RetrogeneDB ID: retro_lafr_176

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_1:19596488..19597236(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSLAFG00000030941
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: IDH2
• Ensembl ID: ENSLAFG00000010171
• Aliases: None
• Description: Isocitrate dehydrogenase [NADP] [Source:UniProtKB/TrEMBL;Acc:G3T543]

Sequence

>retro_lafr_176
GCGGATAAGAGGATCAAGGTGCCCAAGCTGGTGGTGGAGATAGGCCACGATGTGATGACCAGTATTATTTGGGAGTTCAT
CAAGGAGAAGCTCACCCTGCCCCATGTGGATGTCCAGCTCAAGTATTTCCACCTTGGGCTCTCAAACCATAAACCAGACC
AAAGACTAGGTCACCACCTATTCTGTACTAGCCACCCAGACATACAATCTGGCTCTCAAGTGTGCCACCATCACCCCTGA
GAAGGCCAGTGTGGATGAGTTCAAACTGAAGAATATGTGGAAAAGTACCAATGAGACCAAGAGGAACATCCTTGGTGGAA
CTGTCTTCTGGAATCCCACCATCTGCAAAAACATCCCAAGCCTCCTACCCAGCTGGACCAAGCCCATCACCATTGGTGGG
CACACCTGTGGCAACCACTACAAAGCCACAGACTTTGTGGTGGACCAGGGGAGGTGTGTTCAAAATGGTCTTCACCCCGA
AGGACAGTAGCAGTGCTAAGGAGTGGGAGGTGTACAGCTTCCCTGCCCACAGTGTGGGCATGGGCTTATACAACACTGAG
AGTCCATCTCAGGTTTTGCTCAAGTCTGCTTCCAGTATGCCACCCAGAATAAGCGGCCTCTGCACATACACACCAAGAAC
ACCATGCTGAAAGCCTATGATGGGCGCTTCAAGGACATCTTCCAGGAGATCTTTGACAAGCAGTATAAGACCGGCTTTGA
CAAAAACAAGATCTGGTGCAAGCACCAG

Alignment

ORF - retro_lafr_176 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.22 %
• Parental protein coverage: 60.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ADKRIKVAKPVVEMDGDEMTRIIWQFIKEKLILPHVDVQLKYFDLGLPNR-DQTNDQVTIDSALATQKYS
          ADKRIKV.K.VVE...D.MT.IIW.FIKEKL.LPHVDVQLKYF.LGL.N...QT.D.VT..S.LATQ.Y.
Retrocopy ADKRIKVPKLVVEIGHDVMTSIIWEFIKEKLTLPHVDVQLKYFHLGLSNH>NQTKD*VTTYSVLATQTYN

Parental  VAVKCATITPDEARVEEFKLKKMWKSPNGTIRNILGGTVFREPIICKNIPRLVPGWIKPITIGRHAHGDQ
          .A.KCATITP..A.V.EFKLK.MWKS.N.T.RNILGGTVF..P.ICKNIP.L.P.W.KPITIG.H..G..
Retrocopy LALKCATITPEKASVDEFKLKNMWKSTNETKRNILGGTVFWNPTICKNIPSLLPSWTKPITIGGHTCGNH

Parental  YKATDFVVD-RAGTFKMVFTPKDGSSAKEWEVFNFRAGGVGMGMYNTD-ESISGFAHSCFQYAIQKKWPL
          YKATDFVVD.R.G.FKMVFTPKD.SSAKEWEV..F.A..VGMG.YNT..ESISGFA..CFQYA.Q.K.PL
Retrocopy YKATDFVVD>RGGVFKMVFTPKDSSSAKEWEVYSFPAHSVGMGLYNTE<ESISGFAQVCFQYATQNKRPL

Parental  YMSTKNTILKAYDGRFKDVFQEIFDKHYKTDFDKNKIWYEHR
          ...TKNT.LKAYDGRFKD.FQEIFDK.YKT.FDKNKIW..H.
Retrocopy HIHTKNTMLKAYDGRFKDIFQEIFDKQYKTGFDKNKIWCKHQ

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_176 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000010171	1 retrocopy	retro_lafr_176 ,
Macropus eugenii	ENSMEUG00000009797	1 retrocopy	retro_meug_124,
Otolemur garnettii	ENSOGAG00000034936	1 retrocopy	retro_ogar_334,