RetrogeneDB ID: retro_lafr_320

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_12:15005446..15005775(-)
• Located in intron of: ENSLAFG00000016039

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2E1
• Ensembl ID: ENSLAFG00000004150
• Aliases: None
• Description: None

Sequence

>retro_lafr_320
AGGATTCAGGAGGAACTGGCAGACATCACTTTAGACTCTTCACCTAACTGCAGTGCTGATCCCAAAGGTGATAAGATCTG
TGAATGAAGATCAACCATTCTAGGGCCTCCAGGATCCGTATATGAGGGTGGTGTATTCTTCCTCAATATCACTTTTACAC
CAGAATATCCCCTTCAAGCCTCCAAAGATTACATTTAGACAAGAACCTACCACTGTAATATTAACAGTCAAGGAGTTACT
GCTGGGACACACTGAAAGATAACTGGAGTCCAGCATTAACCATTTCCAAATGGTTACAGACTTCTCACAGACTGTTACCT
TGCCGACCC

Alignment

ORF - retro_lafr_320 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.07 %
• Parental protein coverage: 57.51 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  RIQKELADITLDPPPNCSAGPKGDNIYEWRSTILGPPGSVYEGGVFFLDITFTPEY-PFKPPKVTFR-TR
          RIQ.ELADITLD..PNCSA.PKGD.I.E.RSTILGPPGSVYEGGVFFL.ITFTPEY.PFKPPK.TFR.TR
Retrocopy RIQEELADITLDSSPNCSADPKGDKICE*RSTILGPPGSVYEGGVFFLNITFTPEY>PFKPPKITFR<TR

Parental  IYHCNINSQGV-ICLDILKDNWSPALTISKVLLSICSLLTDCNP
          .YHCNINSQGV..C.D.LKDNWSPALTISK.L.....LL..C.P
Retrocopy TYHCNINSQGV<YCWDTLKDNWSPALTISKWLQTSHRLL-PCRP

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_320 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 11 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ciona intestinalis	ENSCING00000006860	1 retrocopy	retro_cint_33,
Cavia porcellus	ENSCPOG00000002251	2 retrocopies	retro_cpor_1036, retro_cpor_52,
Gorilla gorilla	ENSGGOG00000008393	1 retrocopy	retro_ggor_76,
Loxodonta africana	ENSLAFG00000004150	1 retrocopy	retro_lafr_320 ,
Loxodonta africana	ENSLAFG00000006878	2 retrocopies	retro_lafr_288, retro_lafr_290,
Macropus eugenii	ENSMEUG00000014517	1 retrocopy	retro_meug_2089,
Mus musculus	ENSMUSG00000021774	3 retrocopies	retro_mmus_2493, retro_mmus_2600, retro_mmus_537,
Otolemur garnettii	ENSOGAG00000007527	3 retrocopies	retro_ogar_2029, retro_ogar_2566, retro_ogar_626,
Pan troglodytes	ENSPTRG00000014693	1 retrocopy	retro_ptro_68,
Rattus norvegicus	ENSRNOG00000008794	3 retrocopies	retro_rnor_1632, retro_rnor_2291, retro_rnor_2343,
Sarcophilus harrisii	ENSSHAG00000001416	1 retrocopy	retro_shar_712,