RetrogeneDB ID: retro_dnov_1608

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_24678:39862..40696(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GNPDA1
• Ensembl ID: ENSDNOG00000007804
• Aliases: None
• Description: glucosamine-6-phosphate deaminase 1 [Source:HGNC Symbol;Acc:4417]

Sequence

>retro_dnov_1608
TCTCACACCAGTGAGTGTGCAGCCAAATACATCAGGAATCACATCATCCAGATTAACCCAGGGCCAGACAAGTACTTCAC
CACGGGGCTCCCTAATGGGTGTACCCCACTTGGCTACTACAAAAAGTTGATTGAGTACTACAAGAACGGGGAACCTGTCC
TTAAAATATATGACCTTCAACAAATATGAGTATGTGGGCCTTCCTTGAGATCACCCAGAGAGTTACCAGTTCTTCAGGTG
AAACAAATTCTTCAAGCACAATGACCTCCATCCAGAAAATACCAATATCCTGGATGGAAATGCACCCAACTTACAGGTTG
GCTGTGATGCCTTTGAAGAGTGGATCATGGCTGTGGGCTGGATCAAGCTGTTTGTTGGAGGCATTAGCCCCAGCAGATAT
ATCACCTTCAACAAACCAGGCTCTAGTCTGGTACCCAGGACCTGTGTGAAGGAACTGGCCATGGACACCATTCTGGCCAA
TCCTAGGTTCTTTGATAGTGATCTTGCCAAGATGCCCACCATGGTCCTGATAGTGGGTGTGGGCACCATCTTGGATGCTA
GAGAGGTGATGATCTTCATACACGTGCACAGAGATGTTTGTTCCGTACAAGGCCATCGAGGAAAGAGTGAGCCACATGTG
GACAGTATCTGCCTTCCAGCAACATTCATGCACATTGTTTGTGTGTGATGAGGATACAACACTAGAGCTGAAAGTGAAGA
CTGTCAAGTATTTCAAAGGTTTAATGCTTGTTCATAACAAGTTGGTGACCCTTGTACAGTATCACAGAGAAGGAAACAGA
GAAAAGCTAGTCTTCTAAAAAACCATATAGTGAT

Alignment

ORF - retro_dnov_1608 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.04 %
• Parental protein coverage: 96.89 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  SQASEWAAKYIRNRIIQFNPGPDKYFTLGLPTGSTPLGCYKKLIEYYKNGD-LSFKYVKTFNMDEYVGLP
          S..SE.AAKYIRN.IIQ.NPGPDKYFT.GLP.G.TPLG.YKKLIEYYKNG..LS.KY..TFN..EYVGLP
Retrocopy SHTSECAAKYIRNHIIQINPGPDKYFTTGLPNGCTPLGYYKKLIEYYKNGE>LSLKYM-TFNKYEYVGLP

Parental  RDHPESYHSFMWNNFFKHIDIHPGNTYILDGNAADLQAECESFEEKITAAGGIELFVGGIGPDGHIAFNE
          .DHPESY..F..N.FFKH.D.HP.NT.ILDGNA..LQ..C..FEE.I.A.G.I.LFVGGI.P...I.FN.
Retrocopy *DHPESYQFFR*NKFFKHNDLHPENTNILDGNAPNLQVGCDAFEEWIMAVGWIKLFVGGISPSRYITFNK

Parental  PGSSLVSRTRVKTLAMDTILANARFFNGELARVPTMALTVGVGTIMDAREVMI-LITGAHKA-FALYKAI
          PGSSLV.RT.VK.LAMDTILAN.RFF...LA..PTM.L.VGVGTI.DAREVMI.L.T.A....F..YKAI
Retrocopy PGSSLVPRTCVKELAMDTILANPRFFDSDLAKMPTMVLIVGVGTILDAREVMI<LHTRAQRC<FVPYKAI

Parental  EEGVSHMWTVSAFQQHPRTVFVCDEDATLELKVKTVKYFKGLMLVHNKLV-DP-LYSIKEKETEKSQSSK
          EE.VSHMWTVSAFQQH..T.FVCDED.TLELKVKTVKYFKGLMLVHNKLV.DP.LYSI.EKETEKS.SSK
Retrocopy EERVSHMWTVSAFQQHSCTLFVCDEDTTLELKVKTVKYFKGLMLVHNKLV<DP<LYSITEKETEKS*SSK

Parental  TPYSD
          .PYSD
Retrocopy KPYSD

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	27.42 RPM
SRP012922_cerebellum	0.00 RPM	3.85 RPM
SRP012922_heart	0.00 RPM	2.09 RPM
SRP012922_kidney	0.00 RPM	24.09 RPM
SRP012922_liver	0.00 RPM	13.00 RPM
SRP012922_lung	0.00 RPM	5.80 RPM
SRP012922_quadricep_muscle	0.00 RPM	1.56 RPM
SRP012922_spleen	0.00 RPM	18.66 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_1608 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 9 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007865	1 retrocopy	retro_btau_535,
Choloepus hoffmanni	ENSCHOG00000009884	2 retrocopies	retro_chof_2278, retro_chof_42,
Dasypus novemcinctus	ENSDNOG00000007804	3 retrocopies	retro_dnov_1363, retro_dnov_1608 , retro_dnov_508,
Macropus eugenii	ENSMEUG00000015442	1 retrocopy	retro_meug_655,
Monodelphis domestica	ENSMODG00000010398	1 retrocopy	retro_mdom_1337,
Mus musculus	ENSMUSG00000052102	1 retrocopy	retro_mmus_2711,
Otolemur garnettii	ENSOGAG00000007303	3 retrocopies	retro_ogar_2251, retro_ogar_2506, retro_ogar_446,
Ictidomys tridecemlineatus	ENSSTOG00000016508	1 retrocopy	retro_itri_1135,
Tupaia belangeri	ENSTBEG00000003330	2 retrocopies	retro_tbel_2431, retro_tbel_59,