RetrogeneDB ID: retro_lafr_419

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_15:48696112..48696592(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PNO1
• Ensembl ID: ENSLAFG00000000046
• Aliases: None
• Description: None

Sequence

>retro_lafr_419
CCGCTCTTCCCACCCCTCTCCTGGGACAGGCTCCTGGGTGGGAAAGAAGAAATAGGGAAAATTCCACTCCCAGCTAACAG
ATACCCACCATTGAAAGAGAACTAGAAGGTATTTACTCCTGTTGTAGAGCATATGGGACTTCAGATACGTTTTAACTTGA
AATCCAGGAATGTAGAAATCAGGACTTGTAAAGAAACCAAGAGTGTTAGTACTCAGACAGAAGCAGGTCATTTTGTGAAA
GCCTTTTTTCTGGGATTTCAGGTGGAGGATGCACCCACCCTCATCAGGTTGGACAGCTACTTCCTAGAGGAGTCTTTTGA
AATTACAGATGTTAAGCCTTTAAAAGGAAACCATCTCTCAAGGGCAGTTGGATGAACTGCTGGCAAAAGAAGAAAAACCA
AATTCACCATAAAGGATGTGACAAGGACACGGATAGTTTTGGCTGATGTGAAAGTTCACATTCTTGGCTCTTTCCGAAAT

Alignment

ORF - retro_lafr_419 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.12 %
• Parental protein coverage: 65.04 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PVFPPLSGDGLLGGKEETRKIPVPANRYTPLKENWMKIFTPVVEHLGLQIRFNLKSRNVEIRTCKETKDV
          P.FPPLS.D.LLGGKEE..KIP.PANRY.PLKEN..K.FTPVVEH.GLQIRFNLKSRNVEIRTCKETK.V
Retrocopy PLFPPLSWDRLLGGKEEIGKIPLPANRYPPLKEN*-KVFTPVVEHMGLQIRFNLKSRNVEIRTCKETKSV

Parental  SALTKAADFVKAFILGFQVEDALALIRLDDLFL-ESFEITDVKPLKGDHLSRAIGRIAGKGGKTKFTIEN
          S..T.A..FVKAF.LGFQVEDA..LIRLD..FL.ESFEITDVKPLKG.HLSRA.G..AGK..KTKFTI..
Retrocopy STQTEAGHFVKAFFLGFQVEDAPTLIRLDSYFLEESFEITDVKPLKGNHLSRAVG*TAGKRRKTKFTIKD

Parental  VTRTRIVLADVKVHILGSFQN
          VTRTRIVLADVKVHILGSF.N
Retrocopy VTRTRIVLADVKVHILGSFRN

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_419 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 14 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003256	1 retrocopy	retro_cfam_1886,
Callithrix jacchus	ENSCJAG00000006564	3 retrocopies	retro_cjac_2615, retro_cjac_273, retro_cjac_4127,
Felis catus	ENSFCAG00000025330	2 retrocopies	retro_fcat_1521, retro_fcat_864,
Loxodonta africana	ENSLAFG00000000046	1 retrocopy	retro_lafr_419 ,
Microcebus murinus	ENSMICG00000010897	1 retrocopy	retro_mmur_516,
Myotis lucifugus	ENSMLUG00000010850	1 retrocopy	retro_mluc_1719,
Macaca mulatta	ENSMMUG00000017461	2 retrocopies	retro_mmul_102, retro_mmul_352,
Nomascus leucogenys	ENSNLEG00000009993	1 retrocopy	retro_nleu_2389,
Oryctolagus cuniculus	ENSOCUG00000006100	1 retrocopy	retro_ocun_47,
Otolemur garnettii	ENSOGAG00000016637	1 retrocopy	retro_ogar_3025,
Pongo abelii	ENSPPYG00000012353	1 retrocopy	retro_pabe_1232,
Rattus norvegicus	ENSRNOG00000005524	1 retrocopy	retro_rnor_712,
Sus scrofa	ENSSSCG00000008352	2 retrocopies	retro_sscr_114, retro_sscr_352,
Tarsius syrichta	ENSTSYG00000004007	1 retrocopy	retro_tsyr_1625,