RetrogeneDB ID: retro_chof_615

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_126888:853..1236(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCHOG00000006784
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: POLR1C
• Ensembl ID: ENSCHOG00000006601
• Aliases: None
• Description: polymerase (RNA) I polypeptide C, 30kDa [Source:HGNC Symbol;Acc:20194]

Sequence

>retro_chof_615
GGCAAAGATCATGCCAAGTTTTCACCTGTGGCCACCACCAGTTACAGGTTCCTGCCTGACATCACCCTCCTTCAACCCAC
GGAAGAGGAGGCAGCAGGGAGCTCAAGCAGTGCTTCTCACCTGGTGTCATTGAGGTGCAGGAAGTTCAAGCTAAAGAGGT
GGCTAGAGTTACCAATCCCCAGTTGGATACCTTCAGAAGGGAAGTCTTCCAGAATGAGAAGCTGAAGAAGGTTGTATGGT
TGGCCCATGTTCGGGATCATTATATTTTCTCTGTAGAGTCAACAGGGGTGTTGCCACCAGATGTGCTGGTAAGTGAAGCC
ATCAAAGTATTGATGGGAAAGTGCTGGCGGTTCTTGGATGAAGTAGATGCAGTTCAGATGGAC

Alignment

ORF - retro_chof_615 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.27 %
• Parental protein coverage: 60.38 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GKDHAKFSPVATASYRLLPDITLLQPVEGEAA-EELRQCFSPGVIEVHEVQGKKVARVANPRLDTFSREV
          GKDHAKFSPVAT.SYR.LPDITLLQP.E.EAA..EL.QCFSPGVIEV.EVQ.K.VARV.NP.LDTF.REV
Retrocopy GKDHAKFSPVATTSYRFLPDITLLQPTEEEAA<RELKQCFSPGVIEVQEVQAKEVARVTNPQLDTFRREV

Parental  FRNEKLKKVVRLARVRDHYIFSVESTGVLPPDVLVSEAIRVLMGKCRRFLDELDAVQMD
          F.NEKLKKVV.LA.VRDHYIFSVESTGVLPPDVLVSEAI.VLMGKC.RFLDE.DAVQMD
Retrocopy FQNEKLKKVVWLAHVRDHYIFSVESTGVLPPDVLVSEAIKVLMGKCWRFLDEVDAVQMD

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_615 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 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006601	1 retrocopy	retro_chof_615 ,
Tarsius syrichta	ENSTSYG00000011921	1 retrocopy	retro_tsyr_739,