2 retrocopies	retro_amel_118, retro_amel_974,
Bos taurus	ENSBTAG00000014970	3 retrocopies	retro_btau_1505, retro_btau_1755, retro_btau_71,
Loxodonta africana	ENSLAFG00000012907	5 retrocopies	retro_lafr_1057, retro_lafr_1061, retro_lafr_1062 , retro_lafr_665, retro_lafr_950,
Macaca mulatta	ENSMMUG00000015023	4 retrocopies	retro_mmul_164, retro_mmul_2452, retro_mmul_440, retro_mmul_499,
Sus scrofa	ENSSSCG00000006807	1 retrocopy	retro_sscr_986,
Ictidomys tridecemlineatus	ENSSTOG00000003401	5 retrocopies	retro_itri_1196, retro_itri_154, retro_itri_198, retro_itri_587, retro_itri_86,