RetrogeneDB ID: retro_tbel_3051

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_128357:67883..68405(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MTHFD2L
• Ensembl ID: ENSTBEG00000009980
• Aliases: None
• Description: methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2-like [Source:HGNC Symbol;Acc:31865]

Sequence

>retro_tbel_3051
TTTCATGTCATAATGTAGGACGAATGTGTTTGGACCAGCATTCCATGTTACTGGCTGCCCCATGGAGTGTGTGGAATATC
ATTAAGTGAACTAACATTCCAACCCTAGAGCAAGAATGTGGTTGTGGCCAGGAGGTCAAAAACTGTTGGGATGCCCATTA
CAGTGTTGCTACACACAGACAGGGCGTATGATAATCCCGGAGATGATGCCGCTATTAAAATAATTCTTTGATACACTCCC
AAAAAGCCATTGAAGAAACATACAATTCTTGCAGATATTGTGGTGCCTGTGGCAGGCATTCTGGATCTGATCACAGCACA
TATGATCAAAAGGGAGCATCAGTCACCGGTGTGGGAATAAACAGAGTTCAAGATGCCATAACTGCTCTACCCAAGTTAGT
TGGAGGTGTAGATTTTGAAAGAGATGGGAAGAAAGCTGGCCTGTGACAGTCCCTGGGAGTGCTGGCCTGTGACAGTGGCT
GTGCTAATGAAGAATACCGTTATTGCTGCAAATAAAGTGCTG

Alignment

ORF - retro_tbel_3051 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.14 %
• Parental protein coverage: 60.9 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  FHII-NIGRLCLDQQSLIPATASAVWEIIKRTGIETF-GKNVLVAGRSKNVGMPIAMLLHTDGEHERPGG
          FH.I.N.GR.CLDQ.S...A....VW.IIK.T.I.T...KNV.VA.RSK.VGMPI..LLHTD.....PG.
Retrocopy FHVI<NVGRMCLDQHSMLLAAPWSVWNIIK*TNIPTL>SKNVVVARRSKTVGMPITVLLHTDRAYDNPGD

Parental  DATVTIAHRYTPKEQLKIHTQLADVIIVAAGIPKLITSDMVK-EGAAVIDVGINYIHDPVTGKTKLVGDV
          DA...I...YTPK..LK.HT.LAD.....AGI..LIT..M.K..GA.V..VGIN...D..T...KLVG.V
Retrocopy DAAIKIIL*YTPKKPLKKHTILADIVVPVAGILDLITAHMIK<KGASVTGVGINRVQDAITALPKLVGGV

Parental  DFEAVKKKASF-ITAVPGGVG-PMTVAMLLKNTLLAAKKII
          DFE...KKA....T.VPG..G.P.TVA.L.KNT..AA.K..
Retrocopy DFERDGKKAGL<VT-VPGSAG<PVTVAVLMKNTVIAANKVL

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_3051 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3051 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 4 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006627	1 retrocopy	retro_chof_2362,
Callithrix jacchus	ENSCJAG00000013883	1 retrocopy	retro_cjac_1764,
Tupaia belangeri	ENSTBEG00000009980	4 retrocopies	retro_tbel_2436, retro_tbel_2590, retro_tbel_3051 , retro_tbel_850,
Tursiops truncatus	ENSTTRG00000002366	1 retrocopy	retro_ttru_397,