RetrogeneDB ID: | retro_btau_1287 | ||
Retrocopy location | Organism: | Cow (Bos taurus) | |
| Coordinates: | 3:80749506..80750066(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | CYB5R3 | ||
| Ensembl ID: | ENSBTAG00000016516 | ||
| Aliases: | None | ||
| Description: | NADH-cytochrome b5 reductase 3 [Source:RefSeq peptide;Acc:NP_001096720] |
Retrocopy-Parental alignment summary:
>retro_btau_1287
AGCACTGCGCCCTAGCCATTTGAAATCCCAGATATCAAGTACTCACTGTGGCTTATTGATGAGGAGATTATCAGCCATAA
CACCAGTGGTTCTACTTCAACCTGCTATATCCCCATCACATCTTGGACCCCCTCATAAGTCATCACATCTAATTTTCAGT
TCAAATCCACCACAACCTAATCACTCAGCCCTACAGCATTTCCAGGCATGATGAAGGGGCTTGATGGGCCCAGTGATCAA
GGTTTACTTCAAAGATACCCATCCCATGTTTCCTATTGGAAGATGTTCCAGTACCTGGAAAACATGAAGACTGGAGACAT
CATTGAGTTTCAGCGCCCAATCTGGCTGCTAGCCTACCAGGGCAAAGAAAAGTTTGCCCTCTGTCCAGACCAGAAATTCA
AGCTCATTATCAAGAGGTGAAGTCTATTCATATGATCATGAGAGGAACAAGCATCACTTTGATGCTATGGGTGATCCACG
CCATCATGAGGGACCTGGATGACCACCCTGTGTGCCAACTGCTCTTTGCTGGTCAGAAAAAGAAGGACATTTTGTTGCAG
ORF - retro_btau_1287 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 50.52 % |
| Parental protein coverage: | 62.91 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 4 |
Retrocopy - Parental Gene Alignment:
| Parental | STPAITLENPDIKYPLRLIDKEVISHDT-RRFRFALPSPEHILGLPVGQHIYLSARIDGNLVIRPYTPVS |
| ST.....E.PDIKY.L.LID.E.ISH.T...F.F.L..P.HIL......HI..S..I..NL...PY...S | |
| Retrocopy | STAP*PFEIPDIKYSLWLIDEEIISHNT<QWFYFNLLYPHHILDPLISHHI*FSVQIHHNLITQPYS-IS |
| Parental | SDDD-KGFVDLVIKVYFKDTHPKFPAGGKMSQYLESMKIGDTIEFRGPNG-LLVYQGKGKFAIRPDKKSD |
| ..D...G....VIKVYFKDTHP.FP..G..S.............F....G.LL.YQGK.KFA..PD.K.. | |
| Retrocopy | RHDE<RGLMGPVIKVYFKDTHPMFPI-GRCSSTWKT*RLETSLSFSAQSG<LLAYQGKEKFALCPDQKFK |
| Parental | PVIK-TVKSVGMIAGGTGITPMLQVIRAIMKDPDDHTVCHLLFANQTEKDILLR |
| ..IK..VKS..MI..GT.IT.ML.VI.AIM.D.DDH.VC.LLFA.Q..KDILL. | |
| Retrocopy | LIIK<EVKSIHMIMRGTSITLMLWVIHAIMRDLDDHPVCQLLFAGQKKKDILLQ |
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 |
|---|---|---|
| ERP005899_liver | 0 .00 RPM | 103 .89 RPM |
| ERP005899_muscle | 0 .05 RPM | 193 .16 RPM |
| SRP017611_brain | 0 .00 RPM | 102 .69 RPM |
| SRP017611_kidney | 0 .00 RPM | 247 .28 RPM |
| SRP017611_liver | 0 .08 RPM | 183 .41 RPM |
| SRP030211_testis | 0 .39 RPM | 96 .75 RPM |
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_1287 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_1287 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_btau_1287 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 4 parental genes, and 6 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Ailuropoda melanoleuca | ENSAMEG00000009549 | 1 retrocopy | |
| Bos taurus | ENSBTAG00000016516 | 2 retrocopies |
retro_btau_1244, retro_btau_1287 ,
|
| Pteropus vampyrus | ENSPVAG00000014126 | 1 retrocopy | |
| Tursiops truncatus | ENSTTRG00000015143 | 2 retrocopies |