RetrogeneDB ID: retro_meug_124

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: GeneScaffold_3494:12072..13114(-)
• Located in intron of: ENSMEUG00000014109

Retrocopy information

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

Parental gene information

• Parental gene symbol: IDH2
• Ensembl ID: ENSMEUG00000009797
• Aliases: None
• Description: isocitrate dehydrogenase 2 (NADP+), mitochondrial [Source:HGNC Symbol;Acc:5383]

Sequence

>retro_meug_124
ATCAATGGAGGTGAGATGACTCGAATCACCTGGCAGTTCATCAAAGTGAACCTCATCCTACCCCATGTGGATGTATAGCT
CAAGTACCTTGAACTGAGGCTTCCACACTATGATCAGACAGATGATTAGGTCACCATCAACTTAGCACTAGCCACTCAGA
AATATATCATGTCTGTCAAGTGTGCTACCATCACTCCAGATGTTGCCCATGTGGAAGAATTCAAGCTAAAGAAAACGTGG
AAAAGCCCCAATGGGACAATAAGGAACATTTTAGGGGGAACTGTATTGAGGGAACCTATCATCTGCAAGAACATCCTTCA
ACTTGTTCCTGGTTGGATGAAACCAATCACCATTGGCAGGCATGCACATGGTCATCAGTCCAAGGCCACTGACTTTGTTG
TAGACAAGGCAGACATTTTCAAGATGGAGTTTATTCCCAAAGATGGAAGTGTTGTAAAGGAATGGGAAGTATTCAACTTC
CCTGCTGGAGTTGTGGGTATGGGCATGTACAACAATGATGAGTCTGTCTCAGATTTTGCACATAGTTACTGCCAGTATGC
CATCCAGAAGAACTGGCCCCTCTACATGAGCACCAAGAACACCATCCTAAAGGTATGTGATGTGACTTCAAAGTCATCTT
CCAGGAAATCTTTGACAAGCACTACAAGACAGTTTTTGACAAGAACATTATTTGGTATGAACACTGACCATTGACGACAT
GGTATCCAAAGTGCTCAAGTTTTCAGGTGGTTTTGTCTGGGCCTGCAAGAATTATGATGGCGATGTGCAGTCTGACATAC
TAGTCCAGGGCTTTGGTTGCCTTGGCCTGAGAACTTCAGTGCTGGTCTGCCCAGATGGGAAGACCATTGAGGCAGGGGCA
ACCCTTGGAACTGTCACTTGACATTACAGAGAGCTCCAGAAGGGCCAACCCACTAGCACCAATCCCATTGCCAGCATCTT
TGCCTGAACAAGAGGTTTAGAGCACCTAGGAAAGGGGGACAGTAACCAGGACTTAATTAGATTCACACAGACTCTGGAGA
GA

Alignment

ORF - retro_meug_124 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.57 %
• Parental protein coverage: 84.26 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MDGDEMTRIIWQFIKEKLILPHVDVQLRYFDLGLPHRDQTDDQVTIDSALATQKYSVAVKCATITPDEGR
          ..G.EMTRI.WQFIK..LILPHVDV.L.Y..L.LPH.DQTDD.VTI..ALATQKY...VKCATITPD...
Retrocopy INGGEMTRITWQFIKVNLILPHVDV*LKYLELRLPHYDQTDD*VTINLALATQKYIMSVKCATITPDVAH

Parental  VEEFKLKKMWKSPNGTIRNILGGTVFREPIICKNIPRLVPGWTKPINIGRHAHGDQYKATDFAIGKAGTF
          VEEFKLKK.WKSPNGTIRNILGGTV.REPIICKNI..LVPGW.KPI.IGRHAHG.Q.KATDF...KA..F
Retrocopy VEEFKLKKTWKSPNGTIRNILGGTVLREPIICKNILQLVPGWMKPITIGRHAHGHQSKATDFVVDKADIF

Parental  KMVFTPKDGSGVKEWEVYNFPAGGVGMGMYNTDESISGFAHSCFQYAIQKKWPLYMSTKNTILKAYDGR-
          KM.F.PKDGS.VKEWEV.NFPAG.VGMGMYN.DES.S.FAHS..QYAIQK.WPLYMSTKNTILK..D...
Retrocopy KMEFIPKDGSVVKEWEVFNFPAGVVGMGMYNNDESVSDFAHSYCQYAIQKNWPLYMSTKNTILKVCDVT<

Parental  FKDIFQEIFEKHYKTDFDKNKIWYEH-RLIDDMVAQVLKSSGGFVWACKNYDGDVQSDILAQGFGSLGLM
          FK.IFQEIF.KHYKT.FDKN.IWYEH...IDDMV..VLK.SGGFVWACKNYDGDVQSDIL.QGFG.LGL.
Retrocopy FKVIFQEIFDKHYKTVFDKNIIWYEH<LTIDDMVSKVLKFSGGFVWACKNYDGDVQSDILVQGFGCLGLR

Parental  TSVLVCPDGKTIEAEAAHGTVTRHYREHQKGRPTSTNPIASIFAWTRGLEHRGKLDGNQDLIRFAQTLEK
          TSVLVCPDGKTIEA.A..GTVT.HYRE.QKG.PTSTNPIASIFA.TRGLEH.GK.D.NQDLIRF.QTLE.
Retrocopy TSVLVCPDGKTIEAGATLGTVT*HYRELQKGQPTSTNPIASIFA*TRGLEHLGKGDSNQDLIRFTQTLER

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Macropus eugenii was not studied using RNA-Seq expression data.

ChIP-Seq

Macropus eugenii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_meug_124 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_124 was not experimentally validated.

Homology

Retrocopy orthology:

Macropus eugenii 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,