RetrogeneDB ID: retro_lafr_535

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_2:79417524..79417864(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GRPEL1
• Ensembl ID: ENSLAFG00000002590
• Aliases: None
• Description: GrpE protein homolog [Source:UniProtKB/TrEMBL;Acc:G3SQS3]

Sequence

>retro_lafr_535
AGGCCCACTCCTTGGTTGCTATGCATGCCCACCAAACAAAAGAACAATGGCCAGAACTTGGAGGAGGACTCAGGTCCAAA
TAAATAGAAGGCACCGTCTCCAGAGAAGGTGCTCCTGGAAAAGAAGGTCAAGCTAGAGGGGCAGCTAAAGAAGGGGATGG
AAAAATACATGTGTGCTCTGGGAGAAACTGAGAACTTGTAGCAAAGAAGCCAAAAATTTGTGCAGGAGGAAAATTATACA
GCATACAGGGCTTCTGCAAGGACCTGCTGGAGGTTGCAGACATTCTGGAGAAGGTCATGCAGGTCAAGGAGGAGATCAGC
AAGCAAACCCTCACCTCAAG

Alignment

ORF - retro_lafr_535 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.83 %
• Parental protein coverage: 55.14 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RPVPRSLCTATKQKNDGQNLEEDSGPNEQKADPPSPEKVLLEEKAKLEEQLKETVEKYKRALADTENLRQ
          RP.P..LC..TKQKN.GQNLEEDSGPN..KA..PSPEKVLLE.K.KLE.QLK...EKY..AL..TENL.Q
Retrocopy RPTPWLLCMPTKQKNNGQNLEEDSGPNK*KA--PSPEKVLLEKKVKLEGQLKKGMEKYMCALGETENL*Q

Parental  RSQKLVEE-AKLYGIQGFCKDLLEVADILEKATQSIPKEEVSED-NPHLK
          RSQK.V.E..KLY.IQGFCKDLLEVADILEK..Q...KEE.S...NPHLK
Retrocopy RSQKFVQE<GKLYSIQGFCKDLLEVADILEKVMQ--VKEEISKQ<NPHLK

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_535 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 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014364	1 retrocopy	retro_cfam_1776,
Homo sapiens	ENSG00000109519	3 retrocopies	retro_hsap_3746, retro_hsap_3864, retro_hsap_3870,
Loxodonta africana	ENSLAFG00000002590	1 retrocopy	retro_lafr_535 ,
Monodelphis domestica	ENSMODG00000002955	1 retrocopy	retro_mdom_28,
Mustela putorius furo	ENSMPUG00000010471	1 retrocopy	retro_mputfur_32,
Nomascus leucogenys	ENSNLEG00000011822	1 retrocopy	retro_nleu_2642,
Otolemur garnettii	ENSOGAG00000032291	1 retrocopy	retro_ogar_1765,
Procavia capensis	ENSPCAG00000011314	1 retrocopy	retro_pcap_388,
Pongo abelii	ENSPPYG00000014573	1 retrocopy	retro_pabe_3235,
Pan troglodytes	ENSPTRG00000015894	3 retrocopies	retro_ptro_2544, retro_ptro_2633, retro_ptro_2636,
Sarcophilus harrisii	ENSSHAG00000007667	1 retrocopy	retro_shar_766,