RetrogeneDB ID: retro_tbel_2436

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_110629:131981..132470(-)
• 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_2436
AAAAGTCAGATGGCTGCTACTGCCAGTGCCATTTGGGAAATCATCAAAAGAACAGGAATTGAAACATTTGGGAAAAATGT
GCTTGTGGCTGGAAGATCCAAGAATGTAGGAATGCCCATCGCCATGTTGTTACCCACAGACGGAGAGCATGAGCGGCAGG
GAGGTGCTGCAACTGTGACAATAGCGCACAGATATACCCTCAAAGAACAATTGAAGATCCACACTCAGTTGGCAGATATT
ATCATAGTAGATCCAAGTATTCCAAAGTTGATTACATCTGATATGGTCAAGGAAGGTGCTGTTATAATTGGTGTGGGTAT
CAACTATATCCATGATCCAGTGAGAGGAAAGACAAAATTAGTTGGAGATGTGGATTTTGAAACTGTGAAGAAGAAAGCCA
GTTTTATCACTCCAGTTCCAGGAGGTGTGGGACCCATGACGGTGGTGATGCTTCTGAACACCCTGTTGGCAGCTAAAAAA
ATCACTTAT

Alignment

ORF - retro_tbel_2436 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.59 %
• Parental protein coverage: 56.75 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QSLIPATASAVWEIIKRTGIETFGKNVLVAGRSKNVGMPIAMLLHTDGEHERPGGDATVTIAHRYTPKEQ
          .S...ATASA.WEIIKRTGIETFGKNVLVAGRSKNVGMPIAMLL.TDGEHER.GG.ATVTIAHRYT.KEQ
Retrocopy KSQMAATASAIWEIIKRTGIETFGKNVLVAGRSKNVGMPIAMLLPTDGEHERQGGAATVTIAHRYTLKEQ

Parental  LKIHTQLADVIIVAAGIPKLITSDMVKEGAAVIDVGINYIHDPVTGKTKLVGDVDFEAVKKKASFITAVP
          LKIHTQLAD.IIV...IPKLITSDMVKEGA..I.VGINYIHDPV.GKTKLVGDVDFE.VKKKASFIT.VP
Retrocopy LKIHTQLADIIIVDPSIPKLITSDMVKEGAVIIGVGINYIHDPVRGKTKLVGDVDFETVKKKASFITPVP

Parental  GGVGPMTVAMLLKNTLLAAKKIIY
          GGVGPMTV.MLL.NTLLAAKKI.Y
Retrocopy GGVGPMTVVMLL-NTLLAAKKITY

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_2436 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2436 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,