RetrogeneDB ID:

retro_dnov_2292

Retrocopy
location
Organism:Armadillo (Dasypus novemcinctus)
Coordinates:scaffold_61338:41238..41873(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:STX16-NPEPL1
Ensembl ID:ENSDNOG00000024609
Aliases:None
Description:STX16-NPEPL1 readthrough (NMD candidate) [Source:HGNC Symbol;Acc:41993]


Retrocopy-Parental alignment summary:






>retro_dnov_2292
CAGTGGATGGAGAAGTTGAATATACATCATGATTTCAGCTGGATTAAACAGAAGATGAAAAAATTAGCCAGCCTTTATAA
AAGCATATAAACAGACCCATGCTGGATGACAGCAATGAGGAAGAGCATGCCACTGAATCACGACAAAAAGATCATCAATT
TCTTCCACAGAGGCCAGCATGAGGTACAGGTCCTGATCAGCCAGGTCCATGGGGTCTGCTCCAAGCAAGAGTGGCTCCTT
TGCAAAGTGGCAACTTCCCTGGTACAGACCCTGCAGGAGCTGACTACATGCTTCTGGCATGATAAGTTGGGCTGTGTCAA
AAGCATGAAGAATTAAAAGGAAAGATCCCAGCATTTTTTGATATATCAGTACCACTAACGACTGATGGTGATGATAATAC
TCCTCTTGATTAGGGTTTTAGAGATGACCAGTTAGTGCTGGTGAAGCAGTGCATGCTGATGGTGGAAGAGAGTGAGCAGG
AGATCTGTCAGATTGTCCAGTTCATCTGTGACCTGAATGAGATCTTTATGGATTTGGGAGCAGTGATTGCCAAACAGGGT
ACAGTTCTTGATGGAATTGACTAAAACACTGAATAATGCTGTGTGAAAACGGAAGATGATTTGAAACAACTTCAC

ORF - retro_dnov_2292 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 58.9 %
Parental protein coverage: 59.61 %
Number of stop codons detected: 4
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalKWVEGVDGIQYDVGRIKQKMKELASLHD-KHLNRPTLDDSSEEEHAIE-ITTQ-EITQLFHRGQRAVQAL
.W.E....I..D...IKQKMK.LASL...KH.NRP.LDDS.EEEHA.E.ITT...I...FHRGQ..VQ.L
RetrocopyQWMEKLN-IHHDFSWIKQKMKKLASLYK<KHINRPMLDDSNEEEHATE<ITTK<KIINFFHRGQHEVQVL
ParentalTSRARGTCSEQEERLLRNVVTSLAQALQELSTSFRHAQSGYLXXMKNREERSQHF-FDTSVPLMDDGDDN
.S...G.CS.QE..LL..V.TSL.Q.LQEL.T.F.H...G....MKN..ERSQHF.FD.SVPL..DGDDN
RetrocopyISQVHGVCSKQEW-LLCKVATSLVQTLQELTTCFWHDKLGCVKSMKN*KERSQHF<FDISVPLTTDGDDN
ParentalTLYDRGFTDDQLVLVEQNTLMVEEREREIRQIVQSISDLNEIFRDLGVMIVEQXXXXXXXXXXXEQSCVK
T..D.GF.DDQLVLV.Q..LMVEE.E.EI.QIVQ.I.DLNEIF.DLG..I..Q...........E..CVK
RetrocopyTPLD*GFRDDQLVLVKQCMLMVEESEQEICQIVQFICDLNEIFMDLGAVIAKQGTVLDGID*NTE*CCVK
Parental-EDGLKQLH
.ED.LKQLH
RetrocopyTEDDLKQLH

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 33 .06 RPM
SRP012922_cerebellum 0 .00 RPM 29 .83 RPM
SRP012922_heart 0 .00 RPM 10 .44 RPM
SRP012922_kidney 0 .00 RPM 6 .57 RPM
SRP012922_liver 0 .00 RPM 11 .30 RPM
SRP012922_lung 0 .00 RPM 21 .53 RPM
SRP012922_quadricep_muscle 0 .00 RPM 15 .75 RPM
SRP012922_spleen 0 .00 RPM 32 .28 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_2292 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 ENSDNOG00000024609 1 retrocopy
retro_dnov_2292 ,


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