RetrogeneDB ID: retro_lafr_990

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_57:5643111..5643623(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPA1
• Ensembl ID: ENSLAFG00000004048
• Aliases: None
• Description: None

Sequence

>retro_lafr_990
TTCACTCTGGAGTACCGAGTCTTCCTCAAAAACGAAAAAGGACAACACATATCTCCATTTCATGATATTCCAATTTATGC
AGATTAGGGTGTGTTCCACATTGTGGTTGAAGTACCACAATAGTCTGATGCAAAAACGGAGATTGCTACAAAGGACCCAT
TAAATCCAATGAAACAAGATGTGAAAATAAGAAAACTCTATTGTGTTGCAAATTTGTTCCCTTATAAAGGATACATCTGG
ACCTATGGCACCCTCCCTCAGACTTGGGAAGACCCAGGACACAACGACAGACACACTGGCTGTTGTGGCAACAATGACCC
AATTGATGTGTGTGAAATTGAAAGCAAGGTATGTGGGAGAGGTGAAATAATCATTGTGAAACTTTTGGACATACTGGCTA
TGATTCATGAAGGGGAAGCCGACTGGAAAGTCGTTGCCATTAATGTGATGCAGCCAGTTATAATGATATTAATGATGTCA
AATGGCTAAAGCGTGGGTGCCTAGACGCTACT

Alignment

ORF - retro_lafr_990 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.29 %
• Parental protein coverage: 59.39 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FTLEYRVFFKNEKGQYISPFHDIPIYAKKDVFHMVVEVPRWSNAKMEIATKDPLNPIKQDVKKGKLRYVA
          FTLEYRVF.KNEKGQ.ISPFHDIPIYA...VFH.VVEVP..S.AK.EIATKDPLNP.KQDVK..KL..VA
Retrocopy FTLEYRVFLKNEKGQHISPFHDIPIYAD*GVFHIVVEVPQ*SDAKTEIATKDPLNPMKQDVKIRKLYCVA

Parental  NLFPYKGYIWNYGAIPQTWEDPGHNDGHTGCCGDNDPIDVCEIGSKVCARGEIISVKVLGILAMIDEGET
          NLFPYKGYIW.YG..PQTWEDPGHND.HTGCCG.NDPIDVCEI.SKVC.RGEII.VK.L.ILAMI.EGE.
Retrocopy NLFPYKGYIWTYGTLPQTWEDPGHNDRHTGCCGNNDPIDVCEIESKVCGRGEIIIVKLLDILAMIHEGEA

Parental  DWKVIAINVDDP-DAANYNDINDVKRLKPGYLEAT
          DWKV.AINV..P......ND....KR...G.L.AT
Retrocopy DWKVVAINVMQP<SYNDINDVKWLKR---GCLDAT

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_990 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 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014033	1 retrocopy	retro_cfam_1040,
Cavia porcellus	ENSCPOG00000014023	1 retrocopy	retro_cpor_615,
Dasypus novemcinctus	ENSDNOG00000014861	1 retrocopy	retro_dnov_1310,
Equus caballus	ENSECAG00000018686	1 retrocopy	retro_ecab_691,
Homo sapiens	ENSG00000180817	2 retrocopies	retro_hsap_2756, retro_hsap_3267,
Loxodonta africana	ENSLAFG00000004048	1 retrocopy	retro_lafr_990 ,
Myotis lucifugus	ENSMLUG00000017790	1 retrocopy	retro_mluc_2469,
Macaca mulatta	ENSMMUG00000006397	1 retrocopy	retro_mmul_1540,
Nomascus leucogenys	ENSNLEG00000016098	1 retrocopy	retro_nleu_7,
Oryctolagus cuniculus	ENSOCUG00000016001	2 retrocopies	retro_ocun_1373, retro_ocun_883,
Procavia capensis	ENSPCAG00000006788	1 retrocopy	retro_pcap_247,
Pongo abelii	ENSPPYG00000029405	1 retrocopy	retro_pabe_37,
Pan troglodytes	ENSPTRG00000002585	2 retrocopies	retro_ptro_1864, retro_ptro_2210,
Tupaia belangeri	ENSTBEG00000008947	3 retrocopies	retro_tbel_3560, retro_tbel_3561, retro_tbel_848,
Tarsius syrichta	ENSTSYG00000005511	1 retrocopy	retro_tsyr_1856,