RetrogeneDB ID: | retro_dnov_51 | ||
Retrocopy location | Organism: | Armadillo (Dasypus novemcinctus) | |
| Coordinates: | GeneScaffold_1019:210283..210877(-) | ||
| Located in intron of: | ENSDNOG00000008173 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | CA2 | ||
| Ensembl ID: | ENSDNOG00000005408 | ||
| Aliases: | None | ||
| Description: | carbonic anhydrase II [Source:HGNC Symbol;Acc:1373] |
Retrocopy-Parental alignment summary:
>retro_dnov_51
CATCACTGGGGAGACAGCAAGCACAATGGACCCAAGCACTGGCCTGAGACATTCCCCATTGCCAAGTCAGAGTATCAATC
TCCTTTAGACATTAAAACCTAAGCAGCCAAGCACCACTCTGCCCTGTAGCCTCTATGCATTTGCTGTAAGGAAGTGATAT
CTTGGAAGATCCTCAACAATGGTCACACTTTCAAGCTGGAGTTTGATGACTCCCAGGACAAAGCAGTGCGGAAAGAAGGA
CCCTTCACTGACACTTAGAGAGTGACTCAGTTTCATTTTCACTGGGGATCTTCTGATAAGCAAGGTTCTTAGTGTACTGT
GGACAAAAAGAAATATGCTACAGAGCAGTAGCTGGTTCATTGGAACACCAAATATGGGGATTTTGGAAAAAGCATGCAAC
AACCTGATGGACTAGTTGTTTGTGGGTATTTTTTTGAAGGTTGGCAGTGCTAAACTAGGCTGTCAGAAAGTTACTGATGT
CCTAGATTCCATTAAAACAAAGGGTAGAGCCTTGAATTCACTAACTTTGATCCTCATGGCCTCCTTCCTGAGAGCTTAGA
CTACTGGACCTATCCAGGCTCACTAACCACCCCC
ORF - retro_dnov_51 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 67.5 % |
| Parental protein coverage: | 76.15 % |
| Number of stop codons detected: | 5 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | NHWGYSKHNGPEHWHKTFPLADGERQSPVDIDTAAVKHDPALQPLSIHYEEASSQKILNSGHSFSVEFDD |
| .HWG.SKHNGP.HW..TFP.A..E.QSP.DI.T.A.KH..AL.PL.I...E..S.KILN.GH.F..EFDD | |
| Retrocopy | HHWGDSKHNGPKHWPETFPIAKSEYQSPLDIKT*AAKHHSAL*PLCICCKEVISWKILNNGHTFKLEFDD |
| Parental | SQDKAVLKGGPLTGTYRLIQFHFHWGSSDHEGSEHSVDKQKYAAELHFVHWNTKYGEFKKAVEHPDGLAV |
| SQDKAV.K.GP.T.T.R..QFHFHWGSSD..GS...VDK.KYA.E...VHWNTKYG.F.K....PDGL.V | |
| Retrocopy | SQDKAVRKEGPFTDT*RVTQFHFHWGSSDKQGS*CTVDKKKYATEQ*LVHWNTKYGDFGKSMQQPDGLVV |
| Parental | -LGIFLKVGSARPGLQKVVDVLDSIKAKGK-SAAFTDFDPTGLLPEKLDYWTYPGSLTTP |
| ..GIFLKVGSA..G.QKV.DVLDSIK.KG..S..FT.FDP.GLLPE.LDYWTYPGSLTTP | |
| Retrocopy | >VGIFLKVGSAKLGCQKVTDVLDSIKTKGR<SLEFTNFDPHGLLPESLDYWTYPGSLTTP |
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 | 7 .39 RPM |
| SRP012922_cerebellum | 0 .00 RPM | 47 .84 RPM |
| SRP012922_heart | 0 .46 RPM | 2 .32 RPM |
| SRP012922_kidney | 0 .00 RPM | 264 .76 RPM |
| SRP012922_liver | 0 .00 RPM | 22 .76 RPM |
| SRP012922_lung | 0 .00 RPM | 29 .93 RPM |
| SRP012922_quadricep_muscle | 0 .00 RPM | 3 .46 RPM |
| SRP012922_spleen | 0 .00 RPM | 343 .73 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_51 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 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Dasypus novemcinctus | ENSDNOG00000005408 | 1 retrocopy |
retro_dnov_51 ,
|
| Dasypus novemcinctus | ENSDNOG00000010755 | 1 retrocopy | |
| Sarcophilus harrisii | ENSSHAG00000008895 | 1 retrocopy |