RetrogeneDB ID: retro_chof_830

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_15328:107..919(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PANK3
• Ensembl ID: ENSCHOG00000011633
• Aliases: None
• Description: pantothenate kinase 3 [Source:HGNC Symbol;Acc:19365]

Sequence

>retro_chof_830
AGATAAAAAAATTTCTCAACATTACACACGGTGCTATGTGCTACAGGAAGTGGTGCTTATAGGTTTGAAAAAGATTTTGG
TACAATTGGAAACCTCTGCCTGCCCAAACTGGTTGAACATGACTGTCTTGTGAAGAGTTTGCTGTATATAGATTCTGTAT
GTTTCAATGGGCAAGCAGAGTGCTATTATTTTGCTAATGCCAAACTGAGAGATCCCAAACCAAAAGATGCCTTTTAACCT
GGATGACCCCTATCCACTCCTGGTAGTGAACATTGGTTCAGGAGTCAGTATTTTAGCAGTCCATTCCAAAGACAACTATA
AACGAGTGACCGGGACAAGTCTTGGTGGAGGTACCTTTCTGGGTTTATGGCAGCTTGTTGACTGGCTGTGAAAGTTTTGA
AGAGGCTCTTGAAATGGCATCCAAAGGTGATAGCACCCAAGCTGACAAGCTGGTCCGTGATATTTATGGAGAAGATTATG
AAAGATTTGGTCTGCCAGGTTGGGCTGTAGCATCTAGTTTCGGTAATATGATTTATAAGGAGAAGCGAGAATCTGTTAGT
AAAGAAGATCTGGCAAGAGCTACTTTAGTTACTATTACCAATAACATTGGTTCTGTGGCACGGATGTGTGCTGTTAATGA
GAAAATAAACAGAGTTGTCTTTGTTGGAAATTTTTACACATCAGTATTCTCAATGAAACTTTTGGCATATGTGCTGGATT
ATTGGTCAAAAGGTCAACTGAAAACATTGTTTCTAGAACATGAGAGATACTTTGGAGCAGTGGGTGCACTTCTTGGACTG
CCAAATTTCAGC

Alignment

ORF - retro_chof_830 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.01 %
• Parental protein coverage: 73.24 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RDKNFSTLHTVLCATGGGAYKFEKDFRTIGNLHLHKLDELDCLVKGLLYIDSVSFNGQAECYYFANASEP
          R.KNFSTLHTVLCATG.GAY.FEKDF.TIGNL.L.KL.E.DCLVK.LLYIDSV.FNGQAECYYFANA...
Retrocopy R*KNFSTLHTVLCATGSGAYRFEKDFGTIGNLCLPKLVEHDCLVKSLLYIDSVCFNGQAECYYFANAKLR

Parental  ERCQK-MPFNLDDPYPLLVVNIGSGVSILAVHSKDNYKRVTGTSLGGGTFLGLC-SLLTGCESFEEALEM
          ....K.MPFNLDDPYPLLVVNIGSGVSILAVHSKDNYKRVTGTSLGGGTFLGL..SLLTGCESFEEALEM
Retrocopy DPKPK>MPFNLDDPYPLLVVNIGSGVSILAVHSKDNYKRVTGTSLGGGTFLGLW>SLLTGCESFEEALEM

Parental  ASKGDSTQADKLVRDIYGGDYERFGLPGWAVASSFGNMIYKEKRESVSKEDLARATLVTITNNIGSVARM
          ASKGDSTQADKLVRDIYG.DYERFGLPGWAVASSFGNMIYKEKRESVSKEDLARATLVTITNNIGSVARM
Retrocopy ASKGDSTQADKLVRDIYGEDYERFGLPGWAVASSFGNMIYKEKRESVSKEDLARATLVTITNNIGSVARM

Parental  CAVNEKINRVVFVGNFLRVNTLSMKLLAYALDYWSKGQLKALFLEHEGYFGAVGALLGLPNFS
          CAVNEKINRVVFVGNF......SMKLLAY.LDYWSKGQLK.LFLEHE.YFGAVGALLGLPNFS
Retrocopy CAVNEKINRVVFVGNFY-TSVFSMKLLAYVLDYWSKGQLKTLFLEHERYFGAVGALLGLPNFS

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_830 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.

---

Parental genes homology:

Parental genes homology involve 8 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011633	4 retrocopies	retro_chof_1188, retro_chof_1391, retro_chof_1837, retro_chof_830 ,
Callithrix jacchus	ENSCJAG00000015550	1 retrocopy	retro_cjac_2037,
Homo sapiens	ENSG00000120137	1 retrocopy	retro_hsap_779,
Gorilla gorilla	ENSGGOG00000004947	1 retrocopy	retro_ggor_646,
Nomascus leucogenys	ENSNLEG00000004896	5 retrocopies	retro_nleu_1430, retro_nleu_144, retro_nleu_2975, retro_nleu_3058, retro_nleu_3099,
Pongo abelii	ENSPPYG00000016024	1 retrocopy	retro_pabe_2848,
Pan troglodytes	ENSPTRG00000017509	1 retrocopy	retro_ptro_608,
Tursiops truncatus	ENSTTRG00000016157	3 retrocopies	retro_ttru_1947, retro_ttru_29, retro_ttru_994,