RetrogeneDB ID: retro_ogar_3068

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873709.1:2138371..2139046(+)
• Located in intron of: ENSOGAG00000008065

Retrocopy information

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

Parental gene information

• Parental gene symbol: MDH2
• Ensembl ID: ENSOGAG00000009705
• Aliases: None
• Description: malate dehydrogenase 2, NAD (mitochondrial) [Source:HGNC Symbol;Acc:6971]

Sequence

>retro_ogar_3068
GGCATGATCCAGTATGACCTGTTCAACACCGGTGCCACAATTGTGGCCACCCTGACTGCTGCCTATGCCCAGCGTTGCCC
TGAAGCCATGATCTGCATTGTCACCAATCGGGTTAACTCCACCATCCCAATCACAGCAGAAGCTTTCAAGAAACATAGAA
TATAGAACCTCAATAAAATCTTTGGTGTGACAACCCTGGACATCATTAGAGCTAACACCTTTGTTGCCAACTGAAGGGTT
TGGACCCAGCTCAAGGTAACGTCCCTGTCATTGGTGGCCATGCTGGGAAGACCATCATCCCCTGTTCTCTCAGTGCACCC
CCAAGGTGGACCTTCCCCAGGATCAGCTGATGGCATTCACTGGGCAGATCCAGGAGGCTGGCACAGAGGTGGTGAAGGCT
AAAGCTGGAGCAGGTTCTGCCACCCTCTCCATGGCATATGCCAGTGCACGTTCATCTTCTCCCTTCTGGATGCAGTGAAC
GGAAAGGAAGGAGCTGTCGAATGTTCCTTTGTTAAGTCACAAGAAATGGACGGTACCTATTTCTCCACACTGTTACTGCT
GGGAAAAAATGGCATTGAGAAGAATCTAGGCATTGGCAAAGTCTCCTCTTTTGAAGAGAAGATGACTACTGAGGCCATTC
CTAAGCTGAAGGCCTCAATCAAGAAAGGAGACGAC

Alignment

ORF - retro_ogar_3068 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.41 %
• Parental protein coverage: 67.66 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GMTRDDLFNTNATIVATLTAACAQHCPEAMICIIANPVNSTIPITAEVFKKHGVYNPNKIFGVTTLDIVR
          GM...DLFNT.ATIVATLTAA.AQ.CPEAMICI..N.VNSTIPITAE.FKKH...N.NKIFGVTTLDI.R
Retrocopy GMIQYDLFNTGATIVATLTAAYAQRCPEAMICIVTNRVNSTIPITAEAFKKHRI*NLNKIFGVTTLDIIR

Parental  ANTFVA-ELKGLDPARVNVPVIGGHAGKTIIP-LISQCTPKVDFPQDQLTALTGRIQEAGTEVVKAKAGA
          ANTFVA..LKGLDPA..NVPVIGGHAGKTIIP.L.SQCTPKVD.PQDQL.A.TG.IQEAGTEVVKAKAGA
Retrocopy ANTFVA<QLKGLDPAQGNVPVIGGHAGKTIIP<LFSQCTPKVDLPQDQLMAFTGQIQEAGTEVVKAKAGA

Parental  GSATLSMAYAGAR-FVFSLLDAVNGKEGVVECSFVKSQETDCTYFSTPLLLGKKGIEKNLGIGKISSFEE
          GSATLSMAYA.AR.F.FSLLDAVNGKEG.VECSFVKSQE.D.TYFST.LLLGK.GIEKNLGIGK.SSFEE
Retrocopy GSATLSMAYASAR<FIFSLLDAVNGKEGAVECSFVKSQEMDGTYFSTLLLLGKNGIEKNLGIGKVSSFEE

Parental  KMIAEAIPELKASIKKGED
          KM..EAIP.LKASIKKG.D
Retrocopy KMTTEAIPKLKASIKKGDD

Legend:

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

Expression

RNA-Seq

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq

Otolemur garnettii was not studied using ChIP-Seq data.

EST

Otolemur garnettii was not studied using EST data.

TSS

Otolemur garnettii was not studied using FANTOM5 data.

Lab

retro_ogar_3068 was not experimentally validated.

Homology

Retrocopy orthology:

Otolemur garnettii 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 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010846	1 retrocopy	retro_amel_361,
Canis familiaris	ENSCAFG00000013515	2 retrocopies	retro_cfam_182, retro_cfam_41,
Myotis lucifugus	ENSMLUG00000017795	1 retrocopy	retro_mluc_1948,
Monodelphis domestica	ENSMODG00000013680	1 retrocopy	retro_mdom_1711,
Mustela putorius furo	ENSMPUG00000016000	2 retrocopies	retro_mputfur_1607, retro_mputfur_478,
Mus musculus	ENSMUSG00000019179	1 retrocopy	retro_mmus_2451,
Otolemur garnettii	ENSOGAG00000009705	1 retrocopy	retro_ogar_3068 ,
Pteropus vampyrus	ENSPVAG00000003397	1 retrocopy	retro_pvam_981,
Tupaia belangeri	ENSTBEG00000003190	1 retrocopy	retro_tbel_440,
Tursiops truncatus	ENSTTRG00000014834	1 retrocopy	retro_ttru_1550,
Drosophila melanogaster	FBgn0262559	2 retrocopies	retro_dmel_54, retro_dmel_76,