RetrogeneDB ID: retro_chof_1771

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_38013:2687..3359(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCHOG00000001086
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_1771
ATAAACACTGACAATCTCGACGAGCAACAGGTTCAACTTCTGGCAGAGATGTGTATTATTATTGATGAAAATGACAATAA
AATTGGAGCTGAGACCAAAAAGAATTGTCACTTGAATGAAAACATTGACAAAGGATTGCTGCATCGAGCTTTTAGTGTCT
TCTTATTCAACACTGAAAATAAGCTCCTACTACAGCAGAGATCAGATGCTAAAATTACCTTTCCAGGTTGTTTTACCAAT
ACTTGTTGCAGTCATCCATTAAGTAATCCAGGAGAACTTGAAGAAAATGATGCAATTGGAGTAAGACGAGCAGCACAGAG
GCGTTTAAAAGCTGAATTAGGAATTCCCATGGAAGAGGTTCCTCCAGAAGAAATTAATTATGTAACACGAATTCACTACA
AGGCTCAATCTGATGGTATTTGGGGTGAACATGAAATTGATTATATTTTGTTTGTGAGGAAGAATGTAACTTTGGATCCA
GATCCTAATGAGATTAAGAGCTATTGTTATGTGTCAAAGGAAGAACTAGAAGAACTTCTGAAAAAAGCAGCCAATGGTAA
AATTAAGATAACCCCATGGTTTAAAATTATTGCAGAGACTTTCCTCTTTAAATGGTGGGATAATTTAAATCATTTGAATC
AGTTTGTTGAACATGAGAAAATATATAGAATG

Alignment

ORF - retro_chof_1771 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.61 %
• Parental protein coverage: 98.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LNLDWIDKQQLWRLKEMLIVVDENDKLIGTDTKKNCHLNENIEKGLLH-AFSVVLFNTENKILIQQRADI
          .N.D..D.QQ...L.EM.I..DEND..IG..TKKNCHLNENI.KGLLH.AFSV.LFNTENK.L.QQR.D.
Retrocopy INTDNLDEQQVQLLAEMCIIIDENDNKIGAETKKNCHLNENIDKGLLHRAFSVFLFNTENKLLLQQRSDA

Parental  KLTFPGDFTDSCSSHPISNPEELEEKDAIGERKAAQRRLQTELGIPQGQISPEDILFMTIYHHKAKSDKI
          K.TFPG.FT..C.SHP.SNP.ELEE.DAIG.R.AAQRRL..ELGIP.....PE.I...T..H.KA.SD.I
Retrocopy KITFPGCFTNTCCSHPLSNPGELEENDAIGVRRAAQRRLKAELGIPMEEVPPEEINYVTRIHYKAQSDGI

Parental  WGEHEICYLLLIRKNVTVNLDPSETKSFCYMTQEELTELLERGTRGEVKVTPWLKTITEKFLYKWWPHLN
          WGEHEI.Y.L..RKNVT...DP.E.KS.CY...EEL.ELL.....G..K.TPW.K.I.E.FL.KWW..LN
Retrocopy WGEHEIDYILFVRKNVTLDPDPNEIKSYCYVSKEELEELLKKAANGKIKITPWFKIIAETFLFKWWDNLN

Parental  EVTQFVVPRKIHRV
          ...QFV...KI.R.
Retrocopy HLNQFVEHEKIYRM

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_1771 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,