RetrogeneDB ID: retro_dnov_2068

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_45446:5790..5981(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SUMO1
• Ensembl ID: ENSDNOG00000015868
• Aliases: None
• Description: small ubiquitin-like modifier 1 [Source:HGNC Symbol;Acc:12502]

Sequence

>retro_dnov_2068
GAGAAAAAGTAAGCAGAATGCATTAAATTGTAAGTCATTAGACAGGATAGCAGTGAGATTCACTAAACAGGGAACTGACA
ATACACCTCAAGAAATACCAAGGTCACTGCCATTGTCAGGGATTTCCAATGAATTCGCTCAGGTATGTCTTTGAAGAACA
GAGAACTGCTGATTATCATAGTCCAAAACAA

Alignment

ORF - retro_dnov_2068 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.58 %
• Parental protein coverage: 57.52 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DKKEGEYIKLKVIGQDSSEIH-FKVKMTTHLKKLKESYCQRQGVPMNSLRFLFEGQRIADNHTPKE
          .KK..E.IKL.VI.QDSSEIH......T.HLKK.....C..QG.PMNSLR..FE.QR.AD.H.PK.
Retrocopy EKK*AECIKL*VIRQDSSEIH<LNRELTIHLKKY-QGHCHCQGFPMNSLRYVFEEQRTADYHSPKQ

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	2.33 RPM
SRP012922_cerebellum	0.00 RPM	2.34 RPM
SRP012922_heart	0.00 RPM	0.93 RPM
SRP012922_kidney	0.00 RPM	3.29 RPM
SRP012922_liver	0.00 RPM	1.39 RPM
SRP012922_lung	0.00 RPM	3.36 RPM
SRP012922_quadricep_muscle	0.00 RPM	0.69 RPM
SRP012922_spleen	0.00 RPM	2.29 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_2068 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 11 parental genes, and 48 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013225	5 retrocopies	retro_amel_1068, retro_amel_233, retro_amel_236, retro_amel_315, retro_amel_49,
Bos taurus	ENSBTAG00000009859	6 retrocopies	retro_btau_112, retro_btau_1512, retro_btau_1705, retro_btau_357, retro_btau_363, retro_btau_499,
Canis familiaris	ENSCAFG00000012431	8 retrocopies	retro_cfam_1226, retro_cfam_1253, retro_cfam_139, retro_cfam_1815, retro_cfam_1912, retro_cfam_2048, retro_cfam_386, retro_cfam_985,
Dasypus novemcinctus	ENSDNOG00000015868	10 retrocopies	retro_dnov_1070, retro_dnov_1324, retro_dnov_1610, retro_dnov_1623, retro_dnov_1826, retro_dnov_1876, retro_dnov_2068 , retro_dnov_2330, retro_dnov_2423, retro_dnov_997,
Felis catus	ENSFCAG00000031005	6 retrocopies	retro_fcat_1520, retro_fcat_218, retro_fcat_26, retro_fcat_472, retro_fcat_6, retro_fcat_862,
Loxodonta africana	ENSLAFG00000022855	5 retrocopies	retro_lafr_111, retro_lafr_1148, retro_lafr_189, retro_lafr_540, retro_lafr_951,
Myotis lucifugus	ENSMLUG00000007504	2 retrocopies	retro_mluc_1346, retro_mluc_188,
Otolemur garnettii	ENSOGAG00000030345	1 retrocopy	retro_ogar_215,
Pongo abelii	ENSPPYG00000013083	3 retrocopies	retro_pabe_11, retro_pabe_1830, retro_pabe_775,
Pan troglodytes	ENSPTRG00000012817	1 retrocopy	retro_ptro_119,
Sarcophilus harrisii	ENSSHAG00000011968	1 retrocopy	retro_shar_375,