RetrogeneDB ID: retro_chof_1881

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_413496:539..1005(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IDI2
• Ensembl ID: ENSCHOG00000008984
• Aliases: None
• Description: isopentenyl-diphosphate delta isomerase 2 [Source:HGNC Symbol;Acc:23487]

Sequence

>retro_chof_1881
AACACTGACAAAGGATATTGCATCGAGCTTTAGTGTCTCTATTCAACACTAAAATAAGCTTCTACAAGAGCAGAGATCAG
ATGCTAAAATTACCTTTCAGGTTGTTTATCAGTATTGTTGCTGTCATCCATTAAGTAATACAGGAGAACTTGAAGAAAAT
GATGCAGTTGGAGTAAGACGAGCAGCACAGAGGCATTTAAAAGCTGAATTAGGAATTCCCATGGAAGAGGTTCCTCCAGA
AGAAATGAATTATGTAACACGAATTCACTACACAGCTTAATCTGATGGTATTTGGGGAGAACATGAAATTGATTACATTC
TGATTATGCGGAAGAATGTAACTTTGGATCTAGATTCTAATGAGATTAAAAGCTATTGTTATGTAGCAAAGGAAGAACTA
GAAGAACTGAAAAAAGCAGCCAGTGGTGAAATTAAGATAACTCCATGGTTCAAAATTATTGCAGAC

Alignment

ORF - retro_chof_1881 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.88 %
• Parental protein coverage: 69.91 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NIEKG-LLHAFSVVLFNTE-NKILIQQRADIKLTFPGDFTDSCSSHPISNPEELEEKDAIGERKAAQRRL
          N..KG..LH...V.LFNT..NK.L..QR.D.K.TF.......C..HP.SN..ELEE.DA.G.R.AAQR.L
Retrocopy NTDKG<ILHRALVSLFNTK<NKLLQEQRSDAKITFQVVY-QYCCCHPLSNTGELEENDAVGVRRAAQRHL

Parental  QTELGIPQGQISPEDILFMTIYHHKAKSDKIWGEHEICYLLLIRKNVTVNLDPSETKSFCYMTQEELTEL
          ..ELGIP.....PE.....T..H..A.SD.IWGEHEI.Y.L..RKNVT..LD..E.KS.CY...EEL.E.
Retrocopy KAELGIPMEEVPPEEMNYVTRIHYTA*SDGIWGEHEIDYILIMRKNVTLDLDSNEIKSYCYVAKEELEE-

Parental  LERGTRGEVKVTPWLKTITE
          L.....GE.K.TPW.K.I..
Retrocopy LKKAASGEIKITPWFKIIAD

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_1881 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 2 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008984	5 retrocopies	retro_chof_1078, retro_chof_1667, retro_chof_1771, retro_chof_1881 , retro_chof_1921,
Macropus eugenii	ENSMEUG00000015260	1 retrocopy	retro_meug_1719,