RetrogeneDB ID: retro_lafr_982

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_56:5124862..5125577(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSLAFG00000000867
• Aliases: None
• Description: None

Sequence

>retro_lafr_982
ATGGTGGAAAATGGTGATAGTGAAAGATGGCTGCACTGCAGGCCAAAATCTGTCATCCAATTGAGTATTATTTTGGTGAG
TTTAATTTTCCATGGGACAAGTTTTTAAAGGAACAGATCAAACTGGATGAAGGCTGGGTACCTTTGGAAATAATGATAAA
ATTCAACAGGCTAAACTGTCTAACAACAGACTTTAATGTAATAGTAAAGCATTGAGCAAATCAAAAGTATAACTCATGGA
AATAAGTGAAGATTAAACTAAAATCAGAAGATCTCCAAGAAAATCCCTCCATGAAGTGATTGATGAGTATAAAAATTATT
TTAAAAAACAGATTTGTTTATATTAAGGCTTCACAACTGATGCAAACTTCAGTGACATAAAAGAATGGTTAGAAGGCAAA
GGTGAAGTACTAAGTATTCTAATGAGAAGAACATTGCACAAAGCATTTAAGGGATCAATATTTGTGGTGTTTGATAGCAC
TGAATCTGCTAAGAAGTTTGTAGATATCCCTGGCCAGAAGTACAAAGACAAAGATTTGCTAACACTTTTCAAGGAAGACT
ACTTTGCAAAAATGAATGAAAAAAGAAAGCAAAATAAACTAGAAGTTAAATTATGAGCTAAACAAGTGCAAGAAGAAAAA
CAGTAGTTAGCAGAAGATGCTGAAATGAAATCTCTAGAAGAAAAGATGGACTGCTTGCTGAGATTTTCAGGTGAG

Alignment

ORF - retro_lafr_982 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.25 %
• Parental protein coverage: 56.64 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAENGDSE-KMAALEAKICHQIEYYFGDFNLPRDKFLKEQIKLDEGWVPLEIMIKFNRLNRLTTDFNVIV
          M.ENGDSE.KMAAL.AKICH.IEYYFG.FN.P.DKFLKEQIKLDEGWVPLEIMIKFNRLN.LTTDFNVIV
Retrocopy MVENGDSE<KMAALQAKICHPIEYYFGEFNFPWDKFLKEQIKLDEGWVPLEIMIKFNRLNCLTTDFNVIV

Parental  -EALSKSKVELMEISEDKTKIRRSPSKPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVL
          ..ALSKSKV.LMEISED.TKIRRSP.K.L.EV.DE.............GF.TDA...DIKEWLE.KG.VL
Retrocopy <KALSKSKV*LMEISED*TKIRRSPRKSLHEVIDEXXXXXXXQICLY*GFTTDANFSDIKEWLEGKGEVL

Parental  NILMRRTLHKAFKGSIFVVFDSIESAKKFVETPGQKYKDTDLLILFKEDYFAKKNEERKQNKLEAKLRAK
          .ILMRRTLHKAFKGSIFVVFDS.ESAKKFV..PGQKYKD.DLL.LFKEDYFAK.NE.RKQNKLE.KL.AK
Retrocopy SILMRRTLHKAFKGSIFVVFDSTESAKKFVDIPGQKYKDKDLLTLFKEDYFAKMNEKRKQNKLEVKL*AK

Parental  QEQEEKQKLAEDAEMKSLEEKMGCLLKFSGD
          Q.QEEKQ.LAEDAEMKSLEEKM.CLL.FSG.
Retrocopy QVQEEKQ*LAEDAEMKSLEEKMDCLLRFSGE

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_982 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 18 parental genes, and 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007763	5 retrocopies	retro_chof_1125, retro_chof_1292, retro_chof_1380, retro_chof_185, retro_chof_2593,
Dasypus novemcinctus	ENSDNOG00000013450	1 retrocopy	retro_dnov_2038,
Echinops telfairi	ENSETEG00000004614	1 retrocopy	retro_etel_2056,
Homo sapiens	ENSG00000138385	1 retrocopy	retro_hsap_448,
Gorilla gorilla	ENSGGOG00000011507	3 retrocopies	retro_ggor_2914, retro_ggor_434, retro_ggor_791,
Gorilla gorilla	ENSGGOG00000023471	4 retrocopies	retro_ggor_2834, retro_ggor_2915, retro_ggor_433, retro_ggor_792,
Loxodonta africana	ENSLAFG00000000867	3 retrocopies	retro_lafr_698, retro_lafr_745, retro_lafr_982 ,
Macropus eugenii	ENSMEUG00000001650	1 retrocopy	retro_meug_1908,
Myotis lucifugus	ENSMLUG00000016316	1 retrocopy	retro_mluc_2493,
Macaca mulatta	ENSMMUG00000023051	2 retrocopies	retro_mmul_1153, retro_mmul_529,
Monodelphis domestica	ENSMODG00000008227	1 retrocopy	retro_mdom_1080,
Nomascus leucogenys	ENSNLEG00000004958	3 retrocopies	retro_nleu_1039, retro_nleu_177, retro_nleu_3011,
Otolemur garnettii	ENSOGAG00000029768	1 retrocopy	retro_ogar_1642,
Pongo abelii	ENSPPYG00000012919	3 retrocopies	retro_pabe_3408, retro_pabe_3641, retro_pabe_424,
Pan troglodytes	ENSPTRG00000012620	1 retrocopy	retro_ptro_2509,
Rattus norvegicus	ENSRNOG00000007998	1 retrocopy	retro_rnor_405,
Tupaia belangeri	ENSTBEG00000009056	4 retrocopies	retro_tbel_1065, retro_tbel_1269, retro_tbel_3318, retro_tbel_4012,
Tursiops truncatus	ENSTTRG00000002152	2 retrocopies	retro_ttru_1926, retro_ttru_466,