RetrogeneDB ID: retro_chof_1078

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_194735:1338..1949(+)
• 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_1078
ATAAATATTGACAATTTTGATGAGCAACTATTTCAATTTCTGGCAGAAATGTGTATTCTTTTTGATGAAAATGGCAATAA
AATTGGACCTGGGACCAAAAAGAATTGTCACATGAATTAAAACATTGAGAAAGGACTATTGTATCGAGCCTAAAGCATCT
TCTTAATCAACACAGAAAATGAACTACTGCAGCAGAGATGATATGCTAAAATTCCCTTTCCAGGCCGTTTTACCAGTAAT
TGTTGTAGTCATCCTTTAAGTAATCCAGGAGAACTTGAAGAAAATGATGCAATTGGAGAAAGCAGAACAGCACAGAGGAC
TTCAAAAGCTGATGTAGGAATTCCCCAAGGAATAAGTTCCTCCAGAAGACATTCCTTATGTAACACAAGTTTGCTACGGG
GCTCTATCTGATGATGTTTGAGGTGAACACGAAATTGATTACTTCCTGTTTGTGAGGAAGAATGTAAGTCTGGATCCAGA
TCCCAATAAGATTAAGAGCTATTGTATGTGTCAAAGGAAGAACTAGAAGAATGGAGAAAAACAGCCAAGGGTGAAATTAA
GATAACTTTGTGGTTAAAATGATTGCAGAGACTTTTCTCTTTAAAAGGTGG

Alignment

ORF - retro_chof_1078 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.63 %
• Parental protein coverage: 90.71 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LNLDWIDKQQLWRLKEMLIVVDENDKLIGTDTKKNCHLNENIEKGLLH-AFSVVLFNTENKILIQQRADI
          .N.D..D.Q....L.EM.I..DEN...IG..TKKNCH.N.NIEKGLL..A.S..L.NTEN..L.QQR...
Retrocopy INIDNFDEQLFQFLAEMCILFDENGNKIGPGTKKNCHMN*NIEKGLLYRA*SIFLINTENE-LLQQR*YA

Parental  KLTFPGDFTDSCSSHPISNPEELEEKDAIGERKAAQRRLQTELGIPQGQ-ISPEDILFMTIYHHKAKSDK
          K..FPG.FT..C.SHP.SNP.ELEE.DAIGE...AQR......GIPQG....PEDI...T.....A.SD.
Retrocopy KIPFPGRFTSNCCSHPLSNPGELEENDAIGESRTAQRTSKADVGIPQGI>VPPEDIPYVTQVCYGALSDD

Parental  IWGEHEICYLLLIRKNVTVNLDPSETKSFC-YMTQEELTELLERGTRGEVKVTPWL-KTITEKFLYKWW
          ..GEHEI.Y.L..RKNV....DP...KS.C.Y...EEL.E.......GE.K.T.WL.K.I.E.FL.K.W
Retrocopy V*GEHEIDYFLFVRKNVSLDPDPNKIKSYC<YVSKEELEE-WRKTAKGEIKITLWL<KMIAETFLFKRW

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_1078 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,