RetrogeneDB ID: retro_chof_323

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_7329:10437..11002(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KCTD9
• Ensembl ID: ENSCHOG00000012157
• Aliases: None
• Description: potassium channel tetramerization domain containing 9 [Source:HGNC Symbol;Acc:22401]

Sequence

>retro_chof_323
AGAAGCAGTTTAGTGAATAAAGAAGCTGATAGTATGCTGGCCTACATGTTTAAAGACAAAGATGTCTGGAGAAACAAGCA
AGATCATAGAGGAGCTTTCTTAATTGACCAAAGTCCTGAGTACTTTGAACCCATTTTGAACTATTTGCATCATGGACAGC
TCATTGTAAATGACGGCATTAATTTATTAGGTGTGTTAGAAGCAGCCAGATTTTTTGGTATTGACTTATTGATTGAACAC
CTTGAAGTGGCAATAAAGAATTCTCAACTGCTAAAGGATCATTCAACAATATGCCAAAAGGAATTTGTCCAGTTTCTACT
AGTTACTCCAACTAAACCAGAATTGTGTTGCCAGGATTTAAACTTTCATGGTGTTATCTTTCTTGCTTGGACTTTCAGTA
CATTAATTTCAAAATGGCCAATTTAAACCGCTGCAATCTTGCACATGCTAATCTCTGCTTTGTAAATCTTGAACAAGCTG
ATCTCTCTGTTTAGTGCTTGATTGTGCAAATCTTTAGGGGGTCAAGATGGTATGTTCTAATGCAGAAGGGGCATCCTTGA
AACTG

Alignment

ORF - retro_chof_323 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.15 %
• Parental protein coverage: 50.4 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RSTLVNKEPDSMLAHMFKDKDVWGNKQDRRGAFLIDRSPEYFEPILNYLRHGQLIVNDGINLLGVLEEAR
          RS.LVNKE.DSMLA.MFKDKDVW.NKQD.RGAFLID.SPEYFEPILNYL.HGQLIVNDGINLLGVLE.AR
Retrocopy RSSLVNKEADSMLAYMFKDKDVWRNKQDHRGAFLIDQSPEYFEPILNYLHHGQLIVNDGINLLGVLEAAR

Parental  FFGIDSLIEHLEVAIKNSQPPEDHSPISRKEFVRFLLATPTKSELRCQGLNFSG-ADLSRLDLRYINFKM
          FFGID.LIEHLEVAIKNSQ...DHS.I..KEFV.FLL.TPTK.EL.CQ.LNF.G...LS.LD..YINFKM
Retrocopy FFGIDLLIEHLEVAIKNSQLLKDHSTICQKEFVQFLLVTPTKPELCCQDLNFHG<CYLSCLDFQYINFKM

Parental  ANLSRCNLAHANLCCANLERADLS-GSVLDCANLQGVKMLCSNAEGASLKL
          ANL.RCNLAHANLC..NLE.ADLS...VLDCANL.GVKM.CSNAEGASLKL
Retrocopy ANLNRCNLAHANLCFVNLEQADLS<CLVLDCANL*GVKMVCSNAEGASLKL

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_323 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 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012157	1 retrocopy	retro_chof_323 ,
Gorilla gorilla	ENSGGOG00000004480	3 retrocopies	retro_ggor_1309, retro_ggor_2264, retro_ggor_2791,
Macaca mulatta	ENSMMUG00000010151	3 retrocopies	retro_mmul_1083, retro_mmul_1218, retro_mmul_2072,
Nomascus leucogenys	ENSNLEG00000016156	3 retrocopies	retro_nleu_1386, retro_nleu_2499, retro_nleu_2990,
Pongo abelii	ENSPPYG00000018452	3 retrocopies	retro_pabe_1527, retro_pabe_2725, retro_pabe_3457,
Pan troglodytes	ENSPTRG00000020092	3 retrocopies	retro_ptro_1225, retro_ptro_2166, retro_ptro_2825,