RetrogeneDB ID: retro_lafr_972

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_54:15482818..15483451(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MDH1
• Ensembl ID: ENSLAFG00000016504
• Aliases: None
• Description: Malate dehydrogenase [Source:UniProtKB/TrEMBL;Acc:G3TH55]

Sequence

>retro_lafr_972
TCTGAACCAATCAGAGTTCTTGTGACTGAAGCAACTGGTCAAATTGCATATTCACTGCTGTACAGTATTGAAAATGGCTC
TATCTTTGGTAAGGACCAGCCCCTGATTCTAGTGCTATTGGATATCACCCCCACAATGGGTGTCCTGGAAGGTGACTTCA
TGGAACTGCATGACTGTGCACTTCCCCTCCTGCATTACATATGCATTACAACATATAAAGAAGAGGTTGTCTTCAAAGAC
CTGGACGTGGCCATTCTTGTGGGTTCCATGCCAAGATGGGAGGGAATGGAGTGGAAAGACTTACTGAAAGCAAATGTAAA
AATCTTCAAATTCCAGGGTGCAGCCTTGGATAAATATGCCAAGAAGTCAGTTAAGGTTGTCGTCGTGGGAAAATCAGCCA
ATACTAACTGCCTCACTGCGATTAAGTCAGCTTCATCTATCCCCAAGGAGATCTTCAGTTGCTTAATTCATTTGGATCGT
AACTGAGCTGTAGGTCAAACTGTTCATAAACTTGGTGTGACTGCTAAAGATGTAAGGAATGTCATCATCTGGGGAAACCA
TTCCTCAATTCAGTATCCAGATGTCAACCGTGCCAAGGTGAAATTTCAAGGAAAGGAAGTTGGCTCAAGGGAG

Alignment

ORF - retro_lafr_972 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.94 %
• Parental protein coverage: 62.87 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SEPIRVLVTGAAGQIAYSLLYSIGNGSIFGKDQPLILLLLDITPMMGVLEGVLMELQDCALPLLTDI-IA
          SEPIRVLVT.A.GQIAYSLLYSI.NGSIFGKDQPLIL.LLDITP.MGVLEG..MEL.DCALPLL..I.I.
Retrocopy SEPIRVLVTEATGQIAYSLLYSIENGSIFGKDQPLILVLLDITPTMGVLEGDFMELHDCALPLLHYICIT

Parental  TDKEEVAFKDLDVAVLVGSMPRREGMERKDLLKANVKIFKSQGAALDKYAKKSVKVIVVGNPANTNCLTA
          T.KEEV.FKDLDVA.LVGSMPR.EGME.KDLLKANVKIFK.QGAALDKYAKKSVKV.VVG..ANTNCLTA
Retrocopy TYKEEVVFKDLDVAILVGSMPRWEGMEWKDLLKANVKIFKFQGAALDKYAKKSVKVVVVGKSANTNCLTA

Parental  IKSAPSIPKENFSCLTRLDHNRAIGQIVLKLGVTAKDVKNVIIWGNHSSTQYPDVSHAKVKFQGKEVGVY
          IKSA.SIPKE.FSCL..LD.N.A.GQ.V.KLGVTAKDV.NVIIWGNHSS.QYPDV..AKVKFQGKEVG..
Retrocopy IKSASSIPKEIFSCLIHLDRN*AVGQTVHKLGVTAKDVRNVIIWGNHSSIQYPDVNRAKVKFQGKEVGSR

Parental  E
          E
Retrocopy E

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_972 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 15 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019295	1 retrocopy	retro_btau_466,
Choloepus hoffmanni	ENSCHOG00000007281	5 retrocopies	retro_chof_1260, retro_chof_1513, retro_chof_1892, retro_chof_2001, retro_chof_90,
Callithrix jacchus	ENSCJAG00000007018	4 retrocopies	retro_cjac_1848, retro_cjac_2407, retro_cjac_2418, retro_cjac_282,
Dasypus novemcinctus	ENSDNOG00000013329	2 retrocopies	retro_dnov_109, retro_dnov_2562,
Homo sapiens	ENSG00000014641	1 retrocopy	retro_hsap_3426,
Gorilla gorilla	ENSGGOG00000007085	1 retrocopy	retro_ggor_2316,
Loxodonta africana	ENSLAFG00000016504	2 retrocopies	retro_lafr_1134, retro_lafr_972 ,
Macaca mulatta	ENSMMUG00000006163	2 retrocopies	retro_mmul_1750, retro_mmul_2496,
Nomascus leucogenys	ENSNLEG00000009823	1 retrocopy	retro_nleu_1363,
Otolemur garnettii	ENSOGAG00000014487	1 retrocopy	retro_ogar_741,
Pongo abelii	ENSPPYG00000012373	1 retrocopy	retro_pabe_2839,
Pan troglodytes	ENSPTRG00000011974	1 retrocopy	retro_ptro_2326,
Sorex araneus	ENSSARG00000007690	1 retrocopy	retro_sara_361,
Sus scrofa	ENSSSCG00000025751	1 retrocopy	retro_sscr_779,
Tarsius syrichta	ENSTSYG00000001215	2 retrocopies	retro_tsyr_1790, retro_tsyr_190,