RetrogeneDB ID: retro_chof_2132

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_52222:4927..5328(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZCCHC10
• Ensembl ID: ENSCHOG00000001420
• Aliases: None
• Description: zinc finger, CCHC domain containing 10 [Source:HGNC Symbol;Acc:25954]

Sequence

>retro_chof_2132
ACTTACGAATATACAGGAAAAAGAAAATACCTACATAGGCCTTCAAGAATAGCAGAACTAAAGAAAGATTTAAAAGAAAA
GTAAAACAGATTATTATTACAAGAAAGCATTGGTTAAACTAATTTAGAAAAAATATCAAGAAAAAAAGGTCTAAGGGTAT
ATCCAGTTCTAACACCAATAGCAGTGACAGTTCAGCCAATTATTCTTCATCAGAAAGGGAAGAAACATGTACCTCATCCT
CCTCTGGGGATAGTGACACTGATGAAAGCTCTTCTTCAGCTTCCTCCATAAGCTCTTCCTCCTCCTCTGATTCAGACTCA
GATTCCAGCTCCTCCAGTAGCAGTAGCACCAGCAGAGATAGCAGCTCTGAAGATGAACCACCAAAGAGGAAGAAAAAGAA
A

Alignment

ORF - retro_chof_2132 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.86 %
• Parental protein coverage: 88.46 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TYECTGKRKYLHRPSRTAELKKALKEKENRLLLQQSIGETNVEKKN-KKKRSKSVTSSSTNSSDSSASDS
          TYE.TGKRKYLHRPSR.AELKK.LKEK.NRLLLQ.SIG.TN.EK...KKKRSK...SS.TNSSDSSA..S
Retrocopy TYEYTGKRKYLHRPSRIAELKKDLKEK*NRLLLQESIG*TNLEKIS<KKKRSKGISSSNTNSSDSSANYS

Parental  SSESEGTSTSSSSEDSDTDESSSSPSSSASSTSSSSSSDSDSDSSSSSSSTTSTDSSSEDEPPKKKKKK
          SSE.E.T.TSSSS.DSDTDESSSS....ASS.SSSSSSDSDSDSSSSSSS.TS.DSSSEDEPPK.KKKK
Retrocopy SSEREETCTSSSSGDSDTDESSSS----ASSISSSSSSDSDSDSSSSSSSSTSRDSSSEDEPPKRKKKK

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_2132 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 10 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000031203	1 retrocopy	retro_cfam_643,
Choloepus hoffmanni	ENSCHOG00000001420	9 retrocopies	retro_chof_1243, retro_chof_1263, retro_chof_1773, retro_chof_2048, retro_chof_2132 , retro_chof_2183, retro_chof_501, retro_chof_790, retro_chof_923,
Dasypus novemcinctus	ENSDNOG00000017302	1 retrocopy	retro_dnov_257,
Myotis lucifugus	ENSMLUG00000011366	4 retrocopies	retro_mluc_172, retro_mluc_2240, retro_mluc_2241, retro_mluc_2574,
Monodelphis domestica	ENSMODG00000013827	1 retrocopy	retro_mdom_1405,
Mus musculus	ENSMUSG00000018239	1 retrocopy	retro_mmus_269,
Otolemur garnettii	ENSOGAG00000032171	1 retrocopy	retro_ogar_3011,
Pongo abelii	ENSPPYG00000015776	1 retrocopy	retro_pabe_2395,
Rattus norvegicus	ENSRNOG00000006943	3 retrocopies	retro_rnor_2037, retro_rnor_2528, retro_rnor_801,
Sorex araneus	ENSSARG00000007221	1 retrocopy	retro_sara_639,