RetrogeneDB ID: retro_lafr_803

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_4:3384917..3385633(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: YBX2
• Ensembl ID: ENSLAFG00000014006
• Aliases: None
• Description: None

Sequence

>retro_lafr_803
GTCTTTGTTCACCAGACAGCTATTAAACGAAACAACCCCAGGAAGTTTCTGCGCAGCGTTGGCGACAGAGAGACTGTGGA
ATTTAACGTCGTGGATGGAGAGAAGGGTGCAGAAGCTGCTAACGTCACTGGCCTGGCGGGGGGGGTGCCAGTGAAGGGCA
GCCCTATGCCCCCAAAGACGTAGGTTCCGCCAATTCATCCCCCGGCCTTGCCAGCTGCCCCAACACCCATGGTGGCAGAG
GCTCCTTCAGGTGGGACGGAACCAGGCAGCCAAAGAAACAGGGCCGAAACTCTGGGCAACGGCCCAGACGGCGGCGCCCA
CCACCCTTCTTCTACCGACAGCGATTTGTGCGAGGCCCTCGGACCCCCAACTAGCAGCAGCCTACAGAGGGCACTGATGG
CGTAGAACCCAAAGAGACAGCCCCACTGGAGGGGGTCCAACAGCAGGGGGATGAGCGGGTCCTCCCACCCAGATTCTGGC
CCAGATACCGAAGGCCTTTCCGCCCCAAAACCCCCCAGCAGCCTCAGACAGAAGGTGGGGATGGTGAGACCAAGCCCAGC
CAAGGCCCCGCTGATGGTTCCCGGCCTGAGCCCCAGCGCCCACAGAACCGCCCCTACTTTCAGCGGCGACGGCAGCAGCC
CCTTGGCCGCCAGCCCACAGCCCCAGAAACTTCAGCCCCCATCAACAGTGGGGATCCTCCCACCACCAAACTGGAG

Alignment

ORF - retro_lafr_803 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.48 %
• Parental protein coverage: 66.57 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  VFVHQTAIKRNNPRKFLRSVGDGETVEFDVVEGEKGAEAANVTG-PGGVPVK-GSRYAPN-RRRFRRFIP
          VFVHQTAIKRNNPRKFLRSVGD.ETVEF.VV.GEKGAEAANVTG..GGVPVK.G..YAP..RRRFR.FIP
Retrocopy VFVHQTAIKRNNPRKFLRSVGDRETVEFNVVDGEKGAEAANVTGLAGGVPVK<GQPYAPK<RRRFRQFIP

Parental  RP-RPAAPPPMVAEAPSGGTEPGSEGERAE-DSGQRPRRRRPPPFFYRRRFVRGPRPPNQQQPIEGTDGV
          RP..PAAP.PMVAEAPSGGTEPGS...RAE..SGQRPRRRRPPPFFYR.RFVRGPR.PN.QQP.EGTDGV
Retrocopy RP<LPAAPTPMVAEAPSGGTEPGSQRNRAE<NSGQRPRRRRPPPFFYRQRFVRGPRTPN*QQPTEGTDGV

Parental  EPKETAPLEGDQQQGDERVPPPRFRPRYRRPFRPRPPQQPTTEGGDGETKPSQGPADGSRPEPQRPRNRP
          EPKETAPLEG.QQQGDERV.PPRF.PRYRRPFRP..PQQP.TEGGDGETKPSQGPADGSRPEPQRP.NRP
Retrocopy EPKETAPLEGVQQQGDERVLPPRFWPRYRRPFRPKTPQQPQTEGGDGETKPSQGPADGSRPEPQRPQNRP

Parental  YFQRRRQQPPGRQPTAPETSASINSGDPPTTILE
          YFQRRRQQP.GRQPTAPETSA.INSGDPPTT.LE
Retrocopy YFQRRRQQPLGRQPTAPETSAPINSGDPPTTKLE

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_803 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 3 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000007597	1 retrocopy	retro_lafr_804,
Loxodonta africana	ENSLAFG00000014006	1 retrocopy	retro_lafr_803 ,
Ochotona princeps	ENSOPRG00000013773	5 retrocopies	retro_opri_326, retro_opri_327, retro_opri_534, retro_opri_760, retro_opri_824,