RetrogeneDB ID: retro_lafr_502

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_2:24484548..24485484(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF2A
• Ensembl ID: ENSLAFG00000003767
• Aliases: None
• Description: None

Sequence

>retro_lafr_502
GGGGGTTTTCATGTAGCTTTAGCCAAAAAAAGTTTCTTTAAGGCTGATAAGTTTACAATGCTGTGGAATAAAAAAAGCTA
CTGCTGTGTTGGTAATAGCTAGTACAGGTTTTGACAAGACAGAAGCTTCCTACTATAAGGGACAAACACTATACCACATT
GCAACAAATGGAGAAAGTGCCGTAGTGCAATTACCAAAAAATGGCCCCATTTATGATACAGTTTGGAATTTTAGTTCTAC
TGAGTTTTGTGCTGTGTATGGTTTTATACCTGCCAAAGCAACAATTTTCAACTTGAAATGTGATCCTGTATTTGACTTTG
GAACTGGACCTCATAATGCAGCCTACTGTAGCCCTTATGGGCATATATTAGTATTAGCTCGATTCAGAAATCTGGGAAGA
CAAATGGAAGTGTGGGATATTAAAAACTAAAACTTATTCCAGACCAGTGACCTCTGATTCTACATATTTTGCTTGGTGCC
TAGATAGTGAGCATATTTTAACAGCCACATGTGCTTCCAGGTTACATGTTAATAATGGGTTCAAGATTTGGCCTCATACC
AGCTCCGTCTTACACAAGTATGATGTGCCATCAAATGCAGAAATATGGCAGGTTTCTTGGCAGCCATTTTTAGATGGAAT
ATTTCTAGCAAAAACAGTAACTTACCAAGCAGTAGCAAGGGAGGTACCCAGTGAGGAACCTAAAGTTGCAACAGCTTAGA
GACTCCCAGCTTTAAGAAAAACCAGTCATCAGTTCTAAACTGTATGAGGAGGAACCACCTTAGAATATGAAACCACAATC
TGGAAGTGCTAAAAAAGAAGAAAAAAAAAAAAAGTAGCCACTATCAAAACCAGCCCTTAAAAATCAAAGAAAACATAAAA
CTAGGAAAGCTGCAAAACAGGAAGCAAGGAAGTGAAAACATCCAGATTTGGCACCT

Alignment

ORF - retro_lafr_502 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.24 %
• Parental protein coverage: 53.5 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  GGPHTALANRSFFKADKVTMLWNKK-ATAVLVIASTDVDKTGASYYGEQTLHYIATNGESAVVQLPKNGP
          GG.H.ALA..SFFKADK.TMLWNKK.ATAVLVIAST..DKT.ASYY..QTL..IATNGESAVVQLPKNGP
Retrocopy GGFHVALAKKSFFKADKFTMLWNKK>ATAVLVIASTGFDKTEASYYKGQTLYHIATNGESAVVQLPKNGP

Parental  IYDVVWNSSSTEFCAVYGFMPAKATIFNLKCDPVFDFGTGPRNAAYFSPHGHILVLAGFGNLRGQMEVWD
          IYD.VWN.SSTEFCAVYGF.PAKATIFNLKCDPVFDFGTGP.NAAY.SP.GHILVLA.F.NL..QMEVWD
Retrocopy IYDTVWNFSSTEFCAVYGFIPAKATIFNLKCDPVFDFGTGPHNAAYCSPYGHILVLARFRNLGRQMEVWD

Parental  VKN-YKLI-SKPVASDSTYFAWCPDGEHILTATCAPRLRVNNGYKIWHYTGSVLHKYDVPSNAEIWQVSW
          .KN..KLI.S.PV.SDSTYFAWC.D.EHILTATCA.RL.VNNG.KIW..T.SVLHKYDVPSNAEIWQVSW
Retrocopy IKN<LKLI<SRPVTSDSTYFAWCLDSEHILTATCASRLHVNNGFKIWPHTSSVLHKYDVPSNAEIWQVSW

Parental  QPFLDGIFPAKTITYQAVPSEVPSEEPKVATAYRPPALRNKP-ITNSKLHEEEPPQNMKPQSGSDKPLSK
          QPFLDGIF.AKT.TYQAV..EVPSEEPKVATA.R.PALR....I......EE.PP.NMKPQSGS.K...K
Retrocopy QPFLDGIFLAKTVTYQAVAREVPSEEPKVATA*RLPALRKTS>ISSKLYEEE-PP*NMKPQSGSAKKEEK

Parental  TALKNQRKHEAKKAAKQEARSDKSPESAPTPVPPSAP
          .......K...K...K...R.....E......P..AP
Retrocopy KKK*PLSKPALKNQRKHKTRKAAKQEARK*KHPDLAP

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_502 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 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001199	1 retrocopy	retro_cjac_968,
Dasypus novemcinctus	ENSDNOG00000014002	1 retrocopy	retro_dnov_1148,
Homo sapiens	ENSG00000144895	1 retrocopy	retro_hsap_565,
Gorilla gorilla	ENSGGOG00000015391	1 retrocopy	retro_ggor_509,
Loxodonta africana	ENSLAFG00000003767	1 retrocopy	retro_lafr_502 ,
Macaca mulatta	ENSMMUG00000017696	1 retrocopy	retro_mmul_2395,
Nomascus leucogenys	ENSNLEG00000003219	1 retrocopy	retro_nleu_2213,
Oryctolagus cuniculus	ENSOCUG00000016095	3 retrocopies	retro_ocun_1771, retro_ocun_1825, retro_ocun_1861,
Pongo abelii	ENSPPYG00000029636	2 retrocopies	retro_pabe_517, retro_pabe_652,
Pan troglodytes	ENSPTRG00000015528	1 retrocopy	retro_ptro_423,
Ictidomys tridecemlineatus	ENSSTOG00000003374	1 retrocopy	retro_itri_1706,