RetrogeneDB ID: retro_tbel_440

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_2089:435493..436119(-)
• Located in intron of: ENSTBEG00000012190

Retrocopy information

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

Parental gene information

• Parental gene symbol: MDH2
• Ensembl ID: ENSTBEG00000003190
• Aliases: None
• Description: malate dehydrogenase 2, NAD (mitochondrial) [Source:HGNC Symbol;Acc:6971]

Sequence

>retro_tbel_440
GTGGTTATTCCAGCTGAGTCCCCAGAAAACCCAGGCATGACGCGAAGATAAGGTGTTCAACACCAATCCCACAATTGTGG
GCCACCTTGGCCACAGCCTGTGCCCAGCACTGTCCTGAGGCCATGATCTGCAATATCGCTAACCCGTTTAACTCCACTAT
CCTGATCACATCGGAAGTTTTCAAGAAACATGGAGTATACAACCTCAGTAAAATCTTTGGTGTGACCACCCTGGACATTG
TCAAAGCCAACACTTGTGTTGCTGAACTGAAGAATTTGGATCCAGCTGGAGTCAATGTTCCTGTAATCGGCGGCCATGCT
GGAAAGACCATCATCCCCCTGATCTCTCAGTGTCCGCCCAAGGTGGACTTTCCCCAGGACCAGCTGACAACGCTCACTGG
ACACATCCAGGAGGCGGAGGCAGGCATGGAGGTGGTCAAGACTAAAGCTGGAGCAGGCTCTGCCACTCTGTCCATGGCAT
ATGCCAGTGCCTGGTTTGTCTTCTCCCTTGTGGATGCAATGAATGGAAAGGGAGGAGTTGTTGAGTGTTCCTTTGTTAAG
TCACAGGAGACGGACTGTACCTATTTCTCCACACCGTTACTGCTAGGGTAAAAGGGCATTGAGAAG

Alignment

ORF - retro_tbel_440 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.33 %
• Parental protein coverage: 63.38 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VVIPAGVPRKPGMTR-DDLFNTNATIV-ATLAAACAQHCPEAMICVIANPVNSTIPITSEVFKKHGVYNP
          VVIPA..P..PGMTR.D..FNTN.TIV.ATLA.ACAQHCPEAMIC.IANP.NSTI.ITSEVFKKHGVYN.
Retrocopy VVIPAESPENPGMTR>DKVFNTNPTIV>ATLATACAQHCPEAMICNIANPFNSTILITSEVFKKHGVYNL

Parental  SKIFGVTTLDIVRANTFVAELKXXXXARVNVPVIGGHAGKTIIPLISQCTPKVDFPQDQLTTLTGRIQ--
          SKIFGVTTLDIV.ANT.VAELK....A.VNVPVIGGHAGKTIIPLISQC.PKVDFPQDQLTTLTG.IQ..
Retrocopy SKIFGVTTLDIVKANTCVAELKNLDPAGVNVPVIGGHAGKTIIPLISQCPPKVDFPQDQLTTLTGHIQEA

Parental  EAGTEVVKAKAGAGSATLSMAYAGARFVFSLVDAMNGKEGVVECSFVKSQETDCTYFSTPLLLGISSFEE
          EAG.EVVK.KAGAGSATLSMAYA.A.FVFSLVDAMNGK.GVVECSFVKSQETDCTYFSTPLLLG....E.
Retrocopy EAGMEVVKTKAGAGSATLSMAYASAWFVFSLVDAMNGKGGVVECSFVKSQETDCTYFSTPLLLG*KGIEK

Legend:

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

Expression

RNA-Seq

Tupaia belangeri was not studied using RNA-Seq expression data.

ChIP-Seq

Tupaia belangeri was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_tbel_440 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_440 was not experimentally validated.

Homology

Retrocopy orthology:

Tupaia belangeri 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,