RetrogeneDB ID: retro_lafr_996

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_58:7086247..7086642(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DUXA
• Ensembl ID: ENSLAFG00000030167
• Aliases: None
• Description: None

Sequence

>retro_lafr_996
AAAAAACCTTACTAAGGTTATGCTTCCAAACAAAAACTTGCTTTAGAAATCAACGATGTAGAGTCTAGAATTTGAATTTG
GTTTCCGAATCGAAGAGTTAGACACTCATTCTAGAGAAGACCAGAGCTTAAGGAAGCTTTGAGATCAAGCCAAGACCATG
GGCAGGATCACCCTGAAGAGAAGATTCAGGGTCGAGAAGTCAGATGGTATCAAATCAGCTACACCTTCTCCCAGTTACAT
ACCCTCATTAAAGCATTTAAGAGCAGCCCTTACCCTGGGATTGATTCTGGAGAACAACTTGGTCAAGAATTGGGGTTCCA
AAGGAAAGAGTACAAATTTGGTTTCAGAATCAAAGATCTGGATTCTCTGCCCAAAAGAAAATGGCTGATGATGAC

Alignment

ORF - retro_lafr_996 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.96 %
• Parental protein coverage: 77.84 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RKPYPNYATRQKLASEINIEEPRIQIWFQNRRARHPFRKRSKPEEALKSSQDHGQGDLEERSQARRSRTY
          .KPY..YA..QKLA.EIN..E.RI.IWF.NRR.RH.F..R....EAL.SSQDHGQ...EE..Q.R..R.Y
Retrocopy KKPY*GYASKQKLALEINDVESRI*IWFPNRRVRHSF*RRPELKEALRSSQDHGQDHPEEKIQGREVRWY

Parental  ---YNCSQLHILVEAFENNPYPGIVSREQLAEE-IGVPESRVQIWFQNRRSRLFSQAKKEPDED
          ...Y..SQLH.L..AF...PYPGI.S.EQL..E.IGVP..RVQIWFQN.RS..FS..KK..D.D
Retrocopy QISYTFSQLHTLIKAFKSSPYPGIDSGEQLGQE<IGVPKERVQIWFQNQRSG-FSAQKKMADDD

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_996 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 42 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000025505	1 retrocopy	retro_dnov_701,
Felis catus	ENSFCAG00000007545	1 retrocopy	retro_fcat_1027,
Homo sapiens	ENSG00000258873	5 retrocopies	retro_hsap_1525, retro_hsap_2454, retro_hsap_4100, retro_hsap_566, retro_hsap_663,
Gorilla gorilla	ENSGGOG00000005650	7 retrocopies	retro_ggor_1017, retro_ggor_1076, retro_ggor_1167, retro_ggor_1528, retro_ggor_2133, retro_ggor_2752, retro_ggor_510,
Loxodonta africana	ENSLAFG00000030167	1 retrocopy	retro_lafr_996 ,
Macaca mulatta	ENSMMUG00000007788	5 retrocopies	retro_mmul_2157, retro_mmul_2363, retro_mmul_2396, retro_mmul_2441, retro_mmul_636,
Nomascus leucogenys	ENSNLEG00000010886	3 retrocopies	retro_nleu_1935, retro_nleu_2214, retro_nleu_568,
Oryctolagus cuniculus	ENSOCUG00000011331	1 retrocopy	retro_ocun_981,
Pongo abelii	ENSPPYG00000010457	8 retrocopies	retro_pabe_1192, retro_pabe_1328, retro_pabe_1805, retro_pabe_3357, retro_pabe_3376, retro_pabe_518, retro_pabe_660, retro_pabe_802,
Pan troglodytes	ENSPTRG00000028871	5 retrocopies	retro_ptro_1034, retro_ptro_1418, retro_ptro_2781, retro_ptro_424, retro_ptro_482,
Pteropus vampyrus	ENSPVAG00000003020	1 retrocopy	retro_pvam_870,
Tupaia belangeri	ENSTBEG00000005321	1 retrocopy	retro_tbel_3384,
Tarsius syrichta	ENSTSYG00000014223	1 retrocopy	retro_tsyr_1577,
Tursiops truncatus	ENSTTRG00000014200	2 retrocopies	retro_ttru_1277, retro_ttru_1768,