RetrogeneDB ID: retro_chof_2362

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_6844:3325..3771(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MTHFD2L
• Ensembl ID: ENSCHOG00000006627
• Aliases: None
• Description: methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2-like [Source:HGNC Symbol;Acc:31865]

Sequence

>retro_chof_2362
ATGTGGGAAATAATCAAGTGAAACAGAATTCCAGAGCTAGGGAAGAAGGTGATTGTGGCTGGAAGAGCAAAGAATGTTGG
AATGTTACTACATGCAGATGGGGCATGTGAATGTCTTGGAGGTGATGCCACTGTTACAATATCCATCACTACACTCCCAA
AGAGAAGCTGAAGAAACATACAATTCTTGCAGATATTGTGGTACCCTCTGCAGGCATTCCAAATCTGATCACAGCAGATA
TGATCAAGGAAGGAGCAGAAGTCATTGATGTGGGAATAAAAAGCATTCAAGATCCCATAACTGCTAAGCCCAAGTTGTTC
AGAGATGTGGATTTTGAAGGAGCCAGGAAGAAAGTCAGTTACATCACTCCAGTCCCTGGGGGCTTCGGTTCCATGACAGT
GGTGATGGTGATGAAGAATACAATTACTGCTGCAAAAAAACTGCTG

Alignment

ORF - retro_chof_2362 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.64 %
• Parental protein coverage: 52.78 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VWEIIK-RTIETFGKNVVVAGRSKNVGMPIAMLLHTDGEHERPGGDATVTIT-HRYTPKEQLKIHTQLAD
          .WEIIK...I...GK.V.VAGR.KNVG....MLLH.DG..E..GGDATVTI..H.YTPKE.LK.HT.LAD
Retrocopy MWEIIK*NRIPELGKKVIVAGRAKNVG----MLLHADGACECLGGDATVTIS<HHYTPKEKLKKHTILAD

Parental  VIIVAAGIPKLITSDMVKEGAAVIDVGINYIQDPVTGKTRLVGDVDFEAVKKKASFITPVPGGVGPMTVA
          .....AGIP.LIT.DM.KEGA.VIDVGI..IQDP.T.K..L..DVDFE...KK.S.ITPVPGG.G.MTV.
Retrocopy IVVPSAGIPNLITADMIKEGAEVIDVGIKSIQDPITAKPKLFRDVDFEGARKKVSYITPVPGGFGSMTVV

Parental  MLLKNTLLAAKKII
          M..KNT..AAKK..
Retrocopy MVMKNTITAAKKLL

Legend:

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

Expression

RNA-Seq

Choloepus hoffmanni was not studied using RNA-Seq expression data.

ChIP-Seq

Choloepus hoffmanni was not studied using ChIP-Seq data.

EST

Choloepus hoffmanni was not studied using EST data.

TSS

Choloepus hoffmanni was not studied using FANTOM5 data.

Lab

retro_chof_2362 was not experimentally validated.

Homology

Retrocopy orthology:

Choloepus hoffmanni 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,