RetrogeneDB ID: retro_dnov_935

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_123449:1089..1505(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: STMN4
• Ensembl ID: ENSDNOG00000003756
• Aliases: None
• Description: stathmin-like 4 [Source:HGNC Symbol;Acc:16078]

Sequence

>retro_dnov_935
GATATCCAGGTGAAAGAAATGGAGAAGTGTACCTCAGGCCAAGTCTTTGAGATGACACTCAGCCCTCTGTCGAAAGACTA
TGTCCCAGAATTTCCCCTTCCCCTCCAAAGAAGAAGGATCTCTCCCTGAAGGAAATTCAAATGAAGTTAGAAGCTGTAGA
AGAAAGATGCAAGTTCCATGAAGCTAAGGTCTTAAAGCAGCTTATTGAGAAATAAGAGGATGAAAAAGAAGTGCCTCAGA
AAATAACAGAAGAGAATAACAACTTCAGTAAAATGGCAGAAAAGTAACTGATACACAAAATGGAAGCCAACAAGGAGAAT
CGAGAGGCACAAATGGCTGCCAAAGTGGAGCATTTGCAAGAAAAGGACAAGCATATTGAACAAGTATGGAAGAAGAAAGA
GTCCAACGATCCTGCT

Alignment

ORF - retro_dnov_935 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.86 %
• Parental protein coverage: 63.85 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DMEVIELNKCTSGQSFEVILKPPSFDGVPEFNASLPRRR-DPSLEEIQKKLEAAEERRKYQEAELLKHLA
          D..V.E..KCTSGQ.FE..L.P.S.D.VPEF...L.RRR.D.SL.EIQ.KLEA.EER.K..EA..LK.L.
Retrocopy DIQVKEMEKCTSGQVFEMTLSPLSKDYVPEFPLPLQRRR<DLSLKEIQMKLEAVEERCKFHEAKVLKQLI

Parental  EKREHEREVIQKAIEENNNFIKMANEKLAQKMES--KEREAHLAAMLERLQ-KDKHAEEVRKNKELKEEA
          EK.E.E.EV.QK..EENNNF.KMA...L..KME.....REA..AA..E.LQ.KDKH.E.V.K.KE....A
Retrocopy EK*EDEKEVPQKITEENNNFSKMAEK*LIHKMEANKENREAQMAAKVEHLQEKDKHIEQVWKKKESNDPA

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	0.19 RPM	0.97 RPM
SRP012922_cerebellum	0.27 RPM	86.88 RPM
SRP012922_heart	0.00 RPM	0.23 RPM
SRP012922_kidney	0.00 RPM	0.00 RPM
SRP012922_liver	0.00 RPM	0.46 RPM
SRP012922_lung	0.00 RPM	0.61 RPM
SRP012922_quadricep_muscle	0.00 RPM	0.00 RPM
SRP012922_spleen	0.00 RPM	0.00 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_935 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 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000003373	3 retrocopies	retro_dnov_2381, retro_dnov_545, retro_dnov_831,
Dasypus novemcinctus	ENSDNOG00000003756	1 retrocopy	retro_dnov_935 ,
Macropus eugenii	ENSMEUG00000006013	1 retrocopy	retro_meug_1456,
Tupaia belangeri	ENSTBEG00000007290	1 retrocopy	retro_tbel_2706,