RetrogeneDB ID: retro_dnov_2405

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_72059:1553..1957(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TPK1
• Ensembl ID: ENSDNOG00000018545
• Aliases: None
• Description: thiamin pyrophosphokinase 1 [Source:HGNC Symbol;Acc:17358]

Sequence

>retro_dnov_2405
TTTTTGCCTAAATACATCAAGGCAGATTTTGATTCCATTAGGCCTGAAGTCAATGGGTACTATACTTGTAAATGATGTGA
GCTGATTTCAACTCCTGATCAAAACTGCACTGACTTTACCAATTACCTTCTAGTACTCTAAAAGAAGATAGATGTAAAAC
ACCTACAGGTTAATATGAATGTCACACTCCCAGGACTTGCTGGACATTTTGAATGGAGTATGGCATCTGTGTGTACCCTA
TTTCAAGTGAATCATATAACTCTTTGCCAATTATAATAATTCAAGAGGAAACTCTCATCTACCTGCCCCAACCAGGAAAG
GAAAAGATTCATGTAAACACTGGAATAGAAGATGATTGTTGTGGCCTTATTCCTGTTGTATGATAACACAATCACATTGC
CACA

Alignment

ORF - retro_dnov_2405 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.71 %
• Parental protein coverage: 55. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FLPEFINGDFDSIRPEVKEYYTSKGCELISTPDQNYTDFTKCLLELQKKIEEKNLEIDMIVTLGGLAGHF
          FLP..I..DFDSIRPEV..YYT.K.CELISTPDQN.TDFT..LL.L.KKI..K.L...M.VTL.GLAGHF
Retrocopy FLPKYIKADFDSIRPEVNGYYTCK*CELISTPDQNCTDFTNYLLVL*KKIDVKHLQVNMNVTLPGLAGHF

Parental  DQIMS---ILFQATHIT-PLPLIIIQEESLIYLPQPGKHKLHVNTGMEGDWCGLVPIGQHCNHVTT
          ...M.....LFQ..HIT..LP.IIIQEE.LIYLPQPGK.K.HVNTG.E.D.CGL.P.....NH..T
Retrocopy EWSMASVCTLFQVNHIT<SLPIIIIQEETLIYLPQPGKEKIHVNTGIEDDCCGLIPVV**HNHIAT

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP012922_ascending_colon	0.00 RPM	0.39 RPM
SRP012922_cerebellum	0.00 RPM	0.27 RPM
SRP012922_heart	0.00 RPM	0.23 RPM
SRP012922_kidney	0.00 RPM	1.37 RPM
SRP012922_liver	0.00 RPM	1.08 RPM
SRP012922_lung	0.00 RPM	1.37 RPM
SRP012922_quadricep_muscle	0.00 RPM	0.35 RPM
SRP012922_spleen	0.00 RPM	0.69 RPM

ChIP-Seq

Dasypus novemcinctus was not studied using ChIP-Seq data.

EST

Dasypus novemcinctus was not studied using EST data.

TSS

Dasypus novemcinctus was not studied using FANTOM5 data.

Lab

retro_dnov_2405 was not experimentally validated.

Homology

Retrocopy orthology:

Dasypus novemcinctus 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,