RetrogeneDB ID:

retro_dnov_879

Retrocopy
location
Organism:Armadillo (Dasypus novemcinctus)
Coordinates:scaffold_11757:82558..83126(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:SSR1
Ensembl ID:ENSDNOG00000015772
Aliases:None
Description:signal sequence receptor, alpha [Source:HGNC Symbol;Acc:11323]


Retrocopy-Parental alignment summary:






>retro_dnov_879
TTTCTAGTAAATAACTTCCTGAAGTTCATGGTAGGCTTTACAAATAAGGGTACAGTAGAATTTATTGTTGAATCCCTAGT
GCCTCATTCCGTTACCCTTAGGACTACCAGTTTTATATCCAGAATTTCACAGCTCTTCCTCTGAACCCTGTAGTGCTACC
CCAGAGACAGGCAACATTTGAGTACTCCTTCATCCCTGCAGAGCCCTGGGTGGGTGAACTTTTGGTCTAGTCATCAATCT
GAAGTACAAAGATCTGAGTAGCAGTGTATTCCAAGATGCTGTCTTCAATCAAACAGTTACAATTACTGAAAGAGAGGATG
GGTTAGATGGAGAAACAGTCTTGTTCCTTATCAGTCTTAGGCTGGCAGTTGTTGCTGTGCTGGCCTTCATCAACTCTTAG
AATCTAAAATGCAAAAGACTGATACATAAAGTAGAAATAGGTACATCAAATCAGAAAAATGTTGATATGAGTTGTATTCC
TTGGAAAACTTTGAATCAGATCAATAAAGTTTCACCAAGAAGATTGCCCTGGAAACAGGCACAGGAAAAACCAGTGGGAT
CTGATGAG

ORF - retro_dnov_879 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 71.28 %
Parental protein coverage: 67.13 %
Number of stop codons detected: 3
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalFPANNIVKFLVGFTNKGTEDFIVESL-DASFRYPQDYQFYIQNFTALPLNTVVPPQRQATFEYSFIPAEP
F..NN..KF.VGFTNKGT..FIVESL..ASFRYP.DYQFYIQNFTALPLN.VV.PQRQATFEYSFIPAEP
RetrocopyFLVNNFLKFMVGFTNKGTVEFIVESL<SASFRYP*DYQFYIQNFTALPLNPVVLPQRQATFEYSFIPAEP
Parental-MGGRPFGLVINLNYKDLNGNVFQDAVFNQTVTIIEREDGLDGETIFMYMFLAGLGLLVVVGLHQLLE-S
..GG..FGLVINL.YKDL...VFQDAVFNQTVTI.EREDGLDGET.....FL..L.L.VV..L.......
Retrocopy<LGG*TFGLVINLKYKDLSSSVFQDAVFNQTVTITEREDGLDGETV---LFLISLRLAVVAVLAFINS*N
ParentalRKRKRTIQKVEMGTSSQNDVDMSWIPQETLNQINKASPRRLPRKRAQKRSVGSDE
.K.KR.I.KVE.GTS.Q..VDMS.IP..TLNQINK.SPRRLP.K.AQ...VGSDE
RetrocopyLKCKRLIHKVEIGTSNQKNVDMSCIPWKTLNQINKVSPRRLPWKQAQEKPVGSDE

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 64 .95 RPM
SRP012922_cerebellum 0 .00 RPM 15 .12 RPM
SRP012922_heart 0 .00 RPM 14 .85 RPM
SRP012922_kidney 0 .00 RPM 30 .94 RPM
SRP012922_liver 0 .15 RPM 31 .12 RPM
SRP012922_lung 0 .31 RPM 34 .82 RPM
SRP012922_quadricep_muscle 0 .17 RPM 17 .48 RPM
SRP012922_spleen 0 .11 RPM 48 .07 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_879 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 7 parental genes, and 7 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000227311 retrocopy
Dasypus novemcinctus ENSDNOG00000015772 1 retrocopy
retro_dnov_879 ,
Equus caballus ENSECAG000000195201 retrocopy
Echinops telfairi ENSETEG000000201111 retrocopy
Oryctolagus cuniculus ENSOCUG000000090831 retrocopy
Otolemur garnettii ENSOGAG000000142341 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000226081 retrocopy



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