RetrogeneDB ID: retro_lafr_578

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_223:52245..53130(+)
• 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_578
GTGCACCGAGATAACCTGCACACTATGAGGGAGTGGTGGGTCCAGGTGGGGTTGCTGGCCGTGTTCCTGCTGGCGGCCTA
CCTGCACATCCCACCCCCTCAGCTTTCCCCTGCTCTTCACTCATGAAAGTCCACAGGCAAATTTTTCACCTATCAGGGAC
TGCGCATCTTTTACCAAGACTCCGTGGGTGTGGTTGGAAGTCCAGAAATAGTTGTGCTCCTATATGGCTTTCCAACATCC
AGCTAGGATTGGTACAAGATTTCGGAAGGTCTGACCCTCAGGTTTCATGAGTAATTGCTCTTGATTTCTTAGGCTTTGGC
TTCAGTGACAAACGGAGACCACACCACTACTCCATATTTGAACAGGCCAGCATGCGGAGGCATGCTTGAGAGGCTTCTGG
TTCTCCAGAACTGTAGGATCAACCACCTATCTCATGACTGTGGAGACATCGTGGCTCAGGAGCTGCTCCATAGGTACAAG
CGGAATCTGTCTGGGCAGCTTACCATAAAGTCTCTGCCTGTCAAATGGAGGTATCTTTTCCGAGACTCATCATCCTCTCC
TTCTCCAGAAGCTTCTTAAAGATGGAGGCATGCTGTCAACCATCCTCACACGTTTGATGAACTTCTTTGTTATTCTCTTG
AGGTCTCATCCCGGTCTTTGGGCCCTACACTTGGCCTCTGAGAGAGAGCTGTGGGACATGTGGGCAGAGATAGCAACAAT
GACAGAGACTTAGTCAATGATAGTCTTCTACGGTATGTTAACCAGAGGGAGAAGTTTAGAAGATGCTGGGTGGGAGCCCT
TGCCTCTGTATCTTTTCCCATTCATTTTATCTGTGGGCCATTGGATCCCATAAATCCTTACCTGGAGTTTTTGGAGCTGT
ATAGG

Alignment

ORF - retro_lafr_578 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.48 %
• Parental protein coverage: 88.36 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  VRRDRLRRMREWWVQVGLLAVPLLAAYLHIPPPQLSPALHSWKSSGKFFTYKGLHIFYQDSMGVVGSPEI
          V.RD.L..MREWWVQVGLLAV.LLAAYLHIPPPQLSPALHS.KS.GKFFTY.GL.IFYQDS.GVVGSPEI
Retrocopy VHRDNLHTMREWWVQVGLLAVFLLAAYLHIPPPQLSPALHS*KSTGKFFTYQGLRIFYQDSVGVVGSPEI

Parental  VVLLHGFPTSSYDWYKIWEGLTLRFHR-VIALDFLGFGFSDKPRPHHYSIFEQASIVE-ALLRHLGLQNR
          VVLL.GFPTSS.DWYKI.EGLTLRFH..VIALDFLGFGFSDK.RPHHYSIFEQAS.....L.R.L.LQN.
Retrocopy VVLLYGFPTSS*DWYKISEGLTLRFHE<VIALDFLGFGFSDKRRPHHYSIFEQASMRR>MLERLLVLQNC

Parental  RINLLSHDYGDTVAQELLYRYKQNRSGRLTIKSLCLSNGGIFPET-HRPLLLQKLLKDGGVLSPILTRLM
          RIN.LSHD.GD.VAQELL.RYK.N.SG.LTIKSL.......F....H..LL.QKLLKDGG.LS.ILTRLM
Retrocopy RINHLSHDCGDIVAQELLHRYKRNLSGQLTIKSLPVKWRYLFRDS>HPLLL-QKLLKDGGMLSTILTRLM

Parental  NFFV-FSRGLTPVFGPYTRP-SESELWDMWAGI-RNNDGNLVIDSLLQYINQRKKFRRRWVGALASVSIP
          NFFV.FS.GL.PVFGPYT.P.SE.ELWDMWA.I..NND..LV.DSLL.Y.NQR.KFRR.WVGALASVS.P
Retrocopy NFFV>FS*GLIPVFGPYTWP<SERELWDMWAEI<SNNDRDLVNDSLLRYVNQREKFRRCWVGALASVSFP

Parental  IHFIYGPLDPVNPYPEFLELYR
          IHFI.GPLDP.NPY.EFLELYR
Retrocopy IHFICGPLDPINPYLEFLELYR

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_578 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.

---

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,