RetrogeneDB ID:

retro_dnov_2429

Retrocopy
location
Organism:Armadillo (Dasypus novemcinctus)
Coordinates:scaffold_74131:7276..8477(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSDNOG00000007470
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:SART1
Ensembl ID:ENSDNOG00000024688
Aliases:None
Description:squamous cell carcinoma antigen recognized by T cells [Source:HGNC Symbol;Acc:10538]


Retrocopy-Parental alignment summary:






>retro_dnov_2429
CGGCTCGCCTCCGAGTACCTCACGCACAAGGAGATGGTGACCTTTAAAAAGTCCAAGTGGAGGGTGAAGAGAATCCGCAA
GAAGGAGAAGGAGGTGGTGGTGCGGGCCGATGACCCGCTGCCTCTCGGGGACCAGACTCAAGATGGGGACTTTGGCTCCA
GACTGCGGGGCCGGGGCCGGCGCCGAGTGCCCGAGGTTGACGAGGAGGCCCAGGAGGAGGAGGAAAAGGAGCCAGTGCCT
CAGCCCCCACAGTCAGACGACACCCGCGTAGAGAACATGGACATCAGTGATGAAAAGGAGGGTGGAGCGCCGTGCTCTGG
GTCCCCAGAAGTGCCGGAGGAGGACGAGGCAGAGCTGGAGCCACAGAAGCAGCTGGAGAAAGGGCGCCAGCTGCGGCAGC
TCCAGCAGCTGCGGGAGAGTGGCGAGAAGGTGGTGGAGATCGTGAAGAAGCTGGAGTCCCGCCAGCGGGCCTGGGAGGAG
GACGAGGACCCTGAGCGGAAGGGGGCCATCGTGTTCAATGCCACCTCGGAGTTCTGCCAGACGCTGGGGGAGATCCCCAC
CTATGGGCTGGCCGGCAACTGGGAGGAGCAGGAGGAGCCAATGGACTTGGAGCGGGATGAGGAGCGCTCGGCCAACGGCG
GCTCCGAATCCGATGAGGAGGAGAACATCGGCTGGAGCACGGTCAACCTGGACGAGGAGAAGCAGCAGCAGGACTTCTCT
GCCTCCTCCACCACCATCCTGGACGAGGAGCCCATCATGAACCGAGGGCTGGCAGCTGCCCTGCTCCTGTGTCAGAACAA
AGGGCTGCTGGAGACCACGGTGCAGAAGGTGGCCACGGGTGAAGGCACCCAACAAGTCGCTGCTGTCCACCGTGTACTGC
ATCGAGGACAAGATGGCCATCGACGACAAGTACAGCCGGCGGGAGGAGTACCGCGGCTCCACCCAGGACTTCAAGGAAAA
GGACGGCTACAAGCCCGACGTCAAGATCGAGTATGTGGACGAGACGGGCTGCAAGCTCACGCCCAAGGAGGCTTTCCGGC
AGCTGTCCCACCGCTTCCACGGCAAGGGCTCAGGCAAGATGAAGACTGAGCGGCGGATGAAGAAGCTGGACGAGGAGGCA
CTGCTGAAGAAGATGAGCTCCAGCGACACGCCCCTGGGCACCGTGGCCTTGCTGCAGAAGAAGCAGAAGGTCGGAAGACC
C

ORF - retro_dnov_2429 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 88.78 %
Parental protein coverage: 50.38 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalRLASEYLTPEEMVTFKKSKRRVKKIRKKEKEVVVRADDLLPLGDQTQDGDFGSRLRGRGRRRVPEAEEE-
RLASEYLT..EMVTFKKSK.RVK.IRKKEKEVVVRADD.LPLGDQTQDGDFGSRLRGRGRRRVPE..EE.
RetrocopyRLASEYLTHKEMVTFKKSKWRVKRIRKKEKEVVVRADDPLPLGDQTQDGDFGSRLRGRGRRRVPEVDEEA
Parental--KEQPVPQP-PQSDD-TRLENMDISDEEEGGVPRSGSPEVLEEDEAELELQKQLEKGRRLRQLQQLRDS
...E...P.P.P...D.TR.ENMDISDE.EGG.P.SGSPEV.EEDEAELE.QKQLEKGR.LRQLQQLR.S
RetrocopyQEEEEKEPVPQPPQSDDTRVENMDISDEKEGGAPCSGSPEVPEEDEAELEPQKQLEKGRQLRQLQQLRES
ParentalGEKXXXXXXXXXXXXXAWEEDEDPERKGAIVFNATSEFCQTLGEIPTYGLAGNWEEQEEPMDLERDEERS
GEK.............AWEEDEDPERKGAIVFNATSEFCQTLGEIPTYGLAGNWEEQEEPMDLERDEERS
RetrocopyGEKVVEIVKKLESRQRAWEEDEDPERKGAIVFNATSEFCQTLGEIPTYGLAGNWEEQEEPMDLERDEERS
ParentalANGGSESDEEENIGWSTVNLDEEKQQQDFSASSTTILDEEPIMNRGLAAALLLCQNKGLLETTVQKVA-R
ANGGSESDEEENIGWSTVNLDEEKQQQDFSASSTTILDEEPIMNRGLAAALLLCQNKGLLETTVQKVA.R
RetrocopyANGGSESDEEENIGWSTVNLDEEKQQQDFSASSTTILDEEPIMNRGLAAALLLCQNKGLLETTVQKVA>R
ParentalVKAPNKSLLSTVYCIEDKMAIDDKYSRREEYRGSTQDFKEKDGYKPDVKIEYVDETGCKLTPKEAFRQLS
VKAPNKSLLSTVYCIEDKMAIDDKYSRREEYRGSTQDFKEKDGYKPDVKIEYVDETGCKLTPKEAFRQLS
RetrocopyVKAPNKSLLSTVYCIEDKMAIDDKYSRREEYRGSTQDFKEKDGYKPDVKIEYVDETGCKLTPKEAFRQLS
ParentalHRFHGKGSGKMKTERRMKKLDEEALLKKMSSSDTPLGTVALLQKKQKRKTP
HRFHGKGSGKMKTERRMKKLDEEALLKKMSSSDTPLGTVALLQKKQK...P
RetrocopyHRFHGKGSGKMKTERRMKKLDEEALLKKMSSSDTPLGTVALLQKKQKVGRP

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 39 .28 RPM
SRP012922_cerebellum 0 .55 RPM 55 .40 RPM
SRP012922_heart 0 .00 RPM 11 .83 RPM
SRP012922_kidney 0 .27 RPM 27 .93 RPM
SRP012922_liver 0 .46 RPM 22 .76 RPM
SRP012922_lung 0 .76 RPM 45 .21 RPM
SRP012922_quadricep_muscle 0 .17 RPM 19 .73 RPM
SRP012922_spleen 0 .34 RPM 51 .62 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_2429 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 ENSDNOG00000024688 1 retrocopy
retro_dnov_2429 ,


Copyright © RetrogeneDB 2014-2017