RetrogeneDB ID: retro_lafr_877

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_43:9431019..9431322(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF1
• Ensembl ID: ENSLAFG00000002852
• Aliases: None
• Description: None

Sequence

>retro_lafr_877
TTTGCTGGTGCAAGTTAGGGTGATAACCTGCTTCCTGCTGGGACTGAAGATTATATCCATAAAAGAATTCAACAGAGAAA
CATCAGGAAGACCCTTACTATTGTCCCAGGGACCACTGATGATTAGGATAAAAAGAAACTAGTGAAAGTGTTTAAGGAGA
AATTTGCCAGCAATGGTACTGGAATTGAGCATCCAGGATATGGAGAAGTAATTCAGCTACAGGGGTGTCGAGGGCGAGAA
CATATGCCAGTCCCTTGTAGAGACTGGTGGGCTAAAGACGACCACTTGAAGGTTCATGGCTTT

Alignment

ORF - retro_lafr_877 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.73 %
• Parental protein coverage: 88.6 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FADASKGDDLLPAGTEDYIHIRIQQRNGRKTLTTVQGIADDYDKKKLVKAFKKKFACNGTVIEHPEYGEV
          FA.AS.GD.LLPAGTEDYIH.RIQQRN.RKTLT.V.G..DD.DKKKLVK.FK.KFA.NGT.IEHP.YGEV
Retrocopy FAGAS*GDNLLPAGTEDYIHKRIQQRNIRKTLTIVPGTTDD*DKKKLVKVFKEKFASNGTGIEHPGYGEV

Parental  IQLQ-GDQRKNICQFLVEIG-LAKDDQLKVHGF
          IQLQ.G....NICQ.LVE.G..AKDD.LKVHGF
Retrocopy IQLQ>GVEGENICQSLVETG<WAKDDHLKVHGF

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_877 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 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002282	1 retrocopy	retro_btau_63,
Callithrix jacchus	ENSCJAG00000012120	6 retrocopies	retro_cjac_1237, retro_cjac_2089, retro_cjac_346, retro_cjac_3815, retro_cjac_600, retro_cjac_84,
Cavia porcellus	ENSCPOG00000014350	3 retrocopies	retro_cpor_42, retro_cpor_613, retro_cpor_643,
Dipodomys ordii	ENSDORG00000013853	4 retrocopies	retro_dord_349, retro_dord_350, retro_dord_663, retro_dord_753,
Felis catus	ENSFCAG00000024455	2 retrocopies	retro_fcat_1555, retro_fcat_74,
Loxodonta africana	ENSLAFG00000002852	2 retrocopies	retro_lafr_386, retro_lafr_877 ,
Myotis lucifugus	ENSMLUG00000005077	3 retrocopies	retro_mluc_233, retro_mluc_305, retro_mluc_330,
Mustela putorius furo	ENSMPUG00000010883	6 retrocopies	retro_mputfur_1019, retro_mputfur_1072, retro_mputfur_1239, retro_mputfur_1299, retro_mputfur_41, retro_mputfur_752,
Nomascus leucogenys	ENSNLEG00000011013	3 retrocopies	retro_nleu_1482, retro_nleu_2005, retro_nleu_92,
Pongo abelii	ENSPPYG00000029667	1 retrocopy	retro_pabe_127,
Rattus norvegicus	ENSRNOG00000032769	1 retrocopy	retro_rnor_520,
Sorex araneus	ENSSARG00000006287	1 retrocopy	retro_sara_36,
Sarcophilus harrisii	ENSSHAG00000005729	1 retrocopy	retro_shar_42,