RetrogeneDB ID: retro_lafr_498

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_2:7688081..7688726(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSLAFG00000028431
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSLAFG00000006271
• Aliases: None
• Description: None

Sequence

>retro_lafr_498
CCCTGCAGAGCTCTGTTGTGGGCGGGCACTGAGCAGCTGCTGCGAGAAATCCATGAGCTATTCCAGCGGCGGCTTGGAGC
CGGCACCCCTGACCGGGAGCGCGATGTCAACCTCTCTCACAATCCGGGTACAGCCATTGTGCGGCGCTGGTTGAAGGTGC
AGCTGGTGGGGGAAGGCAGGAAGCCGCGCTTGCACCAGCGACACTACGTCTACAAGCTAGTGAAGGAAAGGAAAGAAAAC
CTGGAGCACATCCTCACGCAATCTGTGGAGGAACTTGGATTCTGGCGCGACCTGGCCTCAGTAAAGAAGTCTGTGAGCGG
TAATGGACTGCTTCTCAAGGACTAGCTGTATATGCATCCCCTGAAAAGAAAAAGCTGTTTGAAGAGGAAAAATCGCTGAG
TCGCGAAGGAAAATTAGAGAAGATCCAAACCAAGGAACATGAAGTAACAGTGAAATTTCTGAGAGGCTGTCATCTGAAAG
TGGGGATGAAGAGCAATGTAACATGGGAGCTAAACCGCGAAATAGCTGCCCGCCATTACTTCAAGAACCTTGGTGTTACG
GTAGTCTCACCATGCCGAAAAGTTACCAGAAGAGCCCATCACACGGTGGGGGGAGTGTTGGTGTGAAGTGATGGTAAATG
GACTG

Alignment

ORF - retro_lafr_498 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.52 %
• Parental protein coverage: 82.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PARALLRAGAEQLLRGGVLGLFRPRLGAGTPGLERDFSLSHSRGTVIVERWWKVPLAGEGRKPRLHRRHR
          P.RALL.AG.EQLLR.....LF..RLGAGTP..ERD..LSH..GT.IV.RW.KV.L.GEGRKPRLH.RH.
Retrocopy PCRALLWAGTEQLLRE-IHELFQRRLGAGTPDRERDVNLSHNPGTAIVRRWLKVQLVGEGRKPRLHQRHY

Parental  VYKLVEDTKHSPKENLELILTQSVEELGIRGDLVSVKKSVGRNRLL-SQGLAVYASPENKKLFEEEKLLR
          VYKLV.......KENLE.ILTQSVEELG...DL.SVKKSV..N.LL.SQGLAVYASPE.KKLFEEEK.L.
Retrocopy VYKLVKER----KENLEHILTQSVEELGFWRDLASVKKSVSGNGLL<SQGLAVYASPEKKKLFEEEKSLS

Parental  QQGKLEKIQTKAGEATVKFLRSCHLEVGMKNNVKWELNPEIVARHFFKNLGVVV-APHAIKLPEEPITRW
          ..GKLEKIQTK..E.TVKFLR.CHL.VGMK.NV.WELN.EI.ARH.FKNLGV.V...HA.KLPEEPITRW
Retrocopy REGKLEKIQTKEHEVTVKFLRGCHLKVGMKSNVTWELNREIAARHYFKNLGVTV>SHHAEKLPEEPITRW

Parental  GEYWCEVTVNGL
          GE.WCEV.VNGL
Retrocopy GECWCEVMVNGL

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_498 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 11 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000258	1 retrocopy	retro_chof_10,
Dasypus novemcinctus	ENSDNOG00000011403	1 retrocopy	retro_dnov_1989,
Homo sapiens	ENSG00000143436	1 retrocopy	retro_hsap_4078,
Gorilla gorilla	ENSGGOG00000001902	1 retrocopy	retro_ggor_2735,
Loxodonta africana	ENSLAFG00000006271	2 retrocopies	retro_lafr_498 , retro_lafr_563,
Nomascus leucogenys	ENSNLEG00000010275	1 retrocopy	retro_nleu_2045,
Oryctolagus cuniculus	ENSOCUG00000001383	1 retrocopy	retro_ocun_725,
Otolemur garnettii	ENSOGAG00000030456	1 retrocopy	retro_ogar_159,
Pongo abelii	ENSPPYG00000000857	1 retrocopy	retro_pabe_3347,
Pan troglodytes	ENSPTRG00000001295	2 retrocopies	retro_ptro_2765, retro_ptro_2996,
Vicugna pacos	ENSVPAG00000000664	1 retrocopy	retro_vpac_123,