RetrogeneDB ID: retro_chof_1927

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_42470:123..708(-)
• 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_1927
TATTCCAATATGGAGCATGTCCTTACCAAGGGGAATTTGAAGCACTGGTTTTTGATTCTGAACCAGCCTTTGGATGACTG
TTTTTGCCATCTTTGGAGCAAAGCTCTTTTAAAAGCCTGTGCTGATGGAGGTGCCAACTGCTTACATTATATCACCAGAG
GACAGCGGGAAAGCTTTTTGCCTGAATTCATCAATGGAGATTTTGATTCTATTAGGCCGGAAGTCAGAGACTACTACAGT
ATTAAGGGTTGTGAGCTGATTTCAACTCCTGATCAAGACCACACAGACTTTACCAAGTGCCTCCAAGTGCTACAAAAGAA
GATAGAAGGAAAATACCTACCAGGTTGACATGATTGTGACACTGGGAGGACTTGGTGGACATTTTGACCAGATTATGGCA
TCTGTGAGCTCCCTATTTCAAGCGACTGATATCACTTCTTTGCTAATTATAATAATTCAAGAGAAATCTCTTATCTACCT
GCTCCAACCAGGAAAGCACAAGTTGCATGTAAACACTGAATGGAAGGTGATTGGTGTGGCCTTATACCTGCTGCACAGCC
TTGAAATCAACAGGCTTAAAGTGGA

Alignment

ORF - retro_chof_1927 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.17 %
• Parental protein coverage: 79.59 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FTPLELLLPSGNLKYCLLILNQPLDDCFRHLWSKALLKACADGGANRLYDITEGERESILPELINGDFDS
          ....E..L..GNLK...LILNQPLDDCF.HLWSKALLKACADGGAN.L..IT.G.RES.LPE.INGDFDS
Retrocopy YSNMEHVLTKGNLKHWFLILNQPLDDCFCHLWSKALLKACADGGANCLHYITRGQRESFLPEFINGDFDS

Parental  IRTEVRKHYSIKGCELISTPDQDNTDFTKCLQVLQKKIEEKAL-QVDMIVTLGGLGGRFDQIMASVNTLF
          IR.EVR..YSIKGCELISTPDQD.TDFTKCLQVLQKKIE.K.L.QVDMIVTLGGLGG.FDQIMASV..LF
Retrocopy IRPEVRDYYSIKGCELISTPDQDHTDFTKCLQVLQKKIEGKYL>QVDMIVTLGGLGGHFDQIMASVSSLF

Parental  QAIDITPLPIIIIQDKSLIYLLQPGKHKLHVNTG-MEGDWCGLIPVGQPCNHVTTTG
          QA.DIT.L.IIIIQ.KSLIYLLQPGKHKLHVNT..MEGDWCGLIP..QP.N.....G
Retrocopy QATDITSLLIIIIQEKSLIYLLQPGKHKLHVNTE<MEGDWCGLIPAAQP*NQQA*SG

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_1927 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,