RetrogeneDB ID:

retro_dnov_1038

Retrocopy
location
Organism:Armadillo (Dasypus novemcinctus)
Coordinates:scaffold_13946:8982..9797(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSDNOG00000025223
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:MRPL44
Ensembl ID:ENSDNOG00000012731
Aliases:None
Description:mitochondrial ribosomal protein L44 [Source:HGNC Symbol;Acc:16650]


Retrocopy-Parental alignment summary:






>retro_dnov_1038
TCTGACAAGCCCAACTGGGATTACCGTGCTGAAATACAAGCATTTGGACATCAGTTACAGGAAGCCTTCTCGGTAGATCT
TCTCAAAACTGCATTTGTTAATAGCTGCTATATTAAAAGTGAGGAGGCCAAACTCCAAAAACTTGGGATAGAAAAGGGAG
CAGTTCTTCTGAATCTTAAAGATAATCGAAACTATCTGAACAAGGACTATCTTTTTCACAAACTTGTCTCACACAATTTT
TTGAAGACGCGTATCCAGACTTGCTCCCTGAAGGCATCAAAAGTCTTGTTGGTGTTCTCACTGGTGAGGACATAGTGTGT
CATGTGGCTAGAAACTTGGCTGTGGAACAGTTAACACTGAGTGTGGAATTTCCTGTCCCCCAAACTGTATTACAACAGAC
TTTCTTTGCAGTAATTGGAGCTCTACTACAGATCAGTGGACCCCAGAGAACTGCAGTTTTCATCAGGGACTTCTTATTTA
CTCAGTTGACTGGAAAAGAGCTCTTTGAGATTTGGATGATAATAAATCCATAGGTCTACTGAAAAAAGAGTTGAAGAAAA
GGAATATTTCACCTCCTGAATCTAGACTTACTAGGCAGTCTGGAGGCACCACAGCGTTGCCTTTATATTTTGTTGGCTTA
TACTGTGATAGAAAGTTGATTGCAGAAGAATCTGGGGAGACAGTGTTGGTTGCAGAAGAAGAAGCTGCTAGAGTGGCAGT
TAGGATATTTTATGGATTCACTGAGAACAGACGTCCCTGGGACTGTTCACAGCTCAAAGAGAATTTAGAGAGCAGAAAAG
ACCATCACTGCCAGC

ORF - retro_dnov_1038 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.27 %
Parental protein coverage: 81.87 %
Number of stop codons detected: 0
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalSEKPNWDYHAEIQAFGHRLHETFSIDLLKTAFVNSCYITSEEAKRQKLGIEKEAVLLNLKDNR-ELSEQG
S.KPNWDY.AEIQAFGH.L.E.FS.DLLKTAFVNSCYI.SEEAK.QKLGIEK.AVLLNLKDNR..LSEQG
RetrocopySDKPNWDYRAEIQAFGHQLQEAFSVDLLKTAFVNSCYIKSEEAKLQKLGIEKGAVLLNLKDNR<KLSEQG
ParentalISFSQTCLTQFFEDAYPNLPPEGIKSLVDFLTGEDIVCHVARNLAVEQLTLSAEFPVPQTVLQQTFFAVI
.SFSQTCLTQFFEDAYP.L.PEGIKSLV..LTGEDIVCHVARNLAVEQLTLS.EFPVPQTVLQQTFFAVI
RetrocopyLSFSQTCLTQFFEDAYPDLLPEGIKSLVGVLTGEDIVCHVARNLAVEQLTLSVEFPVPQTVLQQTFFAVI
ParentalGALLQSSGPQRTAVFIRDFLITQLTGKELFEIWTIINP-MGLLVEELKKRNISPPESRLTRQSGSTTALP
GALLQ.SGPQRTAVFIRDFL.TQLTGKELFEIW.IINP..GLL..ELKKRNISPPESRLTRQSG.TTALP
RetrocopyGALLQISGPQRTAVFIRDFLFTQLTGKELFEIWMIINP<IGLLKKELKKRNISPPESRLTRQSGGTTALP
ParentalL-FVGLYCDRKLIAEGPGETVLVAEEEAARVALRKIYGFTENRRPWDYSQPKENL-RTEKTITAS
L.FVGLYCDRKLIAE..GETVLVAEEEAARVA.R..YGFTENRRPWD.SQ.KENL.R.EKTITAS
RetrocopyLYFVGLYCDRKLIAEESGETVLVAEEEAARVAVRIFYGFTENRRPWDCSQLKENL>RAEKTITAS

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 .00 RPM 23 .73 RPM
SRP012922_cerebellum 0 .00 RPM 11 .27 RPM
SRP012922_heart 0 .00 RPM 22 .28 RPM
SRP012922_kidney 0 .00 RPM 37 .51 RPM
SRP012922_liver 0 .00 RPM 34 .68 RPM
SRP012922_lung 0 .00 RPM 16 .65 RPM
SRP012922_quadricep_muscle 0 .17 RPM 48 .29 RPM
SRP012922_spleen 0 .00 RPM 17 .17 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_1038 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 1 parental gene, and 1 retrocopy.

Species Parental gene accession Retrocopies number
Dasypus novemcinctus ENSDNOG00000012731 1 retrocopy
retro_dnov_1038 ,




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