RetrogeneDB ID:

retro_dnov_161

Retrocopy
location
Organism:Armadillo (Dasypus novemcinctus)
Coordinates:GeneScaffold_2241:124028..124419(-)
Located in intron of:ENSDNOG00000013369
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:SUB1
Ensembl ID:ENSDNOG00000007611
Aliases:None
Description:SUB1 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:19985]


Retrocopy-Parental alignment summary:






>retro_dnov_161
ATGCCTAAATCAAAGGAACTTGTTTCTTCAAGTTCATCTGGTAGTGATTCTGATAGTGAACTTGACAAAACGCTAAGGAG
GAAAAAGCAAGTTACTCTGGAAAAACCTGTAAAGAAGCAAAAGAAACTTTGCTCTTGAAACCTCAAGAGCTCTGTCATCT
CCCAAGCAGAGCAGCAGCAGCAGAGGAGATGATAACATGTTCCAGATTGGAAAAATGAGGTACGTCAGTGTCAGGGACTT
TAAAGGAAAAGTCCTAATTGACATTAGAGAATATTGGATAGATCCAGAAGGTGAAATGAAACCAGGAAGGAAAGATACTT
CTTTAAATCCTGAGTAATGGAGCCAGCTGAAGAAACAGATTTCTGACATTGAAGATGCTGTAAGGAAACTG

ORF - retro_dnov_161 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 73.28 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 1
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalMPKSKELVSSSSSGS--DSDSEVDKKLKRKKQIPPEKPVKKQKTG-ETSRALSSSKQSSSSR-DDNMFQI
MPKSKELVSSSSSGS..DS........K............K.....ETSRALSS.KQSSSSR.DDNMFQI
RetrocopyMPKSKELVSSSSSGSDSDSELDKTLRRKKQVTLEKPVKKQKKLCS>ETSRALSSPKQSSSSRGDDNMFQI
ParentalGKMRYVSVRDFKGKVLIDIREYWMDPEGEMKPGRKGISLNPEQWSQLKEQISDIDDAVRKL
GKMRYVSVRDFKGKVLIDIREYW.DPEGEMKPGRK..SLNPE.WSQLK.QISDI.DAVRKL
RetrocopyGKMRYVSVRDFKGKVLIDIREYWIDPEGEMKPGRKDTSLNPE*WSQLKKQISDIEDAVRKL

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






RNA-Seq - click to see more details

(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 .58 RPM 82 .65 RPM
SRP012922_cerebellum 0 .00 RPM 62 .82 RPM
SRP012922_heart 0 .00 RPM 75 .18 RPM
SRP012922_kidney 0 .00 RPM 115 .27 RPM
SRP012922_liver 0 .00 RPM 51 .24 RPM
SRP012922_lung 0 .00 RPM 114 .70 RPM
SRP012922_quadricep_muscle 0 .00 RPM 49 .85 RPM
SRP012922_spleen 0 .00 RPM 203 .97 RPM

ChIP-Seq - click to see more details

Dasypus novemcinctus was not studied using ChIP-Seq data.

EST - click to see more details

Dasypus novemcinctus was not studied using EST data.

TSS - click to see more details

Dasypus novemcinctus was not studied using FANTOM5 data.

Lab - click to see more details

retro_dnov_161 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 22 parental genes, and 77 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000188795 retrocopies
retro_cfam_1266, retro_cfam_1536, retro_cfam_1916, retro_cfam_2010, retro_cfam_215,
Callithrix jacchus ENSCJAG000000187182 retrocopies
retro_cjac_1908, retro_cjac_484,
Cavia porcellus ENSCPOG000000055844 retrocopies
retro_cpor_1114, retro_cpor_1481, retro_cpor_834, retro_cpor_854,
Dasypus novemcinctus ENSDNOG00000007611 5 retrocopies
retro_dnov_1230, retro_dnov_161 , retro_dnov_1822, retro_dnov_2156, retro_dnov_400,
Dipodomys ordii ENSDORG000000139162 retrocopies
retro_dord_85, retro_dord_98,
Homo sapiens ENSG000001133872 retrocopies
retro_hsap_1662, retro_hsap_3934,
Gorilla gorilla ENSGGOG000000270333 retrocopies
retro_ggor_1063, retro_ggor_1254, retro_ggor_2645,
Loxodonta africana ENSLAFG000000110061 retrocopy
retro_lafr_19,
Macropus eugenii ENSMEUG000000077704 retrocopies
retro_meug_1155, retro_meug_1820, retro_meug_2038, retro_meug_500,
Microcebus murinus ENSMICG000000145352 retrocopies
retro_mmur_1115, retro_mmur_17,
Myotis lucifugus ENSMLUG000000136856 retrocopies
retro_mluc_1649, retro_mluc_1696, retro_mluc_1785, retro_mluc_226, retro_mluc_2346, retro_mluc_621,
Macaca mulatta ENSMMUG000000114702 retrocopies
retro_mmul_2318, retro_mmul_993,
Monodelphis domestica ENSMODG000000204103 retrocopies
retro_mdom_840, retro_mdom_841, retro_mdom_895,
Mustela putorius furoENSMPUG000000151852 retrocopies
retro_mputfur_186, retro_mputfur_295,
Mus musculus ENSMUSG000000222054 retrocopies
retro_mmus_1118, retro_mmus_2304, retro_mmus_2586, retro_mmus_3606,
Oryctolagus cuniculus ENSOCUG000000062625 retrocopies
retro_ocun_1227, retro_ocun_1313, retro_ocun_1661, retro_ocun_1714, retro_ocun_902,
Otolemur garnettii ENSOGAG000000090126 retrocopies
retro_ogar_1130, retro_ogar_1272, retro_ogar_218, retro_ogar_2481, retro_ogar_340, retro_ogar_525,
Pongo abelii ENSPPYG000000153792 retrocopies
retro_pabe_124, retro_pabe_1371,
Rattus norvegicus ENSRNOG0000005056312 retrocopies
retro_rnor_1040, retro_rnor_1137, retro_rnor_1203, retro_rnor_1496, retro_rnor_1692, retro_rnor_1693, retro_rnor_1863, retro_rnor_2721, retro_rnor_2986, retro_rnor_420, retro_rnor_572, retro_rnor_735,
Sarcophilus harrisii ENSSHAG000000149861 retrocopy
retro_shar_628,
Ictidomys tridecemlineatus ENSSTOG000000193642 retrocopies
retro_itri_570, retro_itri_571,
Tarsius syrichta ENSTSYG000000140692 retrocopies
retro_tsyr_528, retro_tsyr_895,


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