RetrogeneDB ID:

retro_dnov_2609

Retrocopy
location
Organism:Armadillo (Dasypus novemcinctus)
Coordinates:scaffold_89837:7553..8193(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:IDO1
Ensembl ID:ENSDNOG00000002167
Aliases:None
Description:indoleamine 2,3-dioxygenase 1 [Source:HGNC Symbol;Acc:6059]


Retrocopy-Parental alignment summary:






>retro_dnov_2609
ATGGCCCATGAGCAGGCATCTCCCATGGAAAGTTCTTGGAGAATCCATGAGGAAGTCCACATAAAGGAAGATGTGGGCTT
TGCTCTGCTAGGTCCACTGGAGGGGTTGCCTAATAAGTATGCCGCCTGGACAGTCATTGTTCAAAACGTGCCTGACCTGA
TTAAGACCAGCCAGTCATGCACAGAAGTTGAAAAGTTGCCAGAACTCAGCATTGATGAGCTTGAAGGACACAAGTTGCAG
CACCTTGCCCACCTGATCTTGGGGTACATCACCATGGCCTACGTGTGGCATCAAGGTGCCCAAGATGTCTGTAAGGTCCT
GCCAAGAAATATTGCCATTTCTCACTGCAAAATCTTGGAGAAGCTGAGACTGCCTCTTAACCTGGTGTATGCAGGTTGTG
TCTTGCAAACTGGAAGAAAAAGGACCCCAGTGGGCCCATGACTTATGAAAACATGGACATCCTCTTCTCCTTCCCTGGTG
GAGACTGCAGAAAAGGTTGCTTCCTGGTGTCACTATTGTGGAAATAGCAGCTGCTTCTGCTATCAAAGAAATTCCTGTTA
TACTCAATGCTAAACAACGTCAGGACCAGGGAACTGTGAGAACAGAACTGGAAAAAATAACTGACTGCCTGAAGAAGGCC

ORF - retro_dnov_2609 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 73.15 %
Parental protein coverage: 53.15 %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMACDQASPMESPWRIREEFHINEDVGFALPDPLEELPKKYDDWMFIAQNLPDLIKTGKLREEVEKLPELS
MA..QASPMES.WRI.EE.HI.EDVGFAL..PLE.LP.KY..W..I.QN.PDLIKT.....EVEKLPELS
RetrocopyMAHEQASPMESSWRIHEEVHIKEDVGFALLGPLEGLPNKYAAWTVIVQNVPDLIKTSQSCTEVEKLPELS
ParentalIDDLEGHKLQRLAHLVLGYITMAYVWDRGDQDVRKVLPRNIAIPYCRISEMLKLPPILSYADCV-LANWK
ID.LEGHKLQ.LAHL.LGYITMAYVW..G.QDV.KVLPRNIAI..C.I.E.L.LP..L.YA.CV.LANWK
RetrocopyIDELEGHKLQHLAHLILGYITMAYVWHQGAQDVCKVLPRNIAISHCKILEKLRLPLNLVYAGCV<LANWK
ParentalKKDPSG---VKNMEILFSFPGGDCGKGFFLVSLL-VEIAAASVIKEIPILINAIQHQDQATVKTELEKIT
KKDPSG.....NM.ILFSFPGGDC.KG.FLVSLL.VEIAAAS.IKEIP...NA.Q.QDQ.TV.TELEKIT
RetrocopyKKDPSGPMTYENMDILFSFPGGDCRKGCFLVSLL<VEIAAASAIKEIPVILNAKQRQDQGTVRTELEKIT
ParentalGCLKEA
.CLK.A
RetrocopyDCLKKA

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 3 .50 RPM
SRP012922_cerebellum 0 .00 RPM 0 .14 RPM
SRP012922_heart 0 .00 RPM 10 .44 RPM
SRP012922_kidney 0 .00 RPM 1 .10 RPM
SRP012922_liver 0 .00 RPM 1 .08 RPM
SRP012922_lung 0 .00 RPM 411 .75 RPM
SRP012922_quadricep_muscle 0 .00 RPM 15 .58 RPM
SRP012922_spleen 0 .00 RPM 29 .42 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_2609 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 3 retrocopies.

Species Parental gene accession Retrocopies number
Dasypus novemcinctus ENSDNOG00000002167 3 retrocopies
retro_dnov_1689, retro_dnov_2547, retro_dnov_2609 ,



Copyright © RetrogeneDB 2014-2017