RetrogeneDB ID: retro_dnov_1040

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_140123:1063..1465(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GEMIN2
• Ensembl ID: ENSDNOG00000018278
• Aliases: None
• Description: gem (nuclear organelle) associated protein 2 [Source:HGNC Symbol;Acc:10884]

Sequence

>retro_dnov_1040
AAATAAAGGCAAACTGTGAATGTATCTCTTTAAGGATGCCAGCCTGCTCCCAAAGGATATTCCCTAATACTGCAAAAGCA
ACAGCAACAAGTGGCACGGTTTTCAACTGTTTGACAGAGTGTGAACAAACATAGAAGGCCCCAGAAACCTCAACAGTTGG
ATAGTAACATGACCATGCCAAAATCGGAGCATGAAGAAGGCTGGAAAATTTTTGTCTTGGTGAAAGATTATGTGCTGGAG
GGACTGCTGGACCAGCTACAAGTGAAAATCCAGAAATTGATTGTGTATAAGTGATTTTCTTCCCTTGCTTAGATTATTAG
CAGAAAGAATCAGGCAATAGTAACTAGCATCTTGGAATACCTTAGTAATTGGTTTGGAGAAAGAGACTTTACTCCAGAAT
TG

Alignment

ORF - retro_dnov_1040 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.64 %
• Parental protein coverage: 63.98 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KRRQTVNVSLSGCQPAPEGYSPTLQWQQQQVAQFSTVRQSMNKHRSHWKSQQLDSNVTMPKSEDEEGWK-
          K.RQTVNVSL.GCQPAP.GYS..LQ.QQQQVA.FSTV.QS.NKHR...K.QQLDSN.TMPKSE.EEGWK.
Retrocopy K*RQTVNVSL*GCQPAPKGYSLILQKQQQQVARFSTV*QSVNKHRRPQKPQQLDSNMTMPKSEHEEGWK<

Parental  KFCLGERLCAEGAPGPATNENPGIDYVQI-GFPPLLSI-VSRMNQATVTSVLEYLSNWFGERDFTPEL
          .FCLGERLCA.G..GPAT.ENP.ID.V....F.PLL....SR.NQA.VTS.LEYLSNWFGERDFTPEL
Retrocopy NFCLGERLCAGGTAGPATSENPEIDCV*V<DFLPLLRL<ISRKNQAIVTSILEYLSNWFGERDFTPEL

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	7.39 RPM
SRP012922_cerebellum	0.00 RPM	19.93 RPM
SRP012922_heart	0.00 RPM	7.89 RPM
SRP012922_kidney	0.00 RPM	5.48 RPM
SRP012922_liver	0.00 RPM	4.49 RPM
SRP012922_lung	0.15 RPM	9.01 RPM
SRP012922_quadricep_muscle	0.00 RPM	5.37 RPM
SRP012922_spleen	0.00 RPM	12.82 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_1040 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016248	1 retrocopy	retro_cjac_2630,
Dasypus novemcinctus	ENSDNOG00000018278	1 retrocopy	retro_dnov_1040 ,
Homo sapiens	ENSG00000092208	1 retrocopy	retro_hsap_455,
Gorilla gorilla	ENSGGOG00000016691	2 retrocopies	retro_ggor_1844, retro_ggor_438,
Microcebus murinus	ENSMICG00000004811	1 retrocopy	retro_mmur_1221,
Myotis lucifugus	ENSMLUG00000002619	1 retrocopy	retro_mluc_1005,
Mus musculus	ENSMUSG00000060121	1 retrocopy	retro_mmus_354,
Pongo abelii	ENSPPYG00000005764	1 retrocopy	retro_pabe_278,
Pan troglodytes	ENSPTRG00000006291	1 retrocopy	retro_ptro_342,