RetrogeneDB ID: retro_lafr_454

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_17:38901026..38901688(+)
• Located in intron of: ENSLAFG00000012261

Retrocopy information

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

Parental gene information

• Parental gene symbol: SDHB
• Ensembl ID: ENSLAFG00000018475
• Aliases: None
• Description: None

Sequence

>retro_lafr_454
GGAGATAAACCTCGCATGCAGATTTACAAAATTGCTTGGAATAAATATGGTCCTATGTATGCTTTGATCAAGATTAAGAA
TGAAATTGATGCTACCCTGACTTTTTGAAGTTCATGCAGAGAAGGTATCTGTGGATCTTATGCAGTGAACATCAATGGAG
GCAACAATCTAACTTATACTTGTGGGATTGACACCAACCTTTATAGAGTCTCAAAAATCTACCCTCTTCCACTTATGTAC
GTGATAAAGGATCTTGCTCCTGATTTGCGTGACTTCTATGCTTAGTACAGATCCACTGAGCCTTATTTGATGAAGAAGAA
TGAATCCCAGGAAGGCAGGAAGTGGTATGTGCAGTCCATAGATGGTGAGAAACCGGACAGGCTGTATGAGTGCATTCTCT
GTGCCTGCTGCACCGCCAGCTGCCCCAGCTACTGGTGGAGTGGAGACAAGTATTTGGGACCTGAGGTTCTTATGTGGGCC
ATGGCTGGATGATTGACTTCAGAAACTACTTCATGGAGGAGCGACTGGCCAAGCTGCAGGACCCTTTCTGTCTGTGCCAT
TGCCACACCATCATGACCTGTCCCAAGGGTCTGAATCCAGCGAAAGCTATAGCGGAAATCAGGATAATGGTGGCAGCCTC
TAAGGAGAAGAAAGCTTCTGCT

Alignment

ORF - retro_lafr_454 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.05 %
• Parental protein coverage: 80.85 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GDKPHMQTYEVDLNKCGPMVLDALIKIKNEIDATLTFRRSCREGICGSCAMNINGGNTLACTRRIDTNLN
          GDKP.MQ.Y....NK.GPM...ALIKIKNEIDATLTF..SCREGICGS.A.NINGGN.L..T..IDTNL.
Retrocopy GDKPRMQIYKIAWNKYGPMY--ALIKIKNEIDATLTF*SSCREGICGSYAVNINGGNNLTYTCGIDTNLY

Parental  KVSKIYPLPHMYVIKDLVPDLSNFYAQYKSIEPYLKKKDESQEGKQQYLQSIEDREKLDGLYECILCACC
          .VSKIYPLP.MYVIKDL.PDL..FYA.Y.S.EPYL.KK.ESQEG...Y.QSI.D.EK.D.LYECILCACC
Retrocopy RVSKIYPLPLMYVIKDLAPDLRDFYA*YRSTEPYLMKKNESQEGRKWYVQSI-DGEKPDRLYECILCACC

Parental  STSCPSYWWNGDKYLGPAVLMQA-YRWMIDSRDDFTEERLAKLQDPFSLYRCHTIMNCTRACPKGLNPGK
          ..SCPSYWW.GDKYLGP.VLM.A...WMID.R..F.EERLAKLQDPF.L..CHTIM.C....PKGLNP.K
Retrocopy TASCPSYWWSGDKYLGPEVLMWA<HGWMIDFRNYFMEERLAKLQDPFCLCHCHTIMTC----PKGLNPAK

Parental  AIAEIKKMMATYKEKKASA
          AIAEI..M.A..KEKKASA
Retrocopy AIAEIRIMVAASKEKKASA

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_454 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 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015832	1 retrocopy	retro_cfam_587,
Choloepus hoffmanni	ENSCHOG00000005664	1 retrocopy	retro_chof_2016,
Callithrix jacchus	ENSCJAG00000007927	1 retrocopy	retro_cjac_2988,
Loxodonta africana	ENSLAFG00000018475	1 retrocopy	retro_lafr_454 ,
Macropus eugenii	ENSMEUG00000004817	1 retrocopy	retro_meug_1106,
Microcebus murinus	ENSMICG00000016629	1 retrocopy	retro_mmur_1062,
Myotis lucifugus	ENSMLUG00000000032	1 retrocopy	retro_mluc_150,
Nomascus leucogenys	ENSNLEG00000013264	1 retrocopy	retro_nleu_1640,
Sorex araneus	ENSSARG00000013780	1 retrocopy	retro_sara_577,
Tupaia belangeri	ENSTBEG00000004803	2 retrocopies	retro_tbel_2480, retro_tbel_2875,
Xenopus tropicalis	ENSXETG00000013435	1 retrocopy	retro_xtro_60,