RetrogeneDB ID: retro_chof_1142

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_210895:24..467(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RCHY1
• Ensembl ID: ENSCHOG00000011650
• Aliases: None
• Description: ring finger and CHY zinc finger domain containing 1, E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:17479]

Sequence

>retro_chof_1142
ATGGCGGCCACTGCGTGGGAAGATGGCGCCTGTGACCAAGAGCAAGGGCAGCGGGGCTGTGGGCACTATGACAGAGGATG
TCTCCTGAAGGCACCTTGCTGTAACAAGCTTTATACCTGCCGATTGTGTCATGATAACAATGAAGATCATCAGCTAGATC
GCTTTAAAGTAAAAGAAGTGCAGTGCATAAACTGTGAAAAAATTCAACATGCCCAAAAGACGTGAAAAAATGCAGCACAT
TGTTTGGAGAATATTATTGCAATATATGCCATCTGTTTGACAAAGACAAGAAGCAGTATCATTGTGAAAACTGTGGAATT
TGTAGGACTGGTCCAAAGGAAGATTTTTTCCACTGTTTGAAATGTAACTTATGTCTAGCTATGAATCTTCAAGGAAAACA
CAAGTGTATTGAAAATCTCCTGGCAGAATTGTCAATATGTCTG

Alignment

ORF - retro_chof_1142 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.67 %
• Parental protein coverage: 57.75 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAATAREDGARGQEQGRRGCEHYDRGCLLKAPCCNKLYTCRLCHDNSEDHQLDRFKVKEVQCINCEKIQH
          MAATA.EDGA..QEQG.RGC.HYDRGCLLKAPCCNKLYTCRLCHDN.EDHQLDRFKVKEVQCINCEKIQH
Retrocopy MAATAWEDGACDQEQGQRGCGHYDRGCLLKAPCCNKLYTCRLCHDNNEDHQLDRFKVKEVQCINCEKIQH

Parental  AQQT-CEKCSTLFGEYYCNICHLFDKDKKQYHCEKCGICRIGPKEDFFHCLKCNLCLAVNLQGKHKCIEN
          AQ.T...KCSTLFGEYYCNICHLFDKDKKQYHCE.CGICR.GPKEDFFHCLKCNLCLA.NLQGKHKCIEN
Retrocopy AQKT<VKKCSTLFGEYYCNICHLFDKDKKQYHCENCGICRTGPKEDFFHCLKCNLCLAMNLQGKHKCIEN

Parental  VSRQNCPICL
          .......ICL
Retrocopy LLAE-LSICL

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_1142 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 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000032536	1 retrocopy	retro_cfam_1449,
Choloepus hoffmanni	ENSCHOG00000011650	1 retrocopy	retro_chof_1142 ,
Macropus eugenii	ENSMEUG00000003266	1 retrocopy	retro_meug_1564,
Monodelphis domestica	ENSMODG00000019197	2 retrocopies	retro_mdom_314, retro_mdom_991,
Rattus norvegicus	ENSRNOG00000002546	2 retrocopies	retro_rnor_1127, retro_rnor_607,
Tursiops truncatus	ENSTTRG00000013786	1 retrocopy	retro_ttru_1333,