RetrogeneDB ID: retro_dnov_1474

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_211890:3256..3497(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDNOG00000007933
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SMIM20
• Ensembl ID: ENSDNOG00000004966
• Aliases: None
• Description: small integral membrane protein 20 [Source:HGNC Symbol;Acc:37260]

Sequence

>retro_dnov_1474
GAAGGGTACTTAGCAGATCAGGGCTGCCCCGCCAGGCACTATGTCCTGCAACCTGAGAACCACATTCATTTTCGTTGGCT
TTATCTCCCTGCTTGGTGCCTTCTTCTACCTCATCTACTTCTGGCCGCTCATGTGGCTGGAGGAGTACTAGAAAGAACAA
GCAATAAACAGAGCTGGTATTTTTCAAGTTGATGTGCAGCCGCTAGGGTTAAAAGTGTGGTTTTATCCGTTTGGCAGGAA
A

Alignment

ORF - retro_dnov_1474 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.31 %
• Parental protein coverage: 79.21 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EGCLAGQGCP-PGAMSRNLRTALVFGGFISLLGAVFYPIYFRPLLRLEEYQKEQAINRAGIVQADVQPPG
          EG.LA.QGCP.PG.MS.NLRT...F.GFISLLGA.FY.IYF.PL..LEEY.KEQAINRAGI.Q.DVQP.G
Retrocopy EGYLADQGCP>PGTMSCNLRTTFIFVGFISLLGAFFYLIYFWPLMWLEEY*KEQAINRAGIFQVDVQPLG

Parental  LKVWSDPFGRK
          LKVW..PFGRK
Retrocopy LKVWFYPFGRK

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	19.06 RPM
SRP012922_cerebellum	0.00 RPM	12.65 RPM
SRP012922_heart	0.00 RPM	34.80 RPM
SRP012922_kidney	0.00 RPM	33.95 RPM
SRP012922_liver	0.00 RPM	19.51 RPM
SRP012922_lung	0.00 RPM	16.95 RPM
SRP012922_quadricep_muscle	0.00 RPM	37.91 RPM
SRP012922_spleen	0.00 RPM	22.89 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_1474 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 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003897	1 retrocopy	retro_btau_95,
Dasypus novemcinctus	ENSDNOG00000004966	2 retrocopies	retro_dnov_1474 , retro_dnov_1529,
Macropus eugenii	ENSMEUG00000002680	1 retrocopy	retro_meug_147,
Microcebus murinus	ENSMICG00000017222	1 retrocopy	retro_mmur_868,
Macaca mulatta	ENSMMUG00000006680	1 retrocopy	retro_mmul_179,
Nomascus leucogenys	ENSNLEG00000016894	1 retrocopy	retro_nleu_216,
Ictidomys tridecemlineatus	ENSSTOG00000004810	1 retrocopy	retro_itri_699,
Tupaia belangeri	ENSTBEG00000015052	2 retrocopies	retro_tbel_1277, retro_tbel_4083,