RetrogeneDB ID:

retro_dnov_2512

Retrocopy
location
Organism:Armadillo (Dasypus novemcinctus)
Coordinates:scaffold_81736:3177..4044(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:HSPD1
Ensembl ID:ENSDNOG00000013226
Aliases:None
Description:heat shock 60kDa protein 1 (chaperonin) [Source:HGNC Symbol;Acc:5261]


Retrocopy-Parental alignment summary:






>retro_dnov_2512
ATGCTTCGATTACCCACAGTCCTTCACCAGATGAGGCCAGTGTCCAGGGCATTGGCTCCTCATCTCATTCGGGCATATGC
CAAAGATGTGAAATTCGGTGCCGATGCCCGAGCCTTAATGCTTCAAGGTGTAGACCTTTTAGCTGATGCTGTAGCCGTTA
CTATGGGGCCAAAGGGAAGAACAGTGATTATTGAACAGAGTTGGGGAAGTCCCAAAGTAACAAAAGATGGTGTGACCATT
GCAAAATCAATTGATTTGAAGGATAAATATAAAAATATTGGAGCTAAACTTGTTCAGGATGTTGCCAATAACACAAATGA
AGAGGCTGGGGATGGCACCACCACTGCTACTGTACTGGCACGCTCTATTGCTAAGGAAGGCTTTGAGAAGATTAGCAAAG
GTGCTAATCCAGTAGAAATCAGGAGAGGTGTGATGTTAGCTGTTGATGCTGTAATTGCTGAACTTAAGAAGCAGTCTAAA
CCTGTGACAACCCCTGAAGAAATTGCTCAGGTTGCTAAAATTTCTGCAAATGGAGACAAAGAAATTGGCAATATCATTTT
TGATGCAATGAAAAAGGTTGGAAGAAAAGGTGTCATCACAGTAAAGGATGGAAAAACATTGAATGATGAATTAGAAATCA
TTGAAGGCATGAAGTTTGATCGGGGTTATATTTCTCCATACTTTATTAATACATCAAAAGGTCAGAAATGTGAATTCCAG
GATGCCTATGTTCTGTTAAGTGAAAAGAAAATTTCTAGCATTCAGTCCATTGTACCTGCTCTTGAAATTGCCAATGCTCA
CCGTAAACCCTTGGTCATAATTGCTGAAGATGTTGATGGAGAAGCTCTAAGTACACTTGTTTTGAAT

ORF - retro_dnov_2512 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 97.58 %
Parental protein coverage: 53.32 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMLRLPAVLRQMRPVSRALAPHLIRAYAKDVKFGADARALMLQGVDLLADAVAVTMGPKGRTVIIEQSWGS
MLRLP.VL.QMRPVSRALAPHLIRAYAKDVKFGADARALMLQGVDLLADAVAVTMGPKGRTVIIEQSWGS
RetrocopyMLRLPTVLHQMRPVSRALAPHLIRAYAKDVKFGADARALMLQGVDLLADAVAVTMGPKGRTVIIEQSWGS
ParentalPKVTKDGVTVAKSIDLKDKYKNIGAKLVQDVANNTNEEAGDGTTTATVLARSIAKEGFEKISKGANPVEI
PKVTKDGVT.AKSIDLKDKYKNIGAKLVQDVANNTNEEAGDGTTTATVLARSIAKEGFEKISKGANPVEI
RetrocopyPKVTKDGVTIAKSIDLKDKYKNIGAKLVQDVANNTNEEAGDGTTTATVLARSIAKEGFEKISKGANPVEI
ParentalRRGVMLAVDAVIAELKKQSKPVTTPEEIAQVATISANGDKEIGNIISDAMKKVGRKGVITVKDGKTLNDE
RRGVMLAVDAVIAELKKQSKPVTTPEEIAQVA.ISANGDKEIGNII.DAMKKVGRKGVITVKDGKTLNDE
RetrocopyRRGVMLAVDAVIAELKKQSKPVTTPEEIAQVAKISANGDKEIGNIIFDAMKKVGRKGVITVKDGKTLNDE
ParentalLEIIEGMKFDRGYISPYFINTSKGQKCEFQDAYVLLSEKKISSIQSIVTALEIANAYRKPLVIIAEDVDG
LEIIEGMKFDRGYISPYFINTSKGQKCEFQDAYVLLSEKKISSIQSIV.ALEIANA.RKPLVIIAEDVDG
RetrocopyLEIIEGMKFDRGYISPYFINTSKGQKCEFQDAYVLLSEKKISSIQSIVPALEIANAHRKPLVIIAEDVDG
ParentalEALSTLVLN
EALSTLVLN
RetrocopyEALSTLVLN

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 5 .06 RPM 108 .32 RPM
SRP012922_cerebellum 1 .65 RPM 29 .56 RPM
SRP012922_heart 4 .64 RPM 46 .41 RPM
SRP012922_kidney 9 .04 RPM 138 .54 RPM
SRP012922_liver 7 .28 RPM 97 .22 RPM
SRP012922_lung 3 .51 RPM 48 .57 RPM
SRP012922_quadricep_muscle 2 .25 RPM 49 .68 RPM
SRP012922_spleen 3 .43 RPM 59 .63 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_2512 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 16 parental genes, and 51 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000137701 retrocopy
retro_amel_771,
Bos taurus ENSBTAG000000125861 retrocopy
retro_btau_988,
Canis familiaris ENSCAFG000000108654 retrocopies
retro_cfam_1185, retro_cfam_1620, retro_cfam_2165, retro_cfam_614,
Callithrix jacchus ENSCJAG000000039906 retrocopies
retro_cjac_1516, retro_cjac_1534, retro_cjac_1975, retro_cjac_3172, retro_cjac_3400, retro_cjac_4096,
Dasypus novemcinctus ENSDNOG00000013226 3 retrocopies
retro_dnov_1990, retro_dnov_2113, retro_dnov_2512 ,
Echinops telfairi ENSETEG000000091844 retrocopies
retro_etel_1440, retro_etel_426, retro_etel_885, retro_etel_925,
Loxodonta africana ENSLAFG000000000531 retrocopy
retro_lafr_476,
Macropus eugenii ENSMEUG000000119872 retrocopies
retro_meug_1688, retro_meug_224,
Myotis lucifugus ENSMLUG000000008714 retrocopies
retro_mluc_1458, retro_mluc_2280, retro_mluc_2348, retro_mluc_601,
Macaca mulatta ENSMMUG000000104891 retrocopy
retro_mmul_83,
Monodelphis domestica ENSMODG000000122893 retrocopies
retro_mdom_427, retro_mdom_493, retro_mdom_756,
Mustela putorius furoENSMPUG000000078183 retrocopies
retro_mputfur_1118, retro_mputfur_245, retro_mputfur_434,
Otolemur garnettii ENSOGAG000000340535 retrocopies
retro_ogar_2335, retro_ogar_2420, retro_ogar_2740, retro_ogar_3221, retro_ogar_3497,
Rattus norvegicus ENSRNOG000000145259 retrocopies
retro_rnor_1000, retro_rnor_1006, retro_rnor_1308, retro_rnor_1578, retro_rnor_1585, retro_rnor_2812, retro_rnor_2835, retro_rnor_596, retro_rnor_905,
Tursiops truncatus ENSTTRG000000034173 retrocopies
retro_ttru_1661, retro_ttru_1798, retro_ttru_951,
Xenopus tropicalis ENSXETG000000075091 retrocopy
retro_xtro_63,


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