RetrogeneDB ID: retro_lafr_504

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_2:34371904..34373316(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GLUD1
• Ensembl ID: ENSLAFG00000012059
• Aliases: None
• Description: None

Sequence

>retro_lafr_504
ATAATGGAATTCATCAAGACCCAGGACAGTGAGGAGCAGAAGCGGAAATGAGTGCTCGGGATTCTGTGAATCATCAAGCC
CTGCAACCGTGTGCTGAGTCTCTCCTTCCCCATCCGGCTCACAGCGGCTCCTGGGAGGCCATTCATGGCTACTGAGCCCA
GCACAGTCAGCACTGCACTCCCTGCAAGGCTGGTATCTGTTAAAGCGCAAATGTGAGTATAAATGAAGTAAAAGCTTTGG
CTGCTTTGATGACATAGAAATGTGCTGTGGTTGATGTGCTCTCTGGGGGTGCTAAAGCTGGTGTTAAGATCAATCCCAAG
AATTATACCCATAATGAATTTGAAAAGATCACAAGGAGGTTCCATGGAATTAGCAAAGAAGGGCTTTATTGGTCCTAGCG
TTGATGTGCTTGCCCCCAGATATGGGCACTGGTGAGCGTGAGATGTCCTGGATTGCTGACACCTATGCCAGCACCATAGG
GTAGTATGATATTAATTCACATGCCTGTGTTACAGGTAAACCCATCAGTCAGGGTGGTATCCATGGACATATCTCTGCTA
CTGGCCATGGTGTTTTCCTTGGTATTGAAAACTTTATCAGTGAAGCTTCTTACATGAACATTTTAGTGTTGACATCAAGA
GTTCAAAATAAAACACTTGTTCAGGGATTTGGTAATATGGGCCATTATACTATAAGATATTTACGTCATTTTGGTGCTAA
ATGTGTTGGTGTTAGTGACTCTCACAGGGGCATATGGAATTCAGATGGTATTGATCCAAAGGAACTGGAGGACTTCAAAT
TGCAACGTGGATCAGTCATGGGTTTCACCAAGGCAAAACCCTATAAAGGAAGCATCTTGGAAGCTGACTGTGACATACTG
ATTCCTGCCGCCAAGGAGAAGCAGTTGACCAAATTCAGTGCACAGAAAGTCAAAGCCAAGACCATTGCTGAAGGTGCCAA
TGAACAGACAACGCCAGAAGTTCATAAGATTTTCCTGGCGAAGAAGATTCTAGTAATCCTTGATCTCTGCTTGAATGCTG
GAGGACTGACAGTATCTTACTTTGAGCGGCTGAAGAATATAAGTCATGTCAGCTATGGCCATTTGACTTTCAAATATGAA
AGGGATTCTACTACCATTTGCTCAGGTCTGCTTAAAAGAGTTTAGAAAGAACATTTGGAAGCTCAGTGGAACTCTTCCCA
TTTTACCCACAGCAGGATTCCAAGATAGACTATCAGGTGCATCTGAGAAAGACATCGTGCACTCTGGCTTAGCTTATACC
ATGGAGTATCCTGCTAGGCAAACCATGAGCACAGCCAGGAAGTATAAACTGGGAATGGATGTGAGAATGGCTGCCTACGT
CATTGCCATTGAGAAAATTGTCAGGGTGTACAATGAAGCTGGTTTGACCTTC

Alignment

ORF - retro_lafr_504 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.8 %
• Parental protein coverage: 84.77 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  LVEDLRTRESEEQKRNRVRGILRIIKPCNHVLSVSFPIR-RDDGSWEVIEGYRAQHSQHRTPCKGGIRYS
          ..E...T..SEEQKR..V.GIL.IIKPCN.VLS.SFPIR....GSWE.I.GY.AQHSQH.TPCK.GI..S
Retrocopy IMEFIKTQDSEEQKRK*VLGIL*IIKPCNRVLSLSFPIR<AHSGSWEAIHGY*AQHSQHCTPCKAGIC*S

Parental  TDVSVDEVKALASLMTYKCAVVDVPFGGAKAGVKINPKNYTDSELEKITRRFTMELAKKG-FIGPGIDVP
          ..VS..EVKALA.LMT.KCAVVDV..GGAKAGVKINPKNYT..E.EKITRRF.....K.G.FIGP..DV.
Retrocopy ANVSINEVKALAALMT*KCAVVDVLSGGAKAGVKINPKNYTHNEFEKITRRF-HGISKEG>FIGPSVDVL

