RetrogeneDB ID: retro_chof_988

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_18117:6528..7221(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TPK1
• Ensembl ID: ENSCHOG00000001227
• Aliases: None
• Description: thiamin pyrophosphokinase 1 [Source:HGNC Symbol;Acc:17358]

Sequence

>retro_chof_988
ATTCCCACTGGGAATTTGAAGTACTGCCTTTCAACTCTGAACCAGCCTTTGGACGACCATTTTTGTCATCTTTGGAGCAA
AGCTCTTTTAAAAGCTTGTGCTGATGGAGATGCCAACCACTTACATGATATCACTGAAGGAGAGCGGGAAGGCTTTTTGC
CCGAATTCATCAGTGGAGATTTTGATTCTGTTAGGCCTGAAGTCAGAGAGTACTACAGTATTAAGGGTTGTGAGCGCACT
TCAACTCCTGATAAAGACCACACTGACTTTACCAAGTGCCTCCAAGTGCCCCAAAAGAAGATAGAAGAAAAAGTCCTATA
GGTTGGTATGATTATGACACTGGGAGGCCTTGATGGACATTTTGACCGGATTAGGGCATCTGTGAGCACCCTGTTCCAGG
CCACTGATGTCACTCCTTTGCCAATTATAATAATTTAAGAGAAATTTCTCATCTACCTGCTCCAACCAGGAAAGCACAAA
TTGCTTATAAACCCTGGAGTGGAAGGTGATTGGTGTGGCCTTATACCTGTTGGACAGCCTTGCAATCAGGTTACCACAAC
AGGCCTAAAGTGGAACCTCGCCAATCATGTGCTTGGTTTCGGAATACTGGTCAGTACCTCTAATACCTACGATGGATCTG
GGGTCGTGACTGTGGAAACTGACCAGTCACTTCTCTGGACCATGGCCATCAAA

Alignment

ORF - retro_chof_988 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.83 %
• Parental protein coverage: 95.1 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LPSGNLKYCLLILNQPLDDCFRHLWSKALLKACADGGANRLYDITEGERESILPELINGDFDSIRTEVRK
          .P.GNLKYCL..LNQPLDD.F.HLWSKALLKACADG.AN.L.DITEGERE..LPE.I.GDFDS.R.EVR.
Retrocopy IPTGNLKYCLSTLNQPLDDHFCHLWSKALLKACADGDANHLHDITEGEREGFLPEFISGDFDSVRPEVRE

Parental  HYSIKGCELISTPDQDNTDFTKCLQVLQKKIEEKALQVDMIVTLGGLGGRFDQIMASVNTLFQAIDITPL
          .YSIKGCE..STPD.D.TDFTKCLQV.QKKIEEK.L.V.MI.TLGGL.G.FD.I.ASV.TLFQA.D.TPL
Retrocopy YYSIKGCERTSTPDKDHTDFTKCLQVPQKKIEEKVL*VGMIMTLGGLDGHFDRIRASVSTLFQATDVTPL

Parental  PIIIIQDKSLIYLLQPGKHKLHVNTGMEGDWCGLIPVGQPCNHVTTTGLKWNLXNHVLGFGILVSTFNTY
          PIIII..K.LIYLLQPGKHKL..N.G.EGDWCGLIPVGQPCN.VTTTGLKWNL.NHVLGFGILVST.N..
Retrocopy PIIII*EKFLIYLLQPGKHKLLINPGVEGDWCGLIPVGQPCNQVTTTGLKWNLANHVLGFGILVSTSN--

Parental  TYDGSGVVTVDTDQPLLWTMAIK
          TYDGSGVVTV.TDQ.LLWTMAIK
Retrocopy TYDGSGVVTVETDQSLLWTMAIK

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_988 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 7 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001227	23 retrocopies	retro_chof_1004, retro_chof_1093, retro_chof_1416, retro_chof_1458, retro_chof_1537, retro_chof_1683, retro_chof_1732, retro_chof_191, retro_chof_1927, retro_chof_2202, retro_chof_2413, retro_chof_2507, retro_chof_2577, retro_chof_468, retro_chof_472, retro_chof_550, retro_chof_630, retro_chof_665, retro_chof_701, retro_chof_801, retro_chof_917, retro_chof_954, retro_chof_988 ,
Dasypus novemcinctus	ENSDNOG00000018545	4 retrocopies	retro_dnov_1080, retro_dnov_1592, retro_dnov_2405, retro_dnov_2523,
Macropus eugenii	ENSMEUG00000010062	1 retrocopy	retro_meug_1153,
Myotis lucifugus	ENSMLUG00000004213	1 retrocopy	retro_mluc_1071,
Monodelphis domestica	ENSMODG00000025468	2 retrocopies	retro_mdom_1299, retro_mdom_1300,
Ornithorhynchus anatinus	ENSOANG00000020728	1 retrocopy	retro_oana_44,
Vicugna pacos	ENSVPAG00000010214	2 retrocopies	retro_vpac_205, retro_vpac_503,