RetrogeneDB ID: retro_lafr_467

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_18:11598267..11598972(+)
• Located in intron of: ENSLAFG00000002485

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMD12
• Ensembl ID: ENSLAFG00000010876
• Aliases: None
• Description: None

Sequence

>retro_lafr_467
AAGAGCAAGCCAGTGGAGTTTATTTTGGAACAAATGAGGCTCTGCCTAGCTGTGAAGGATTACATTAGTACACAAATAAT
CAGCAAGAAAATTAATACTAAGTTTTTCCAGGAAGAAAATACAGAGAAAATAAAGGTGAAATATTATAACTTAATGATTC
AGCTGGATAAACATGAGGGATATTATTTGTCTATTTGTAAGCACTACAGAACAATATATGACACTTCCTCTATATGGGCA
GAAAGTGAAACATGAAAACAGAATCTAAAAAGTGTTGTTCTTTATGCTATCCTGGCTCCTTTTGACAATGAACAGTCAGA
TTTGGTTCACCGAATAAGTGGTGATAAGAAGTTAGAAGAAATTCCCAAGTGCGAGGATATTTTAAAGCTTTTTGCCACAA
GGGAGTTGATGGGTTGGTCCACACTTGTTGAGGACTATGGAATGGAATTAAGAAAAGGTTCTCAGGACAGTCCAGAAACT
GATGTTTTGGGCTATACAGAGGAAGATGAAAAAAGGTGGAAAGACATGACGAACAAGAGTTGTTGGACATAGTATTAGAG
TAATGGCCAAATATTATATGAGGATAATGGCAAAGAGGATGGCACAGTTTCTAGATCTATCCATCGACGAATCAGAGGAT
TTCTCTCAAATCTAGTAGTTAACAAGACCATCTTTACTAAAGTAGACAGGTGGGCAGGAATTATC

Alignment

ORF - retro_lafr_467 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.43 %
• Parental protein coverage: 51.54 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KKERVEFILEQMRLCLAVKDYIRTQIISKKINTKFFQEENTEKLKLKYYNLMIQLDQHEGSYLSICKHYR
          K...VEFILEQMRLCLAVKDYI.TQIISKKINTKFFQEENTEK.K.KYYNLMIQLD.HEG.YLSICKHYR
Retrocopy KSKPVEFILEQMRLCLAVKDYISTQIISKKINTKFFQEENTEKIKVKYYNLMIQLDKHEGYYLSICKHYR

Parental  AIYDTPCIQAESEKWQQALKSVVLYVILAPFDNEQSDLVHRISGDKKLEEIPKYKDLLKLFTTMELMRWS
          .IYDT..I.AESE...Q.LKSVVLY.ILAPFDNEQSDLVHRISGDKKLEEIPK..D.LKLF.T.ELM.WS
Retrocopy TIYDTSSIWAESET*KQNLKSVVLYAILAPFDNEQSDLVHRISGDKKLEEIPKCEDILKLFATRELMGWS

Parental  TLVEDYGMELRKGSRESPATDVFGSTEEGEKRWKDLKN-RVVEHNIRIMAKYYTRITMKRMAQLLDLSVD
          TLVEDYGMELRKGS..SP.TDV.G.TEE.EKRWKD..N.RVV.H.IR.MAKYY.RI..KRMAQ.LDLS.D
Retrocopy TLVEDYGMELRKGSQDSPETDVLGYTEEDEKRWKDMTN>RVVGHSIRVMAKYYMRIMAKRMAQFLDLSID

Parental  ESE-AFLSNLVVNKTIFAKVDRLAGII
          ESE..FLSNLVVNKTIF.KVDR.AGII
Retrocopy ESE<GFLSNLVVNKTIFTKVDRWAGII

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_467 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 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000008691	2 retrocopies	retro_cjac_1400, retro_cjac_2793,
Homo sapiens	ENSG00000197170	1 retrocopy	retro_hsap_2801,
Gorilla gorilla	ENSGGOG00000014761	1 retrocopy	retro_ggor_1947,
Loxodonta africana	ENSLAFG00000010876	1 retrocopy	retro_lafr_467 ,
Nomascus leucogenys	ENSNLEG00000001265	1 retrocopy	retro_nleu_1541,
Pongo abelii	ENSPPYG00000008565	1 retrocopy	retro_pabe_2223,
Pan troglodytes	ENSPTRG00000022722	1 retrocopy	retro_ptro_1898,
Tupaia belangeri	ENSTBEG00000014760	1 retrocopy	retro_tbel_443,
Tarsius syrichta	ENSTSYG00000013154	1 retrocopy	retro_tsyr_1670,