RetrogeneDB ID:

retro_dnov_1317

Retrocopy
location
Organism:Armadillo (Dasypus novemcinctus)
Coordinates:scaffold_18076:12589..12936(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PFDN6
Ensembl ID:ENSDNOG00000011211
Aliases:None
Description:prefoldin subunit 6 [Source:HGNC Symbol;Acc:4926]


Retrocopy-Parental alignment summary:






>retro_dnov_1317
GTGGAAAAATATCAGCAGCTATAGAAGGACTTGAGCAAGTCCAAGTCAGGGAGGCAGAAGTTAGAGGCACAACTAACAGA
AAATAATATCGCGAAGGAGGAATTGGCCCTGCTGGATGGATCCAATGTGGTCTTTAAACTCCTGGGTCTGGTATTGCTCA
AAAAGGAGCTGCAGGAGGCCCAAGCCACAGTGGGGACAAGGCTGGACCATATTACAGCTGAAATTAAATGATACAAGTCC
CAGTTCCGGGACCTTGAGCGGCAGTCCGAGCAACAGAGGGAGATGCTTGCTCAGCTGAGCAGGAAATCCAGCAGGCCCTG
GCAGCAAAAGCAGGGGCTCCTAAGAAG

ORF - retro_dnov_1317 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 82.91 %
Parental protein coverage: 89.92 %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalVEKYQQLQKDLSKSMSGRQKLEAQLTENNIVKEELALLDGSNVVFKLLGPVLVKQELGEAQATVGKRLDY
VEKYQQL.KDLSKS.SGRQKLEAQLTENNI.KEELALLDGSNVVFKLLG.VL.K.EL.EAQATVG.RLD.
RetrocopyVEKYQQL*KDLSKSKSGRQKLEAQLTENNIAKEELALLDGSNVVFKLLGLVLLKKELQEAQATVGTRLDH
ParentalITAEIKRYESQLRDLERQSERQRETLAQL-QQEFQRAQAAKAGAPEK
ITAEIK.Y.SQ.RDLERQSE.QRE.LAQL..QE.Q.A.AAKAGAP.K
RetrocopyITAEIK*YKSQFRDLERQSEQQREMLAQL<EQEIQQALAAKAGAPKK

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 30 .53 RPM
SRP012922_cerebellum 0 .00 RPM 35 .74 RPM
SRP012922_heart 0 .00 RPM 30 .63 RPM
SRP012922_kidney 0 .00 RPM 55 .31 RPM
SRP012922_liver 0 .00 RPM 21 .36 RPM
SRP012922_lung 0 .00 RPM 32 .68 RPM
SRP012922_quadricep_muscle 0 .00 RPM 24 .23 RPM
SRP012922_spleen 0 .00 RPM 27 .47 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_1317 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 6 parental genes, and 10 retrocopies.

Species Parental gene accession Retrocopies number
Dasypus novemcinctus ENSDNOG00000011211 2 retrocopies
retro_dnov_1317 , retro_dnov_2064,
Loxodonta africana ENSLAFG000000129671 retrocopy
Macropus eugenii ENSMEUG000000167781 retrocopy
Otolemur garnettii ENSOGAG000000283414 retrocopies
Ochotona princeps ENSOPRG000000009831 retrocopy
Procavia capensis ENSPCAG000000060191 retrocopy



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