Parental  A-PDMSTGEREMSWIADTYASTIGHYDINAHACVTGKPISQGGIHGRISATGRGLFHGIENFINEASYMS
          A.PDM.TGEREMSWIADTYASTIG.YDIN.HACVTGKPISQGGIHG.ISATG.G.F.GIENFI.EASYM.
Retrocopy A>PDMGTGEREMSWIADTYASTIG*YDINSHACVTGKPISQGGIHGHISATGHGVFLGIENFISEASYMN

Parental  ILGMTPGFGDKTFVVQGFGNVGLHSMRYLHRFGAKCVGVAESEGSIWNPDGIDPKELEDFKLQHGSIMGF
          IL..T.....KT..VQGFGN.G....RYL..FGAKCVGV..S...IWN.DGIDPKELEDFKLQ.GS.MGF
Retrocopy ILVLTSRVQNKT-LVQGFGNMGHYTIRYLRHFGAKCVGVSDSHRGIWNSDGIDPKELEDFKLQRGSVMGF

Parental  PKAKPYEGSILEADCDILIPAASEKQLTKSNAPRVKAKIIAEGANGPTTPEADKIFLERNIMVIPDLYLN
          .KAKPY.GSILEADCDILIPAA.EKQLTK..A..VKAK.IAEGAN..TTPE..KIFL...I.VI.DL.LN
Retrocopy TKAKPYKGSILEADCDILIPAAKEKQLTKFSAQKVKAKTIAEGANEQTTPEVHKIFLAKKILVILDLCLN

Parental  AGGVTVSYFEWLKNLNHVSYGRLTFKYERDSN-YHLLMSVQESLERKFG-KHGGTIPIVPTAEFQDRISG
          AGG.TVSYFE.LKN..HVSYG.LTFKYERDS..YHLL.S...SLER.FG.K..GT.PI.PTA.FQDR.SG
Retrocopy AGGLTVSYFERLKNISHVSYGHLTFKYERDST<YHLLRSA*KSLERTFG<KLSGTLPILPTAGFQDRLSG

Parental  ASEKDIVHSGLAYTMERSARQIMRTAMKYNLGLDLRTAAYVNAIEKVFKVYNEAGVTF
          ASEKDIVHSGLAYTME..ARQ.M.TA.KY.LG.D.R.AAYV.AIEK...VYNEAG.TF
Retrocopy ASEKDIVHSGLAYTMEYPARQTMSTARKYKLGMDVRMAAYVIAIEKIVRVYNEAGLTF

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_504 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 20 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007540	2 retrocopies	retro_btau_1413, retro_btau_1741,
Canis familiaris	ENSCAFG00000016095	1 retrocopy	retro_cfam_747,
Choloepus hoffmanni	ENSCHOG00000001101	1 retrocopy	retro_chof_2002,
Callithrix jacchus	ENSCJAG00000011633	1 retrocopy	retro_cjac_2830,
Dipodomys ordii	ENSDORG00000009767	1 retrocopy	retro_dord_400,
Equus caballus	ENSECAG00000007371	2 retrocopies	retro_ecab_886, retro_ecab_919,
Echinops telfairi	ENSETEG00000019638	2 retrocopies	retro_etel_141, retro_etel_2024,
Homo sapiens	ENSG00000148672	1 retrocopy	retro_hsap_31,
Gorilla gorilla	ENSGGOG00000015770	1 retrocopy	retro_ggor_2954,
Loxodonta africana	ENSLAFG00000012059	1 retrocopy	retro_lafr_504 ,
Microcebus murinus	ENSMICG00000016526	1 retrocopy	retro_mmur_524,
Monodelphis domestica	ENSMODG00000002756	1 retrocopy	retro_mdom_124,
Nomascus leucogenys	ENSNLEG00000011658	1 retrocopy	retro_nleu_36,
Otolemur garnettii	ENSOGAG00000003641	1 retrocopy	retro_ogar_2757,
Procavia capensis	ENSPCAG00000008662	1 retrocopy	retro_pcap_11,
Pongo abelii	ENSPPYG00000002827	3 retrocopies	retro_pabe_3109, retro_pabe_3213, retro_pabe_79,
Pan troglodytes	ENSPTRG00000002711	4 retrocopies	retro_ptro_3162, retro_ptro_3283, retro_ptro_3285, retro_ptro_3290,
Ictidomys tridecemlineatus	ENSSTOG00000012843	1 retrocopy	retro_itri_737,
Tarsius syrichta	ENSTSYG00000001578	1 retrocopy	retro_tsyr_313,
Tursiops truncatus	ENSTTRG00000008145	1 retrocopy	retro_ttru_950,