RetrogeneDB ID: retro_lafr_748

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_341:74656..75540(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MEST
• Ensembl ID: ENSLAFG00000006066
• Aliases: None
• Description: None

Sequence

>retro_lafr_748
GTGCACCGAGATAACCTGCACACGGTGAGGGAATGGTGGGTCCAGGTGGGGTTGCTGGCCGTGCTCCTGCTGGCGGCCTA
CCTGCACATCCCACCCCCTCAGCTTTCCCCTGCTCTTAACTCATGAAAGTCCACAGGCAAATTTTTCACCTATCAGGGAC
TGCGCATCTTTTACCAAGACTCCGTGGGTGTGGTTGGAAGTCCAGAAATAGTTGTGCTCCTATATGGCTTTCCAACATCC
AGCTATGATGGTACAAGATTTCGGAAGGTCTGACCCTCAGGTTTCATGAGTAATTGCTCTTGATTTCTTAGGCTTTGGCT
TCAGTGACAAACGGAGACCACACCACTACTCCATATTTGAACAGGCCAGCATGCGGAGGCATGCTTGAGAGGCTTCTGGT
TCTCCAGAACTGTAGGATCAACCACCTATCTCATGACTATGGAGACATCGTGGCTCAGGAGCTGCTCCATAGGTACAAGT
GGAATCCGTCTGGGCAGCTTACCATAAAGTCTCTGCCTGTCAAATGGAGGTATCTTTTCCGAGACTCATCATCCTCTCCT
TCTCCAGAAGCTTCTTAAAGATGGAGGCATGCTGTCAACCATCCTCACACGTTTGATGAACTTCTTTGTTATTCTCTTGA
GGTCTCATCCCGGTCTTTGGGCCCTACACTTGGCCTCTGAGAGTGACCTGTGGGACGTATGGGCAGAGATAGTAACAATG
ACAGAGACTTAGTCATTGATAGTCTTCTACAGTATGTTAACCAGAGGAAGAAGTTTAGAAGATGCTGGGTGGGAGCCCTT
GCCTCTGTATCTATTCCCATTCATTTTATCTGTGGGCCATTGGATCCCATAAATCCTTACCTGGAGTTTTTGGAGCTGTA
TAGG

Alignment

ORF - retro_lafr_748 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.22 %
• Parental protein coverage: 88.36 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  VRRDRLRRMREWWVQVGLLAVPLLAAYLHIPPPQLSPALHSWKSSGKFFTYKGLHIFYQDSMGVVGSPEI
          V.RD.L...REWWVQVGLLAV.LLAAYLHIPPPQLSPAL.S.KS.GKFFTY.GL.IFYQDS.GVVGSPEI
Retrocopy VHRDNLHTVREWWVQVGLLAVLLLAAYLHIPPPQLSPALNS*KSTGKFFTYQGLRIFYQDSVGVVGSPEI

Parental  VVLLHGFPTSSYD-WYKIWEGLTLRFHR-VIALDFLGFGFSDKPRPHHYSIFEQASIVE-ALLRHLGLQN
          VVLL.GFPTSSYD.WYKI.EGLTLRFH..VIALDFLGFGFSDK.RPHHYSIFEQAS.....L.R.L.LQN
Retrocopy VVLLYGFPTSSYD<WYKISEGLTLRFHE<VIALDFLGFGFSDKRRPHHYSIFEQASMRR>MLERLLVLQN

Parental  RRINLLSHDYGDTVAQELLYRYKQNRSGRLTIKSLCLSNGGIFPET-HRPLLLQKLLKDGGVLSPILTRL
          .RIN.LSHDYGD.VAQELL.RYK.N.SG.LTIKSL.......F....H..LL.QKLLKDGG.LS.ILTRL
Retrocopy CRINHLSHDYGDIVAQELLHRYKWNPSGQLTIKSLPVKWRYLFRDS>HPLLL-QKLLKDGGMLSTILTRL

Parental  MNFFV-FSRGLTPVFGPYTRP-SESELWDMWAGI-RNNDGNLVIDSLLQYINQRKKFRRRWVGALASVSI
          MNFFV.FS.GL.PVFGPYT.P.SES.LWD.WA.I..NND..LVIDSLLQY.NQRKKFRR.WVGALASVSI
Retrocopy MNFFV>FS*GLIPVFGPYTWP<SESDLWDVWAEI<SNNDRDLVIDSLLQYVNQRKKFRRCWVGALASVSI

Parental  PIHFIYGPLDPVNPYPEFLELYR
          PIHFI.GPLDP.NPY.EFLELYR
Retrocopy PIHFICGPLDPINPYLEFLELYR

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_748 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 15 parental genes, and 35 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005659	2 retrocopies	retro_amel_1177, retro_amel_1874,
Callithrix jacchus	ENSCJAG00000010760	2 retrocopies	retro_cjac_1563, retro_cjac_3931,
Felis catus	ENSFCAG00000022984	5 retrocopies	retro_fcat_1067, retro_fcat_1645, retro_fcat_1693, retro_fcat_2004, retro_fcat_326,
Loxodonta africana	ENSLAFG00000006066	3 retrocopies	retro_lafr_578, retro_lafr_584, retro_lafr_748 ,
Macropus eugenii	ENSMEUG00000008227	1 retrocopy	retro_meug_885,
Microcebus murinus	ENSMICG00000006129	1 retrocopy	retro_mmur_1091,
Macaca mulatta	ENSMMUG00000009499	2 retrocopies	retro_mmul_1936, retro_mmul_94,
Nomascus leucogenys	ENSNLEG00000012841	3 retrocopies	retro_nleu_1065, retro_nleu_515, retro_nleu_790,
Otolemur garnettii	ENSOGAG00000009224	1 retrocopy	retro_ogar_3464,
Pongo abelii	ENSPPYG00000018006	4 retrocopies	retro_pabe_2337, retro_pabe_2510, retro_pabe_2511, retro_pabe_866,
Pan troglodytes	ENSPTRG00000019698	2 retrocopies	retro_ptro_1769, retro_ptro_2045,
Sorex araneus	ENSSARG00000000502	1 retrocopy	retro_sara_352,
Ictidomys tridecemlineatus	ENSSTOG00000020977	2 retrocopies	retro_itri_1210, retro_itri_1610,
Tupaia belangeri	ENSTBEG00000008404	2 retrocopies	retro_tbel_1480, retro_tbel_526,
Tursiops truncatus	ENSTTRG00000004934	4 retrocopies	retro_ttru_1026, retro_ttru_1115, retro_ttru_1133, retro_ttru_1907,