RetrogeneDB ID: retro_lafr_517

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_2:102747527..102748195(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DEK
• Ensembl ID: ENSLAFG00000004470
• Aliases: None
• Description: None

Sequence

>retro_lafr_517
TCCTCATTAAAGAAGAATGTGGGTCAGTTCGATGGCTTTCCATTTGAAAAAGGAAGTGCCCAACATAAAAAGAAGGATGA
AATGTTGAAAAAATTCAGAAATGCCATGTTAAAGAGCATCTGCAGAGTTCTTGATATGGAGAGATCAGGTGTAAATAGTG
AACTGGTGAAGCGGCTCTTGACTTTCTTAATGCATCCAAAGCCTTCTAGCAAACCATTGCCAAAATCCAAAAACACTTCC
AGTAAAGGCAGCAGTAAGGAACAGAACAGCTCTAGAGTGGCAAGGAAGGCTAAGCGAACCAAATGTCCTGAGATTCTGTC
AGATGAATCTTGTAGTGATGAAGATGCCAAGAAAAACCAGGAAGAATCTTCAGATGATGAAGATAAAGTGAAGAGGAGCA
GCCACCAAAAAAGACATCTAAAAGAGAAAAACCTAGACCAGAAACCACTTCTAAAAGTAAAAAATCCATAAACAGTGCTA
ATGTTAGGAAGGCAGATAGCAACATCACCAAGAAGAATCAAAACAGCCCCCAAAAAGAAAGTGAATCTGAGGATAGTTCA
GATGATGAACCTTTAATTTAAAAATTGAAGAAATCTCCCACAGCTGAAGAGTTAAAGGAAACAGTAAAGGAATTATTGGC
AAATGCTGACTTAGAGGAAGTCACAGTG

Alignment

ORF - retro_lafr_517 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.56 %
• Parental protein coverage: 59.57 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SSLKKNVGQFSGFPFEKGSVQYKKKEEMLKKFRNAMLKSICEVLDLERSGVNSELVKRILNFLMHPKPSG
          SSLKKNVGQF.GFPFEKGS.Q.KKK.EMLKKFRNAMLKSIC.VLD.ERSGVNSELVKR.L.FLMHPKPS.
Retrocopy SSLKKNVGQFDGFPFEKGSAQHKKKDEMLKKFRNAMLKSICRVLDMERSGVNSELVKRLLTFLMHPKPSS

Parental  KPLPKSKKTSSKGSKKERNSSGMARKAKQTKCPEILSDESSSDEDEKKNQEESSDDEDK-ESEEEQPPKK
          KPLPKSK.TSSKGS.KE.NSS..ARKAK.TKCPEILSDES.SDED.KKNQEESSDDEDK...EE.QPPKK
Retrocopy KPLPKSKNTSSKGSSKEQNSSRVARKAKRTKCPEILSDESCSDEDAKKNQEESSDDEDK<SEEE-QPPKK

Parental  TSKREKPKPKATSKSKKSVKSANVKKADSSTTKKNQNSSKKESESEDSSDDEPLIKKLKKPPTDEELKET
          TSKREKP.P..TSKSKKS..SANV.KADS..TKKNQNS..KESESEDSSDDEPLI.KLKK.PT.EELKET
Retrocopy TSKREKPRPETTSKSKKSINSANVRKADSNITKKNQNSPQKESESEDSSDDEPLI*KLKKSPTAEELKET

Parental  VKKLLANANLEEVTM
          VK.LLANA.LEEVT.
Retrocopy VKELLANADLEEVTV

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_517 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.

---

Parental genes homology:

Parental genes homology involve 7 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000010184	1 retrocopy	retro_cfam_1362,
Echinops telfairi	ENSETEG00000018188	1 retrocopy	retro_etel_1367,
Loxodonta africana	ENSLAFG00000004470	1 retrocopy	retro_lafr_517 ,
Macaca mulatta	ENSMMUG00000019763	2 retrocopies	retro_mmul_1266, retro_mmul_2627,
Oryctolagus cuniculus	ENSOCUG00000003869	4 retrocopies	retro_ocun_1583, retro_ocun_1791, retro_ocun_1851, retro_ocun_1857,
Otolemur garnettii	ENSOGAG00000007750	1 retrocopy	retro_ogar_3258,
Sus scrofa	ENSSSCG00000001075	1 retrocopy	retro_sscr_203,