RetrogeneDB ID: retro_lafr_1168

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_8:28564969..28565381(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2V2
• Ensembl ID: ENSLAFG00000017749
• Aliases: None
• Description: None

Sequence

>retro_lafr_1168
GGAGTTACAGTTTCTTGTAATTTTTGCTTGTTGGAAGAACTTGAAGAAGGACAAAAAGGAGTAAGTGATGTATGGTTAGC
CTTGAAGATGATGAAGATATGACACTTACAAGGTAGACAGACATGATAATTGGGCCACCAAGGACAAATTATGAAAACAG
AATATATAGCCTGAAAGTCGTATGTGGGTCTAAATACCCAGAAGCTCCTCCATCATATAGATTTATAACGAAAACTAATA
TGAATGGAATAAATAATTCCAGGGGAATGGTGGATGCATGGAGCATATCAATGTCAGCAAAATGGCAAATTCATATAGCA
TTAAAGTTGCACTTCAAAAGCTAGGACCTCTAATGCTATCCAAAGAAAATATGAAGCTTCCACAACCACCAGAAAGCCAA
ACATACAACAAT

Alignment

ORF - retro_lafr_1168 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.24 %
• Parental protein coverage: 95.24 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GVKVPRNFRLLEELEEGQKGVGD-GTVSWGLEDDEDMTLTRWTGMIIGPPRTNYENRIYSLKVECGPKYP
          GV.V..NF.LLEELEEGQKGV.D...VS.....D...T..R.T.MIIGPPRTNYENRIYSLKV.CG.KYP
Retrocopy GVTVSCNFCLLEELEEGQKGVSD<CMVSLEDDEDMTLT--R*TDMIIGPPRTNYENRIYSLKVVCGSKYP

Parental  EAPPSVRFVTKINMNGINNSSGVVDARSIPVLAKWQ-NSYSIKVVLQELRRLMMSKENMKLPQPPEGQTY
          EAPPS.RF.TK.NMNGINNS.G.VDA.SI...AKWQ.NSYSIKV.LQ.L..LM.SKENMKLPQPPE.QTY
Retrocopy EAPPSYRFITKTNMNGINNSRGMVDAWSISMSAKWQ<NSYSIKVALQKLGPLMLSKENMKLPQPPESQTY

Parental  NN
          NN
Retrocopy NN

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_1168 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 10 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000032182	1 retrocopy	retro_cjac_814,
Loxodonta africana	ENSLAFG00000017749	1 retrocopy	retro_lafr_1168 ,
Loxodonta africana	ENSLAFG00000027359	2 retrocopies	retro_lafr_1026, retro_lafr_1221,
Macropus eugenii	ENSMEUG00000016581	1 retrocopy	retro_meug_2093,
Monodelphis domestica	ENSMODG00000010191	10 retrocopies	retro_mdom_1065, retro_mdom_1151, retro_mdom_1167, retro_mdom_1435, retro_mdom_1660, retro_mdom_173, retro_mdom_1979, retro_mdom_736, retro_mdom_786, retro_mdom_979,
Mus musculus	ENSMUSG00000022674	4 retrocopies	retro_mmus_1385, retro_mmus_189, retro_mmus_2048, retro_mmus_2770,
Oryctolagus cuniculus	ENSOCUG00000006933	1 retrocopy	retro_ocun_5,
Procavia capensis	ENSPCAG00000000293	1 retrocopy	retro_pcap_138,
Sus scrofa	ENSSSCG00000022190	1 retrocopy	retro_sscr_524,
Tursiops truncatus	ENSTTRG00000008325	1 retrocopy	retro_ttru_1623,