RetrogeneDB ID: retro_dnov_1064

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_142462:3194..3479(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GLO1
• Ensembl ID: ENSDNOG00000019598
• Aliases: None
• Description: glyoxalase I [Source:HGNC Symbol;Acc:4323]

Sequence

>retro_dnov_1064
CCTCAGCTCGCGGCCGGCAGCTTACCGACGAGGCTGCAGTCAATTGCTGCTCCAATGCGGACCCCCAGCACCAAGGATTT
TCTATTGCAGCAGACCATGTTACGAATTAAAGATCCTAAGACGTCATTGGATTTTGATACTAGAATTCTTGGAATGACGC
TAATTGAAGAATTAGATTTTCCCACTATGAAATGTTCACTCTATTTTTTGGCTTATGAGGATAAAAATGACATCCCCAAA
GATTAAAATGAAAAAGTGGCATGGTTTTTCTCCAGAAAAGGTACT

Alignment

ORF - retro_dnov_1064 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.38 %
• Parental protein coverage: 51.1 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PQPAPGGL-TDEAAFSCCSDADP-STKDFLLQ-TMLQIKHPKKSLDFYAR-LGMTLIEKLDFPTMKFSLY
          PQ.A.G.L.TDEAA..CCS.ADP.STKDFLLQ.TML.IK.PK.SLDF..R.LGMTLIE.LDFPTMK.SLY
Retrocopy PQLAAGSL<TDEAAVNCCSNADP>STKDFLLQQTMLRIKDPKTSLDFDTRILGMTLIEELDFPTMKCSLY

Parental  FLAYEDKNDIPKDKNEKVAWLFSRKAT
          FLAYEDKNDIPKD.NEKVAW.FSRK.T
Retrocopy FLAYEDKNDIPKD*NEKVAWFFSRKGT

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	0.97 RPM	33.25 RPM
SRP012922_cerebellum	0.69 RPM	46.74 RPM
SRP012922_heart	1.39 RPM	76.80 RPM
SRP012922_kidney	0.27 RPM	47.09 RPM
SRP012922_liver	0.46 RPM	71.99 RPM
SRP012922_lung	0.46 RPM	22.60 RPM
SRP012922_quadricep_muscle	1.21 RPM	98.31 RPM
SRP012922_spleen	0.57 RPM	40.29 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_1064 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 12 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012703	2 retrocopies	retro_btau_1003, retro_btau_1513,
Cavia porcellus	ENSCPOG00000010050	1 retrocopy	retro_cpor_1482,
Dasypus novemcinctus	ENSDNOG00000019598	6 retrocopies	retro_dnov_1016, retro_dnov_1064 , retro_dnov_1411, retro_dnov_1759, retro_dnov_2560, retro_dnov_735,
Dipodomys ordii	ENSDORG00000006369	1 retrocopy	retro_dord_21,
Macropus eugenii	ENSMEUG00000005978	1 retrocopy	retro_meug_1641,
Mus musculus	ENSMUSG00000024026	1 retrocopy	retro_mmus_1902,
Otolemur garnettii	ENSOGAG00000007945	2 retrocopies	retro_ogar_2541, retro_ogar_681,
Rattus norvegicus	ENSRNOG00000000541	2 retrocopies	retro_rnor_1012, retro_rnor_1024,
Sus scrofa	ENSSSCG00000027778	1 retrocopy	retro_sscr_853,
Ictidomys tridecemlineatus	ENSSTOG00000005821	1 retrocopy	retro_itri_1626,
Tupaia belangeri	ENSTBEG00000014386	1 retrocopy	retro_tbel_4376,
Tursiops truncatus	ENSTTRG00000004664	1 retrocopy	retro_ttru_90,