RetrogeneDB ID: retro_dnov_1363

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_187131:4022..4484(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDNOG00000025610
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_1363
GAGGTGACTAAGTACTACAAGAAAGGGAACCTCTCTTCAAATACGACCTTCGACATGGACAAGAATGCGGGCTTTCCTCA
AGACCACCCTGAGAGTCATCACTTCTCATGTGGAATGGCTTCCTCAATGACACTGACATCCATCCAGAAAACACCAGTAT
TCTGGAGGGGAATGCAGCTGACCTGCAAGCTGAGCGGGACGCCTTTGGAGAGAAGAACACGGCTGCGGCAGGGATTGAGC
TGCACTGGGGCACTGGCCCCAATCACACATCTCCTTCAATGCAGCAGGCTCCAGTCTGGTGCCCAGGACGCATGTGAAGA
CCCTGGCTGTGGACACCACCCTGGCCAACACTAGGTTCTTCAAAGGAGATCTCGCCAAGGTGCCACAATGCCCTGGATGG
TGAGCGAGGGCGTCTTCACGGATGCTAGAGAGGTGATGATCCTCAGCAAGGGCATACGCAAG

Alignment

ORF - retro_dnov_1363 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.01 %
• Parental protein coverage: 54.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KLIEYYKNGDLSFKYVKTFNMDEYVGLPRDHPESYHS-FMWNNFFKHIDIHPGNTYILDGNAADLQAECE
          ....YYK.G.LS.....TF.MD...G.P.DHPES.H...MWN.F....DIHP.NT.IL.GNAADLQAE..
Retrocopy EVTKYYKKGNLSSN--TTFDMDKNAGFPQDHPESHHF<LMWNGFLNDTDIHPENTSILEGNAADLQAERD

Parental  SFEEKITAAGGIELFVGGIGPD-GHIAFNEPGSSLVSRTRVKTLAMDTILANARFFNGELARVP-TMALT
          .F.EK.TAA.GIEL...G.GP...HI.FN..GSSLV.RT.VKTLA.DT.LAN.RFF.G.LA.VP.TM...
Retrocopy AFGEKNTAAAGIELH-WGTGPN<SHISFNAAGSSLVPRTHVKTLAVDTTLANTRFFKGDLAKVP<TMPWM

Parental  VGVGTIMDAREVMILITGAHK
          V..G...DAREVMIL..G..K
Retrocopy VSEGVFTDAREVMILSKGIRK

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	0.78 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	0.15 RPM	5.80 RPM
SRP012922_quadricep_muscle	0.17 RPM	1.56 RPM
SRP012922_spleen	0.34 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_1363 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,