RetrogeneDB ID:

retro_dnov_1437

Retrocopy
location
Organism:Armadillo (Dasypus novemcinctus)
Coordinates:scaffold_203809:0..598(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSDNOG00000019471
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:CYTH1
Ensembl ID:ENSDNOG00000005074
Aliases:None
Description:cytohesin 1 [Source:HGNC Symbol;Acc:9501]


Retrocopy-Parental alignment summary:






>retro_dnov_1437
GGGGAGACTCAGAGCACTGATGGCAGGATGGAGGCCTTGGTGGCATGCTGCTCCCCGTGTCACCCCGAGGTCTTCCAGCC
CACAGACACGTGCTCCACACTGTCCTTCACCTCATCCTGCTCAACACCAGCCTCCACAACCACATCGTGCGGGACAAGCC
CACGGCCGAGCGCTCAGGCCCCAGGAGCAGGGCACCCACGAGGGCAGGGACCTGCCTGAGCAGGGGCTGCAGAATTTATA
TCAAAGTGTTCAACACGAACCGTTTACAGCCCAGAGGACAATGGCAATGCCCTGAGGCACATGTTCTTCCATCCTGAACC
CGGGGGCTGGCTCCTGACGCCCGGGGGCGAGTGGAGCCCTGGAAGGGCTGCTGGTTCATCCTGTCCCTCTACCGCCCCTA
CTTCCTCAAACACACACCAGGTAAGGAGCCCAGGCAGGGCAACTCGCTGGAAACCCTCAGCATAAGAGAACTGCAAGACC
TGCGTGAGCCCAACTGTTTCAGCTTCATACCCCGAGCCACAAAGGGCAAGTTATCCAAGCCTGGAAGACAGAAGCAGAGG
ACTCAGGACTCAGCAGCCACGTGGTGCTCCGCATCTCA

ORF - retro_dnov_1437 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 50.48 %
Parental protein coverage: 50.37 %
Number of stop codons detected: 0
Number of frameshifts detected 5


Retrocopy - Parental Gene Alignment:

ParentalGEAQKIDRMMEAFAQRYCQCNSGVFQSTDTCYVLSFA-IIMLNTSLHNPNVKDKPTVERFIAMNR-GIND
GE.Q..D..MEA.......C...VFQ.TDTC..LSF...I.LNTSLHN..V.DKPT.ER.....R.G...
RetrocopyGETQSTDGRMEALVACCSPCHPEVFQPTDTCSTLSFT<LILLNTSLHNHIVRDKPTAERSGPRSR<GTHE
ParentalGGDLPEELLRNLYESIKNEPFKI-PEDDGNDLTHTFFNPDREGWLLKLAGG-RVKTWKRRWFILTDNCLY
G.DLPE..L.NLY.S...EPF...PED.GN.L.H.FF.P...GWLL...GG.RV..WK..WFIL.....Y
RetrocopyGRDLPEQGLQNLYQSVQHEPFTA<PEDNGNALRHMFFHPEPGGWLL-TPGG<RVEPWKGCWFILSLYRPY
ParentalYFEYTTDKEPRGIIPLENLSIREVEDSKKPNC-FELYIPDNKDRVIKACKTEADGRVVEGNHTVYRIS
....T..KEPR....LE.LSIRE..D...PNC.F.L..P..K..VI.A.KTEA........H.V.RIS
RetrocopyFLKHTPGKEPRQGNSLETLSIRELQDLREPNC<FQLHTPSHKGQVIQAWKTEAEDSGL-SSHVVLRIS

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 14 .20 RPM
SRP012922_cerebellum 0 .00 RPM 23 .37 RPM
SRP012922_heart 0 .00 RPM 5 .10 RPM
SRP012922_kidney 0 .00 RPM 3 .29 RPM
SRP012922_liver 0 .00 RPM 4 .64 RPM
SRP012922_lung 0 .00 RPM 17 .87 RPM
SRP012922_quadricep_muscle 0 .00 RPM 6 .23 RPM
SRP012922_spleen 0 .00 RPM 33 .54 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_1437 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 ENSDNOG00000005074 3 retrocopies
retro_dnov_1437 , retro_dnov_2322, retro_dnov_2337,


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