RetrogeneDB ID: retro_dnov_1278

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_17501:87425..88255(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSPC1
• Ensembl ID: ENSDNOG00000011078
• Aliases: None
• Description: paraspeckle component 1 [Source:HGNC Symbol;Acc:20320]

Sequence

>retro_dnov_1278
CAGACACCACCACCACCAATACCTGCAAATGGGCAACAGACCAGCAACCAAAATGAAGGCTTGACTATGGACCTGAAGAA
TTTAAAGAAACCAGGAAAGCAAACCTTCACCCAACAGAGCTCTCTCACAAGCAATCTTCCTCCTAACATCACTGAGGAGG
AAACGAGGAAACCATTTGAAAAATATGGGAAAGTAGACAAGGTCTTCATTCATAAGGATAAAGGCTTTGGCTTTATCCAC
TTGGAAACACAAACCCTAGCAGAGTTTGCCAAAGTGGAGCTGGACAACATGCCACTCTGTGGAAAGTAGCTGCGAGTGTG
CTTTGCCTGCCATAGTGCATCCCTTACAGTCAGAAACCTTCCTCAGTAAGTGTCCAATGAACTGCTGGAGGAGGCCTTTT
CTGTGTTTGGTCAGGTGGAGAGGGCTGTAGTCATTGAGGATGATTGAGGAAGTCCCTCAGGAAAAGACATTGTTGAGTTC
TCAGGAAAGCCAGCTGCTCAGAAAGCTCTGGGACAGATGCAGTGAAGGCTCCTTCCTGCTAGTCACATTTCCTGGATCTG
TGACTGTGAAGCCAATGGACTGGTTAGATGATGGAGAGGGACTTCCAGAGAAGCTGGTTATAAAGAACCAGCAAGTTTGC
AAGGAGAGAGAGCAGCCACCCAGATTTGCACAGCCTGACTCTTTTGAGTCTGAGTATGCCATGTACTGCAAGACACTCAC
TGAGAGGGAGGAAAAGCAGCAGACCAAGAAGACTGTACATCAAGGAAGCTCGTGAGAAGCTGAAAATGGAGATGGAGGCT
GCTCGTCATGAGCACCAGGTCATGTTCATG

Alignment

ORF - retro_dnov_1278 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.09 %
• Parental protein coverage: 52.88 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  QAPPPAAPA--EDHPEEDAGFTIDIKSFLKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVF
          Q.PPP..PA..........G.T.D.K...KPG..T.TQ...L...NLP..ITEE.....FE.YG....VF
Retrocopy QTPPPPIPANGQQTSNQNEGLTMDLKNLKKPGKQTFTQQSSL-TSNLPPNITEEETRKPFEKYGKVDKVF

Parental  INRDRGFGFIRLXXXXXAE-AKAELDGTIFKSRPLRIRFATHGAALTVKNLSPVVSNELLEQAFSQFGPV
          I..D.GFGFI.L.....AE.AK.ELD........LR..FA.H.A.LTV.NL...VSNELLE.AFS.FG.V
Retrocopy IHKDKGFGFIHLETQTLAEFAKVELDNMPLCGK*LRVCFACHSASLTVRNLPQ*VSNELLEEAFSVFGQV

Parental  EKAVVVVDDRGRATGKGFVEFAAKPPARKAL-ERCGDGAFLLTTTPRPVIVEPMEQFDDEDGLPEKLMQK
          E.AVV..DD.G...GK..VEF..KP.A.KAL..RC..G.FLL.T.P..V.V.PM...DD..GLPEKL..K
Retrocopy ERAVVIEDD*GSPSGKDIVEFSGKPAAQKAL>DRCSEGSFLLVTFPGSVTVKPMDWLDDGEGLPEKLVIK

Parental  TQQYHKEREQPPRFAQPGTFEFEYASRWKALDEMEKQQR-EQVDRNIR-EAKEKLEAEMEAARHEHQLML
          .QQ..KEREQPPRFAQP..FE.EYA...K.L.E.E..Q...Q.D...R.EA.EKL..EMEAARHEHQ.M.
Retrocopy NQQVCKEREQPPRFAQPDSFESEYAMYCKTLTEREEKQQ<DQEDCTSR<EAREKLKMEMEAARHEHQVMF

Parental  M
          M
Retrocopy M

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	3.31 RPM	60.29 RPM
SRP012922_cerebellum	1.51 RPM	46.74 RPM
SRP012922_heart	0.23 RPM	9.05 RPM
SRP012922_kidney	0.55 RPM	15.33 RPM
SRP012922_liver	0.77 RPM	18.73 RPM
SRP012922_lung	1.83 RPM	28.71 RPM
SRP012922_quadricep_muscle	0.17 RPM	7.44 RPM
SRP012922_spleen	2.52 RPM	39.72 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_1278 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	ENSDNOG00000011078	2 retrocopies	retro_dnov_1278 , retro_dnov_488,
Tupaia belangeri	ENSTBEG00000002361	2 retrocopies	retro_tbel_2388, retro_tbel_3616,
Xiphophorus maculatus	ENSXMAG00000007929	1 retrocopy	retro_xmac_3,
Drosophila melanogaster	FBgn0004227	1 retrocopy	retro_dmel_11,