RetrogeneDB ID: retro_lafr_725

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_33:11393903..11394634(+)
• Located in intron of: ENSLAFG00000003622

Retrocopy information

• Ensembl ID: ENSLAFG00000026897
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PSME3
• Ensembl ID: ENSLAFG00000013446
• Aliases: None
• Description: None

Sequence

>retro_lafr_725
ATGGCTTCCCCCCTGAAGCTAGAGCAGGACGTTCAGGGGAAGGTGGATTCGTTTCGGGCCCGCATCGCCCAGGAGGCCGA
GGATCTGGTGTCCACCTTCTTCCCTCAGAAGCTGTCGGAACTGGATAGCCGGGTCCAGGAGCTCCGCCTGCAAGACCTGT
CCAGGATCCGTTCGGTGCCCTGTCCCGAGCCCCCTGCGGCCACAGACACCGTGGGGGATGGCCCCAACCGGGAGCCGCAG
TCTCTGCAGACCCAGTCCGCGACCAAGGTACCAGCACTGCCGGGGGGCGAGGGACAGCTTTTGAGGAGCAATCAGCATCT
GGTGGAGCTGATTGAGCGGGTAAAGCCTGAGATCGAGCTGCTGAGAGAGAAATGCAACACGGTACGGATGTGGGTGCAGC
TGCTGATCCCGAAGGTGGAGGATGGCAACAACTTCGGGGTGTCTATCCAGGAAGACACGGTGGACCAGCTGTGGACGGTG
GAGAGCACGGCGGCCTCCTATCTGCGCCGCTTCTCCACCTACTACAACACGCGGGCCAAACTGGTTTCCAAGATCGTGAG
TACCCCCAGGTGGAAGATTACTGCCGCACTGTAGCCGAGGTCGACGAAAACGAGTACCTGAGTGTGCGCCAGATTCTGCT
GCACGTTCGGAACCAGTATGCCACCTTACATGATGTAATCCTCAAAAACATCGAGAAGATAAAGACTCCTCGAGCATTAT
CACTGACAACC

Alignment

ORF - retro_lafr_725 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.98 %
• Parental protein coverage: 99.21 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MASLLKVDQEVKLKVDSFRERITSEAEDLVANFFPKKLLELDSFLKEPILNIHDLTQIHSDMNLPVPDPI
          MAS.LK..Q.V..KVDSFR.RI..EAEDLV..FFP.KL.ELDS...E..L...DL..I.S....P.P.P.
Retrocopy MASPLKLEQDVQGKVDSFRARIAQEAEDLVSTFFPQKLSELDSRVQE--LRLQDLSRIRS---VPCPEPP

Parental  LLTNSHDGLDGPTYKKRRLDECEEAFQGTKVFVMPNG---MLKSNQQLVDIIEKVKPEIRLLIEKCNTVK
          ..T......DGP......L.........TKV...P.G....L.SNQ.LV..IE.VKPEI.LL.EKCNTV.
Retrocopy AATDTVG--DGPNREPQSL----QTQSATKVPALPGGEGQLLRSNQHLVELIERVKPEIELLREKCNTVR

Parental  MWVQLLIPRIEDGNNFGVSIQEETVAELRTVESEAASYLDQISRYYITRAKLVSKIA-KYPHVEDYRRTV
          MWVQLLIP..EDGNNFGVSIQE.TV..L.TVES.AASYL...S.YY.TRAKLVSKI...YP.VEDY.RTV
Retrocopy MWVQLLIPKVEDGNNFGVSIQEDTVDQLWTVESTAASYLRRFSTYYNTRAKLVSKIV<EYPQVEDYCRTV

Parental  TEIDEKEYISLRLIISELRNQYVTLHDMILKNIEKIKRPRSSNAET
          .E.DE.EY.S.R.I....RNQY.TLHD.ILKNIEKIK.PR.....T
Retrocopy AEVDENEYLSVRQILLHVRNQYATLHDVILKNIEKIKTPRALSLTT

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_725 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 13 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000013688	2 retrocopies	retro_acar_118, retro_acar_37,
Bos taurus	ENSBTAG00000019918	2 retrocopies	retro_btau_1249, retro_btau_941,
Callithrix jacchus	ENSCJAG00000013111	1 retrocopy	retro_cjac_2307,
Cavia porcellus	ENSCPOG00000012552	1 retrocopy	retro_cpor_1204,
Equus caballus	ENSECAG00000012620	2 retrocopies	retro_ecab_29, retro_ecab_827,
Homo sapiens	ENSG00000131467	1 retrocopy	retro_hsap_245,
Loxodonta africana	ENSLAFG00000013446	1 retrocopy	retro_lafr_725 ,
Mustela putorius furo	ENSMPUG00000010027	1 retrocopy	retro_mputfur_619,
Oryctolagus cuniculus	ENSOCUG00000015986	1 retrocopy	retro_ocun_641,
Pongo abelii	ENSPPYG00000008372	1 retrocopy	retro_pabe_413,
Pan troglodytes	ENSPTRG00000009225	1 retrocopy	retro_ptro_212,
Sus scrofa	ENSSSCG00000017385	1 retrocopy	retro_sscr_784,
Ictidomys tridecemlineatus	ENSSTOG00000028833	1 retrocopy	retro_itri_153,