RetrogeneDB ID: retro_dnov_2615

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_90776:1222..2063(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RASGEF1B
• Ensembl ID: ENSDNOG00000005271
• Aliases: None
• Description: RasGEF domain family, member 1B [Source:HGNC Symbol;Acc:24881]

Sequence

>retro_dnov_2615
ATACAAAGGGACATCATTACTGTCTGCAGTGACCCTTACGTGTTGGCCCAGTAGCTGATTCACATAGAACTGGAGAGGCT
CAATTTCATCGGACCAGAAGAATTTGTTCAGGCATTTGTTCAGAAGGACCCTTCGGACAATGACAAGAGTTGTTACGGCG
AGCGGAAGAAAATACACAACTTAGAAGCTTAGGTAGAATGGTTTAATCACCTCAGTTACTTGGTTGCTATAGAAATTTGC
ATGCCCGTAAAGAAGAAGCATCAAGAAAGAATAACAGAATAATATTTCTTTGACGTGGCAAGGGAGTGTTTTAACATTGG
CAACTTTAATTCCTTGATGGTGATCATCTCCGGCATGAATATGAGCCCCATCTCTCGACTAAAGAAAACTTGGGCCAAAG
TGAAGACTGCAAAGTTTGACATTCTTGATTATCAGATGGACCTTTCCAGCAATTTCTATAATTATCAAACAGCTCTTCAT
GGGGCAGCACAAAGGTCTTTAACTGCTCATAGTAGCAGAGAGAAGACTGTGATACCATTCTTCAGTCTCTTGATCAAAGA
TATTTATTTTCTCAATAAAGTCTGTGCCAATCAGCTTCCAAATAGCCATGTCAATTTTGAGAAATTTTGGGAACTGGCCA
AAACAAGTTAGTGAATTCATGATGTGGAAACAAGTCGGATGCCCATTTGAGAGGGGCCAGAAGATCTTACAGTATCTGCT
CACGGTACCAGTCTTCAGTGAAGATGCTCTCTACTTGGCTTCATGTGAGGGTGAAGGAACTGAAAATCATATAGAGAAAG
ACAGTTGGAAGTCTTTAAGGTCGAGCCTCCTAGGCAGAATT

Alignment

ORF - retro_dnov_2615 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.83 %
• Parental protein coverage: 56.14 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IQRDIITVCSDPYTLAQQLTHIELERLNYIGPEEFVQAFVQKDPLDNDKSCYGERKKTRNLEAYVEWFNR
          IQRDIITVCSDPY.LAQ.L.HIELERLN.IGPEEFVQAFVQKDP.DNDKSCYGERKK..NLEA.VEWFN.
Retrocopy IQRDIITVCSDPYVLAQ*LIHIELERLNFIGPEEFVQAFVQKDPSDNDKSCYGERKKIHNLEA*VEWFNH

Parental  LSYLVATEICMPVKKKHRARIIE-YFIDVARECFNIGNFNSLMAIISGMNMSPVSRLKKTWAKVKTAKFD
          LSYLVA.EICMPVKKKH..RI.E.YF.DVARECFNIGNFNSLM.IISGMNMSP.SRLKKTWAKVKTAKFD
Retrocopy LSYLVAIEICMPVKKKHQERITE*YFFDVARECFNIGNFNSLMVIISGMNMSPISRLKKTWAKVKTAKFD

Parental  ILEHQMDPSSNFYNYRTALRGAAQRSLTAHSSREKIVIPFFSLLIKDIYFLNEGCANRLPNGHVNFEKFW
          IL..QMD.SSNFYNY.TAL.GAAQRSLTAHSSREK.VIPFFSLLIKDIYFLN..CAN.LPN.HVNFEKFW
Retrocopy ILDYQMDLSSNFYNYQTALHGAAQRSLTAHSSREKTVIPFFSLLIKDIYFLNKVCANQLPNSHVNFEKFW

Parental  ELA-KQVSEFMTWKQVECPFERDRKILQYLLTVPVFSEDALYLASYESEGPENHIEKDRWKSLRSSLLGR
          ELA.KQVSEFM.WKQV.CPFER..KILQYLLTVPVFSEDALYLAS.E.EG.ENHIEKD.WKSLRSSLLGR
Retrocopy ELA>KQVSEFMMWKQVGCPFERGQKILQYLLTVPVFSEDALYLASCEGEGTENHIEKDSWKSLRSSLLGR

Parental  V
          .
Retrocopy I

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	7.97 RPM
SRP012922_cerebellum	0.00 RPM	1.92 RPM
SRP012922_heart	0.00 RPM	0.70 RPM
SRP012922_kidney	0.00 RPM	6.84 RPM
SRP012922_liver	0.00 RPM	1.86 RPM
SRP012922_lung	0.00 RPM	6.41 RPM
SRP012922_quadricep_muscle	0.00 RPM	1.73 RPM
SRP012922_spleen	0.80 RPM	20.95 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_2615 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000003412	1 retrocopy	retro_cpor_56,
Dasypus novemcinctus	ENSDNOG00000005271	1 retrocopy	retro_dnov_2615 ,