RetrogeneDB ID: retro_chof_1494

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_30800:3170..3564(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TM2D1
• Ensembl ID: ENSCHOG00000013535
• Aliases: None
• Description: TM2 domain containing 1 [Source:HGNC Symbol;Acc:24142]

Sequence

>retro_chof_1494
TACAAACAACACAGTTCATGTTTTCCAGCACCCAACATAACTTGTAAGGATTTCATTGGCAATGAAATAATTTTCCTGGA
AACGAAGTTGGTGTTTTCTCAAGCCTATATCGTGCCAAAATGTAAATGGCTATTCATACTAAGTGGCAGTTGCACTGTCT
CTTTTTCTTGGATGATTGGGAACAGATAAATTTTATCCTGGTTACCCTGCCTTGGGTTTGTTAAAGTTTAGTACTGTAGG
GTTGTGTGGAATTGAGAGCTTAATTGATTTCACTCTTATTTCAATCAGATAGTTGGACCTTCAGATGGAAGTAGTTACAT
TATAGCTTATTATGAAACCAGACTTACAAGACTAAGTATTACTAATGGAAATATTTAGAAAAACACAGTTATAC

Alignment

ORF - retro_chof_1494 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.87 %
• Parental protein coverage: 50.58 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  YTAHVPCFPAPNITCKDFSGNETHFTGNEVGF-LKPISCRNVNGYSYKVAVALSLFLGWLGADRFYLGYP
          Y..H..CFPAPNITCKDF.GNE..F......F.LKPISC.NVNGYSY.VAVALSLFLG.LG.D.FY.GYP
Retrocopy YKQHSSCFPAPNITCKDFIGNEIIFLETKLVF>LKPISCQNVNGYSY*VAVALSLFLG*LGTDKFYPGYP

Parental  ALGLLKFCTVGFCGIGSLIDFILISM-QIVGPSDGSSYIIDYYGTRLIRLSITN-ETFRKTQLY
          ALGLLKF.TVG.CGI.SLIDF.LIS..QIVGPSDGSSYII.YY.TRL.RLSITN.E.FRKTQLY
Retrocopy ALGLLKFSTVGLCGIESLIDFTLISI<QIVGPSDGSSYIIAYYETRLTRLSITN>EIFRKTQLY

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_1494 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 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011705	1 retrocopy	retro_amel_1290,
Canis familiaris	ENSCAFG00000018838	1 retrocopy	retro_cfam_1213,
Choloepus hoffmanni	ENSCHOG00000013535	1 retrocopy	retro_chof_1494 ,
Cavia porcellus	ENSCPOG00000012287	1 retrocopy	retro_cpor_471,
Equus caballus	ENSECAG00000015035	1 retrocopy	retro_ecab_556,
Erinaceus europaeus	ENSEEUG00000001567	1 retrocopy	retro_eeur_708,
Loxodonta africana	ENSLAFG00000013979	1 retrocopy	retro_lafr_662,
Mus musculus	ENSMUSG00000028563	2 retrocopies	retro_mmus_1412, retro_mmus_1981,
Rattus norvegicus	ENSRNOG00000007527	1 retrocopy	retro_rnor_1104,
Tupaia belangeri	ENSTBEG00000002089	3 retrocopies	retro_tbel_1156, retro_tbel_1730, retro_tbel_201,