RetrogeneDB ID: retro_lafr_580

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_23:26458178..26458632(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ANP32E
• Ensembl ID: ENSLAFG00000026778
• Aliases: None
• Description: None

Sequence

>retro_lafr_580
CTCAGCACAGTAGAAGCTCTGCAAAATCCTAAAACTTTGTTATGTCTTGACTTGTTCAACCGTGAGATAGCAAACCTTAA
GGATTATAGAGGAAGTACTTTTGAACTGCTGCAGACAGTTACACACTTAGATGAATTTGATTAAGAGGATAATGAAGCAC
CTGAAACACTTCAAGAGGGCGATGATGAGAATGGAGCTGAAGACGAAGAGGATGAAGAAGATGAAGCTAGTCCACCTGAA
GGATATGAGGAAGGGGAAGGAAGTAGAGGAGGATGAGGGTGGCGATGACAATGAAGCAGGCTCAGATTTCAGAGAGGGAG
CAGAGGAAGTGGGCCTCTCATATTTAATGAAAGAAGAAATTCAGTGTGAAGAAGATGATGGTGACTGTGACGAAGAAGGG
GAGGAAGAGGAAGAAAAAGAAGAAGAAGGTCTTCAAGGGGAGAATGAAACGAGA

Alignment

ORF - retro_lafr_580 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.21 %
• Parental protein coverage: 57.2 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LSTVEALQNLKNLKSLDLFNCEITNLEDYRESIFELLQQITYLDGFDQEDNEAPEASEEEDDDDGDEDDE
          LSTVEALQN.K.L..LDLFN.EI.NL.DYR.S.FELLQ..T.LD.FD.EDNEAPE...E.DD..G.....
Retrocopy LSTVEALQNPKTLLCLDLFNREIANLKDYRGSTFELLQTVTHLDEFD*EDNEAPETLQEGDDENGAXXXX

Parental  DEDDDEAGPPEEYEEEE-EEEE-EDDDDDEAGSELGEGEEEVGLSYLMKEEIQDEEDDDDYVEEGEEEEE
          ........P.E.YEE.E.E.EE.E..DD.EAGS...EG.EEVGLSYLMKEEIQ.EEDD.D..........
Retrocopy XXXXXXSPP-EGYEEGE>EVEEDEGGDDNEAGSDFREGAEEVGLSYLMKEEIQCEEDDGDCDXXXXXXXX

Parental  EEEEGLRGEKRKR
          .....L.GE...R
Retrocopy XXXXXLQGENETR

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_580 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 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009710	1 retrocopy	retro_cjac_2926,
Dipodomys ordii	ENSDORG00000011690	4 retrocopies	retro_dord_311, retro_dord_358, retro_dord_495, retro_dord_777,
Loxodonta africana	ENSLAFG00000022560	1 retrocopy	retro_lafr_679,
Loxodonta africana	ENSLAFG00000026778	1 retrocopy	retro_lafr_580 ,
Microcebus murinus	ENSMICG00000015265	1 retrocopy	retro_mmur_115,
Monodelphis domestica	ENSMODG00000027412	2 retrocopies	retro_mdom_1802, retro_mdom_569,
Ochotona princeps	ENSOPRG00000010058	3 retrocopies	retro_opri_1223, retro_opri_52, retro_opri_774,
Ictidomys tridecemlineatus	ENSSTOG00000004170	5 retrocopies	retro_itri_1003, retro_itri_1031, retro_itri_1359, retro_itri_394, retro_itri_955,
Tupaia belangeri	ENSTBEG00000001989	1 retrocopy	retro_tbel_918,