RetrogeneDB ID:

retro_dnov_544

Retrocopy
location
Organism:Armadillo (Dasypus novemcinctus)
Coordinates:GeneScaffold_597:94967..95425(+)
Located in intron of:ENSDNOG00000016582
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:SRGN
Ensembl ID:ENSDNOG00000006889
Aliases:None
Description:serglycin [Source:HGNC Symbol;Acc:9361]


Retrocopy-Parental alignment summary:






>retro_dnov_544
ACGATGCAGAGATTCAAGTGCAGTAGGCTTGCCTTCACTCCCTCCCACATCCTGTTTGGGAACATTCAGTTTAAGGTTAT
CCCATGCAGACAGGCAGGTACCAGTGAGTACACTGCAGTCCAGAGAGTAATTCTGCAAACTGTATTGAGGAAAGGGGACC
AATGTTAGACCTACCTCCAGGCAAGTCTAGCAGGCTCCTCCTTCCAAGGACAGACAGTTTTTAAATGACAAGGTGCCAGA
ACAAGCATGATATCTTTGCTCTTTCTGAGGACTATTCTGGGTCAGGCTCTGGCTCTGGATTGAACTCTGAAAGTGGCTTT
CCAGCTGAAATCAAACAAGGATACCAAGCAATATATGAAGATGATGCTTTCTATTATAGTGCTTGGCTTCTCAAGCGGAA
TCTGCCCTCAGACAACCAGCACTTGGATCAAGATGGATCAGGAATGGATTTTATTATT

ORF - retro_dnov_544 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 70.51 %
Parental protein coverage: 100. %
Number of stop codons detected: 3
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalTMPRFLQSSRLVLALSLLLF-WESSVQGYPMRRGRYQWVRCNPESNSANCIEEGGPMFDLPPGESNRILP
TM.RF...SRL....S..LF.WE.SV.GYPM..GRYQ.V.C.PESNSANCIEE.GPM.DLPPG.S.R.L.
RetrocopyTMQRF-KCSRLAFTPSHILF<WEHSV*GYPMQTGRYQ*VHCSPESNSANCIEERGPMLDLPPGKSSRLLL
ParentalPRTDPFSMTRFQNMRDTFPLSEDYSSGSGSGSGFN---GFPAEIEQEYQAIDEDDAFYYNAQPLERNLPS
PRTD.F.MTR.QN..D.F.LSEDY.SGSGSGSG.N...GFPAEI.Q.YQAI.EDDAFYY.A..L.RNLPS
RetrocopyPRTDSF*MTRCQNKHDIFALSEDY-SGSGSGSGLNSESGFPAEIKQGYQAIYEDDAFYYSAWLLKRNLPS
ParentalDNQHMDQDGSEDDFII
DNQH.DQDGS..DFII
RetrocopyDNQHLDQDGSGMDFII

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP012922_ascending_colon 0 .00 RPM 41 .62 RPM
SRP012922_cerebellum 0 .00 RPM 3 .16 RPM
SRP012922_heart 0 .00 RPM 10 .67 RPM
SRP012922_kidney 0 .00 RPM 6 .02 RPM
SRP012922_liver 0 .00 RPM 17 .18 RPM
SRP012922_lung 0 .00 RPM 210 .30 RPM
SRP012922_quadricep_muscle 0 .35 RPM 4 .33 RPM
SRP012922_spleen 0 .00 RPM 196 .87 RPM
Dasypus novemcinctus was not studied using ChIP-Seq data.
Dasypus novemcinctus was not studied using EST data.
Dasypus novemcinctus was not studied using FANTOM5 data.
retro_dnov_544 was not experimentally validated.

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.

Parental genes homology:
Parental genes homology involve 3 parental genes, and 12 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000179691 retrocopy
Choloepus hoffmanni ENSCHOG000000004489 retrocopies
Dasypus novemcinctus ENSDNOG00000006889 2 retrocopies
retro_dnov_1745, retro_dnov_544 ,



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