RetrogeneDB ID: retro_lafr_750

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_35:4526630..4526857(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TAF10
• Ensembl ID: ENSLAFG00000029330
• Aliases: None
• Description: TAF10 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 30kDa [Source:HGNC Symbol;Acc:11543]

Sequence

>retro_lafr_750
TCCAGCACGTCTCTGGTAAACCTCCTGATGCAGCTAAAGGACTACCCACCCCCTATCCCAGATGCACTGACTGGTTACTG
CCTGACCCTGCTTACTTTGAGACTTGAGATCCATGCCTAATCCTAGTCATCACCCTAGCGGTCCAAAAATTTATCTCAAA
TAGGGGCGAAGATTCTCTACAGCACTGCAAAATTTAGGGCCCAGCCTCCGGCAGTTCCCAAAGCAAA

Alignment

ORF - retro_lafr_750 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.34 %
• Parental protein coverage: 70.37 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SSTPLVDFLMQLEDYTPTIPDAVTGYYL-NRAGFEASDPRIIRLISLAAQKFISDIANDALQHCKMKGTA
          SST.LV..LMQL.DY.P.IPDA.TGY.L...A.FE..DP..I..I.LA.QKFIS....D.LQHCK..G.A
Retrocopy SSTSLVNLLMQLKDYPPPIPDALTGYCL<DPAYFET*DPCLILVITLAVQKFISNRGEDSLQHCKI*GPA

Parental  SGSSRSK
          SGSS.SK
Retrocopy SGSSQSK

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_750 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 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016278	2 retrocopies	retro_amel_1088, retro_amel_297,
Dasypus novemcinctus	ENSDNOG00000000814	1 retrocopy	retro_dnov_592,
Equus caballus	ENSECAG00000007794	1 retrocopy	retro_ecab_525,
Echinops telfairi	ENSETEG00000008886	1 retrocopy	retro_etel_2090,
Loxodonta africana	ENSLAFG00000029330	1 retrocopy	retro_lafr_750 ,
Macropus eugenii	ENSMEUG00000008216	2 retrocopies	retro_meug_1645, retro_meug_992,
Myotis lucifugus	ENSMLUG00000024459	1 retrocopy	retro_mluc_1960,
Macaca mulatta	ENSMMUG00000007743	1 retrocopy	retro_mmul_1144,
Mus musculus	ENSMUSG00000043866	1 retrocopy	retro_mmus_35,