RetrogeneDB ID:

retro_dnov_2514

Retrocopy
location
Organism:Armadillo (Dasypus novemcinctus)
Coordinates:scaffold_81790:2292..2902(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:GHITM
Ensembl ID:ENSDNOG00000018880
Aliases:None
Description:growth hormone inducible transmembrane protein [Source:HGNC Symbol;Acc:17281]


Retrocopy-Parental alignment summary:






>retro_dnov_2514
TATACGTACTTAGCAGGAATATTGGCTTAACAGCTTTGTTTGGCCTTGAAGGGAGCAGATCTCCTGTTCTTATGACCTTC
ATGATGTAAGGCTCTTGGGTGACAAATGGTGCAACCTTTGTAGCCACGATTGGAGTTGGAATGCTGGTGTGAATGATACC
CTATGACCAGAGTCCTGCCTGGCCCAAACATTTTACTTGGTTGCTATACTGTGGTATGATGGTGCAGTAGAGGCTCTTCT
GGCAATATTAGGGGTCGTTTTCTCAGCAGAGCTGCTTGGTACAGAGCCAGCATTGTGAGCAGCCTCTCCACTGTGGCCAT
GTGTGCTCCCAGAGAGAAATTTATGGACATGAGCATACCCCTGGAGTGGGCTTAGTCTCTTCTTTGTGTTCTTATGGGGC
TCTATGTTTCTTCCACCTACCACAGTGGCTGGTGCCACTCTGTACTCAGTGGCAATTTACCATGGATTAGTTCTTTTTAG
CATGCTCCTCTTGTTTGACACCCGGAAAGTAATCAGGTGTACCTAAGTAGTACCATTATATGGAGATCAAAAATATGATC
CCATTGTTTCGATGATGGGAATATACATGGATACATTAAATATATTTATG

ORF - retro_dnov_2514 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 69.05 %
Parental protein coverage: 59.24 %
Number of stop codons detected: 3
Number of frameshifts detected 5


Retrocopy - Parental Gene Alignment:

ParentalYMYLAG-SIGLTALSALAMTRSPALMGFMMRGSWVTIGATFAAMIGAGMLVRSIPYDQSPG-PKHLAWLL
Y.YLAG..IGLTAL..L...RSP.LM.FMM.GSWVT.GATF.A.IG.GMLV..IPYDQSP..PKH..WLL
RetrocopyYTYLAG<NIGLTALFGLEGSRSPVLMTFMM*GSWVTNGATFVATIGVGMLV*MIPYDQSPAWPKHFTWLL
ParentalHSGVM-GAVVAPLAILG-GPLLIRAAWYTAGIVGGLSTVAMCAPSEKFMNMGAPL-GVGL-GLVFVSSLG
..G.M.GAV.A.LAILG.G..L.RAAWY.A.IV..LSTVAMCAP.EKFM.M..PL.GVGL..L.FV...G
RetrocopyYCGMM<GAVEALLAILG<GRFLSRAAWYRASIVSSLSTVAMCAPREKFMDMSIPL<GVGL<SLFFVFLWG
ParentalSMFLPPTTVAGATLYSVAVYGGLVLFSMFLLYDTQKVIWRAEGAPLYGVQKYDPINT--GIYIDALNLFM
SMFLPPTTVAGATLYSVA.Y.GLVLFSM.LL.DT.KVI......PLYG.QKYDPI....GIY.D.LN.FM
RetrocopySMFLPPTTVAGATLYSVAIYHGLVLFSMLLLFDTRKVIRCT*VVPLYGDQKYDPIVSMMGIYMDTLNIFM

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 .19 RPM 148 .18 RPM
SRP012922_cerebellum 0 .55 RPM 145 .30 RPM
SRP012922_heart 0 .00 RPM 71 .23 RPM
SRP012922_kidney 0 .00 RPM 130 .87 RPM
SRP012922_liver 0 .15 RPM 73 .38 RPM
SRP012922_lung 0 .31 RPM 61 .85 RPM
SRP012922_quadricep_muscle 0 .00 RPM 97 .79 RPM
SRP012922_spleen 0 .00 RPM 59 .86 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_2514 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 18 parental genes, and 28 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000097531 retrocopy
Bos taurus ENSBTAG000000328292 retrocopies
Choloepus hoffmanni ENSCHOG000000015761 retrocopy
Cavia porcellus ENSCPOG000000064321 retrocopy
Dasypus novemcinctus ENSDNOG00000018880 5 retrocopies
Dipodomys ordii ENSDORG000000011091 retrocopy
Echinops telfairi ENSETEG000000017961 retrocopy
Loxodonta africana ENSLAFG000000096461 retrocopy
Macropus eugenii ENSMEUG000000098613 retrocopies
Microcebus murinus ENSMICG000000116211 retrocopy
Monodelphis domestica ENSMODG000000016933 retrocopies
Oryctolagus cuniculus ENSOCUG000000060931 retrocopy
Otolemur garnettii ENSOGAG000000121201 retrocopy
Rattus norvegicus ENSRNOG000000139611 retrocopy
Sus scrofa ENSSSCG000000103451 retrocopy
Tupaia belangeri ENSTBEG000000163652 retrocopies
Tarsius syrichta ENSTSYG000000063671 retrocopy
Drosophila melanogaster FBgn00302631 retrocopy



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