RetrogeneDB ID: retro_tbel_850

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_3150:245839..246323(-)
• Located in intron of: ENSTBEG00000017669

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_850
CTAAATAGTGATAATAATATAGATGGCCTCCTTACTCAGCTGCCTCTTCCAGAGCACACTGATGAGAGAAAGATCTGCAA
TGCCCTTTCTACAGACAAAAATGTTGATGACTTTCATGTCATTAATGTAGGGCAAATGTGTTTGGATCAGTATTCCATGT
TACTGGCTATCCCATGGGGTGTCTGGGAAATCATTAAACGAACTGTCATTCTAACCCTAGGGAAGAATGTGGTTGTGACT
GGAAGGTCAAAAAATGTAGTAAATGATGTTACTACACACACAGATAGGGCACGTGAACACCACGGAGGTGATGCCACTGT
TACAATTCTCATTGATATACTCCCAAAGAGCAGCTGAAGAAACATACAATTCTCGCAGATATTCTGGTATCTGCTGCAGG
CCTTCCAAATCTGGTAACAGCAGATATTTCAATGAGAGATCAGCTGTCATTGATGTGGGAATAAAGAGTTCAGATCCCAT
ATCT

Alignment

ORF - retro_tbel_850 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.89 %
• Parental protein coverage: 57.09 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LNMDPRVSGILVQLPLPDHIDERTICNGIAPEKDVDGFHIINIGRLCLDQQSLIPATASAVWEIIKRTGI
          LN.D....G.L.QLPLP.H.DER.ICN.....K.VD.FH.IN.G..CLDQ.S...A....VWEIIKRT.I
Retrocopy LNSDNNIDGLLTQLPLPEHTDERKICNALSTDKNVDDFHVINVGQMCLDQYSMLLAIPWGVWEIIKRTVI

Parental  ETFGKNVLVAGRSKNVGMPIAMLLHTDGEHERPGGDATVTI-AHRYTPKEQLKIHTQLADVIIVAAGIPK
          .T.GKNV.V.GRSKNV........HTD...E..GGDATVTI..H.YTPKEQLK.HT.LAD....AAG.P.
Retrocopy LTLGKNVVVTGRSKNVVNDVT--THTDRAREHHGGDATVTI<SH*YTPKEQLKKHTILADILVSAAGLPN

Parental  LITSDM-VKEGAAVIDVGINYIHDPVT
          L.T.D....E..AVIDVGI....DP..
Retrocopy LVTADI<FNERSAVIDVGIK-SSDPIS

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_850 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_850 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.

---

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,