RetrogeneDB ID: retro_lafr_205

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_1:48843831..48844358(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AK3
• Ensembl ID: ENSLAFG00000001126
• Aliases: None
• Description: None

Sequence

>retro_lafr_205
ATTGGTGTGTTGGCCAAGACTTTCATTGACCAAGGGATGCTCATCCCAGACTACGTCATGCCTTAGATGGACCTGGAGGA
GCTGAAAAATCTCACCCAGTATAGCTGGCTGTTGTGTGGTTTTCCAAGGACACCTCCACAGGCGGAAGCCCTGGACAGAG
TTTATAAAATAGACTAGTGATTAACCTGAACGTGCCCTTTCTGGTCATTAAGCAACGCCTCACTGCTCGCTGGATTCATC
TAGCCAGTGGCCGAATCTCTAATCTCAAATTCAACCCTCCCAAAGCCATAGGCATTGATGATCTAACTGGAGAGCCTCTC
GTTCAGTGTGAGGATGATAGGCCAGAGACGGTTATTAAGAGACTGAAGGTTTATGAAGCACAACTCCAACTGGTTCTGGA
ATGTTAGCAGAAAAAAGGCATGTTGGAAACATTCTCCGGAACAGAAACTGACAAGATCTGGCCCCAAGTATATGCTTTCC
TACAAACAAAAGTTCCACAAATAAACCAGAAAGCATCGGTTACTCCA

Alignment

ORF - retro_lafr_205 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.33 %
• Parental protein coverage: 97.28 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IGVLAKTFIDQGKLIPDDVMTRLVLHELKHLTQYSWLLDVVKGFPRTVPQAEALDKVYQID-TVINLNVP
          IGVLAKTFIDQG.LIPD.VM....L.ELK.LTQYSWLL....GFPRT.PQAEALD.VY.ID..VINLNVP
Retrocopy IGVLAKTFIDQGMLIPDYVMP*MDLEELKNLTQYSWLLC---GFPRTPPQAEALDRVYKID<LVINLNVP

Parental  FEVIKQRLTARWIHPASGRVYNIDFNPPKSVGIDDLTGEPLVQREDDRPETVIKRLKAYEAQTEPVLDYY
          F.VIKQRLTARWIH.ASGR..N..FNPPK..GIDDLTGEPLVQ.EDDRPETVIKRLK.YEAQ...VL...
Retrocopy FLVIKQRLTARWIHLASGRISNLKFNPPKAIGIDDLTGEPLVQCEDDRPETVIKRLKVYEAQLQLVLEC*

Parental  QKKGVLETFSGTETNKIWPHVYAFLQTKVPQINHTASVSP
          QKKG.LETFSGTET.KIWP.VYAFLQTKVPQIN..ASV.P
Retrocopy QKKGMLETFSGTETDKIWPQVYAFLQTKVPQINQKASVTP

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_205 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 24 parental genes, and 47 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002640	3 retrocopies	retro_amel_1009, retro_amel_1916, retro_amel_1931,
Bos taurus	ENSBTAG00000017147	1 retrocopy	retro_btau_323,
Callithrix jacchus	ENSCJAG00000011188	1 retrocopy	retro_cjac_1940,
Equus caballus	ENSECAG00000011235	2 retrocopies	retro_ecab_317, retro_ecab_914,
Echinops telfairi	ENSETEG00000000829	1 retrocopy	retro_etel_57,
Felis catus	ENSFCAG00000028063	2 retrocopies	retro_fcat_162, retro_fcat_1982,
Homo sapiens	ENSG00000147853	3 retrocopies	retro_hsap_1163, retro_hsap_3228, retro_hsap_555,
Gorilla gorilla	ENSGGOG00000028122	3 retrocopies	retro_ggor_2195, retro_ggor_503, retro_ggor_908,
Loxodonta africana	ENSLAFG00000001126	1 retrocopy	retro_lafr_205 ,
Microcebus murinus	ENSMICG00000013112	3 retrocopies	retro_mmur_1474, retro_mmur_1559, retro_mmur_1579,
Myotis lucifugus	ENSMLUG00000017272	1 retrocopy	retro_mluc_535,
Macaca mulatta	ENSMMUG00000000143	2 retrocopies	retro_mmul_2032, retro_mmul_898,
Mustela putorius furo	ENSMPUG00000005006	2 retrocopies	retro_mputfur_1163, retro_mputfur_890,
Nomascus leucogenys	ENSNLEG00000008885	3 retrocopies	retro_nleu_2638, retro_nleu_2653, retro_nleu_948,
Oryctolagus cuniculus	ENSOCUG00000011411	1 retrocopy	retro_ocun_716,
Otolemur garnettii	ENSOGAG00000007477	2 retrocopies	retro_ogar_3482, retro_ogar_3492,
Pongo abelii	ENSPPYG00000019245	3 retrocopies	retro_pabe_2676, retro_pabe_3588, retro_pabe_967,
Pan troglodytes	ENSPTRG00000020742	5 retrocopies	retro_ptro_1785, retro_ptro_2180, retro_ptro_2895, retro_ptro_416, retro_ptro_796,
Pteropus vampyrus	ENSPVAG00000015751	1 retrocopy	retro_pvam_269,
Sus scrofa	ENSSSCG00000023595	1 retrocopy	retro_sscr_641,
Ictidomys tridecemlineatus	ENSSTOG00000000021	1 retrocopy	retro_itri_933,
Tupaia belangeri	ENSTBEG00000008054	3 retrocopies	retro_tbel_1463, retro_tbel_3247, retro_tbel_3397,
Tursiops truncatus	ENSTTRG00000016524	1 retrocopy	retro_ttru_1036,
Vicugna pacos	ENSVPAG00000009187	1 retrocopy	retro_vpac_137,