RetrogeneDB ID: retro_chof_1424

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_289700:443..1380(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCHOG00000005547
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000008413
• Aliases: None
• Description: None

Sequence

>retro_chof_1424
CAGGCGAAGCTGACATTATGATCTTCATGCAGAGAGCATGGAGACTTCTACCCTTTTGATGGAAAAAATGGGGTTTTAGC
CCATGATTTTGGAGCTGGAGCTGGTATTAGAGGAGACACTCATTTTGATGAGGATGAAATCTGGACTATAAACTCCAGAG
GCATAAACTTATTTCTTGTTGTGGTTCATGAGATTGACCATTCCTTGGATCTTAACCATTCCAATGATCCAAAGGCCATA
ATGTTTCCCACCTACAGTTATGTTGACTCCCACACATTTAGCTTCTCTTCTGATGACATACATGGCATTCAGTTCCTCTA
TGGAGGCCCAGAACAGCACCAACCCAAGCCAGATCCCAACCAGATAGACATCTGTGACCCCAATTTGAGATTCAGTGCTG
TCACTACAGTTGGCAGTAAAATCTTTTTCTTTAAAGACAGGTTCTTCTGGTGGAAGCATGCAGAGACACCTAAGATCAGT
GTTAGTTCAATTTCTATCTTAGGGCCAACTTTGCCATTTGGTATTCAAGCTGTCTATGAAATTGGATCTAGAAATGAAGT
TTTTCTTTTTAAAGATGACAAGTACTGGTTAATCAGCAATTTAAGAATACATCCAAAACTATCCCAAGAACATATATTCT
TTGGGTTTCCCTGCCTCTGTGAAAAAAATTGATGCAGCCGTTTTCCACCCAGTTTTTTACAAGACCTACTTCTTTGACGA
TAACTGGTATTGGAGGTACGATGAGAGGAGACAACTCATGGATGCTGATTATCCCAAATCGATTACCAAAAGCTTTCCAG
GAATTGGACCTAAAATCGATGCAACCTTCTACTGCAAGGGTCACTATTATTTCTTCCAGGGATCTCACCAACTTAAATAT
AACATCCTATCCAACCATGTCACCAGAAGGTTGAAAAGCAATAGAAGGTTGGGTTGT

Alignment

ORF - retro_chof_1424 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.11 %
• Parental protein coverage: 66.74 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EADIMILFSRREHGDFYPFDGKNGILAHAFGPGAGIGGDAHFDDDEIWTKNSRGHNFFLVAVHEIGHSLG
          .A......S.REHGDFYPFDGKNG.LAH.FG.GAGI.GD.HFD.DEIWT.NSRG.N.FLV.VHEI.HSL.
Retrocopy QAKLTL*SSCREHGDFYPFDGKNGVLAHDFGAGAGIRGDTHFDEDEIWTINSRGINLFLVVVHEIDHSLD

Parental  LDHSNDPKAIMFPTYRYVDLHTFSLSSDDIRGIQFLYGGPEQHQPKPVPDE-DVCDPNLRFNAVTTVGNK
          L.HSNDPKAIMFPTY.YVD.HTFS.SSDDI.GIQFLYGGPEQHQPKP.P...D.CDPNLRF.AVTTVG.K
Retrocopy LNHSNDPKAIMFPTYSYVDSHTFSFSSDDIHGIQFLYGGPEQHQPKPDPNQIDICDPNLRFSAVTTVGSK

Parental  IFFFKDRFFWWKHVETPKISISSISNLWPTLPSGIQAAYEIGARNEVFLFKDDKYWLISNLRIHP-DYPK
          IFFFKDRFFWWKH.ETPKIS.SSIS.L.PTLP.GIQA.YEIG.RNEVFLFKDDKYWLISNLRIHP..YPK
Retrocopy IFFFKDRFFWWKHAETPKISVSSISILGPTLPFGIQAVYEIGSRNEVFLFKDDKYWLISNLRIHP>NYPK

Parental  SIYSLGLPASVKKIDAAVFHPVLYKTYFFVDNWYWRYDERRQLMDSDYPKLITKNFPGIGPKIDAAFYYK
          .IYSLG.PASVKKIDAAVFHPV.YKTYFF.DNWYWRYDERRQLMD.DYPK.ITK.FPGIGPKIDA.FY.K
Retrocopy NIYSLGFPASVKKIDAAVFHPVFYKTYFFDDNWYWRYDERRQLMDADYPKSITKSFPGIGPKIDATFYCK

Parental  GHYYFFQGSHQLEFNTLSNRVTRRLKSNSGLGC
          GHYYFFQGSHQL..N.LSN.VTRRLKSN..LGC
Retrocopy GHYYFFQGSHQLKYNILSNHVTRRLKSNRRLGC

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_1424 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 5 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008413	6 retrocopies	retro_chof_1424 , retro_chof_1611, retro_chof_2207, retro_chof_325, retro_chof_595, retro_chof_645,
Equus caballus	ENSECAG00000019445	1 retrocopy	retro_ecab_153,
Loxodonta africana	ENSLAFG00000010062	1 retrocopy	retro_lafr_147,
Macaca mulatta	ENSMMUG00000004250	1 retrocopy	retro_mmul_2325,
Otolemur garnettii	ENSOGAG00000010221	1 retrocopy	retro_ogar_965,