RetrogeneDB ID:

retro_dnov_327

Retrocopy
location
Organism:Armadillo (Dasypus novemcinctus)
Coordinates:GeneScaffold_3651:112032..112435(-)
Located in intron of:ENSDNOG00000012645
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS18
Ensembl ID:ENSDNOG00000012084
Aliases:None
Description:ribosomal protein S18 [Source:HGNC Symbol;Acc:10401]


Retrocopy-Parental alignment summary:






>retro_dnov_327
ATGTCTCTCGTGATCCCTGAGAAGTTCCACTGCATTTTGCAAGTACTCAATACCAACATCTATGGGTGGCAGAAAATAGC
CTTTGCCATCACGGCCATTAAGGGCATGGGGCAAAGGTATGCTTGTGTGGTGTTGAGGAAAGCAGATATAAACCTCACCA
AGAGGGCAGGAGAGCTCACTGAGGATGAGGGGGAACATGTGATCACCATTATGCAGAATCCACGCTAGTACAGGATCCCT
GACTGGTTCCTGAACAGACTGAAGGATGTCAAGGATGGAAAATCCAGCCAGGTCCTGGGCCAGTGGTCTGGACAATAAGC
TCCATGAAGACCTGGAGCAACTGAAGAAGATTCAGGCGCAATGGGGGCTGCGCCACTTCTGGGGCCTTCGTGTCCGAGGC
CGA

ORF - retro_dnov_327 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 82.22 %
Parental protein coverage: 88.16 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMSLVIPEKFQHILRVLNTNIDGRRKIAFAITAIKGVGRRYAHVVLRKADIDLTKRAGELTEDEVERVITI
MSLVIPEKF..IL.VLNTNI.G..KIAFAITAIKG.G.RYA.VVLRKADI.LTKRAGELTEDE.E.VITI
RetrocopyMSLVIPEKFHCILQVLNTNIYGWQKIAFAITAIKGMGQRYACVVLRKADINLTKRAGELTEDEGEHVITI
ParentalMQNPRQYKIPDWFLNRQKDVKDGKYSQVL-ANGLDNKLREDLERLKKIRAHRGLRHFWGLRVRGQ
MQNPR.Y.IPDWFLNR.KDVKDGK.SQVL.A.GLDNKL.EDLE.LKKI.A..GLRHFWGLRVRG.
RetrocopyMQNPR*YRIPDWFLNRLKDVKDGKSSQVL>ASGLDNKLHEDLEQLKKIQAQWGLRHFWGLRVRGR

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 1233 .12 RPM
SRP012922_cerebellum 0 .96 RPM 490 .76 RPM
SRP012922_heart 0 .23 RPM 542 .95 RPM
SRP012922_kidney 0 .00 RPM 1375 .55 RPM
SRP012922_liver 0 .00 RPM 802 .67 RPM
SRP012922_lung 0 .31 RPM 1687 .30 RPM
SRP012922_quadricep_muscle 0 .00 RPM 918 .73 RPM
SRP012922_spleen 0 .00 RPM 2480 .37 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_327 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 21 parental genes, and 134 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000026482 retrocopies
Callithrix jacchus ENSCJAG000000216505 retrocopies
Dasypus novemcinctus ENSDNOG00000012084 13 retrocopies
Erinaceus europaeus ENSEEUG000000102978 retrocopies
Homo sapiens ENSG000002315002 retrocopies
Gorilla gorilla ENSGGOG000000065715 retrocopies
Loxodonta africana ENSLAFG000000321731 retrocopy
Macropus eugenii ENSMEUG0000001677011 retrocopies
Myotis lucifugus ENSMLUG000000073602 retrocopies
Macaca mulatta ENSMMUG000000038671 retrocopy
Oryctolagus cuniculus ENSOCUG000000105461 retrocopy
Otolemur garnettii ENSOGAG000000062257 retrocopies
Pongo abelii ENSPPYG0000002595314 retrocopies
Pan troglodytes ENSPTRG000000180391 retrocopy
Pteropus vampyrus ENSPVAG000000019026 retrocopies
Rattus norvegicus ENSRNOG000000285054 retrocopies
Sarcophilus harrisii ENSSHAG000000068572 retrocopies
Sarcophilus harrisii ENSSHAG000000086581 retrocopy
Sus scrofa ENSSSCG000000015025 retrocopies
Tupaia belangeri ENSTBEG0000001270840 retrocopies
Tursiops truncatus ENSTTRG000000043023 retrocopies



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