RetrogeneDB ID: | retro_rnor_2919 | ||
Retrocopy location | Organism: | Rat (Rattus norvegicus) | |
| Coordinates: | X:50542915..50543786(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Slc3a2 | ||
| Ensembl ID: | ENSRNOG00000018487 | ||
| Aliases: | Slc3a2, Mdu1 | ||
| Description: | 4F2 cell-surface antigen heavy chain [Source:UniProtKB/Swiss-Prot;Acc:Q794F9] |
Retrocopy-Parental alignment summary:
>retro_rnor_2919
TACCACATTGGCAACCTTCAGGCCTTTGTAGGCCGGGAAGCAGGAAGCATAGATGATGTGAAGAACCATCTGGATTATTT
GAGAACCCTGAAGGTGAAGGGCCTAGTTTTGGGCCCAATTCACAAGAACCAGAAGGATGAAGTCAATGAAACCAACTTGA
AACAGATTGATCCCGCTTTAGGCTCCCAGGAAGATTTTTAAGACCTTCTACAAAGTGCCAAGAAAAAAGAGCATTCACAT
CATATTGGACCTCACTCCCAACTACAAGGACCAGAATGTAGTTCTTCCCTCCTCAGGCTGGCTTGTAGCCACCAAAATGA
AGGAAGCTCTGAGTACTTGGTTGCAGGACAATGTGGATGGGTTCCAAGTTTGGGATGTGGGAAAGCTGGCAAATGCATCC
TTGTACTTGACTGAGTAGAATATCACCAAGAACTTCAGTGAGGACAGGCTTTTGATTGCAGGGACTGAGTCCTCTGGCCT
GCAACAAATTGGCAACATACTTGAATCCACCAGCGACCTACTGCTAACTAGCTCATACCTGTCACAGTCCATTTTCACTG
GGAAGCACACAGGATTCTTAGTGACTAAGTATTTGAATGCCACTGGCAGTTGCTGGTTCAGCTGGAGTGAGTTGCAGGCA
AGACTCCTGACAGCTTCTATACCGGCTCAGTTTCTCTGACTCTATCAGCTGCTGCTCTTCACTCTGACAGGGACTCCTGT
TTTCAGCTATGGTGATGAGCTTGGCCTTCAGGCAGCTAACCTTTCTGGACAGCCTATGGAGGCCCCATTCATGCCGTGGA
ATGAGTCTGGCATCTCCCACACCTCAAGACCTGTAAGCCTCAACATGACAGTGAAGGGTCGGAATGAAGAC
ORF - retro_rnor_2919 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 80.55 % |
| Parental protein coverage: | 55.41 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | YRIGDLQAFVGPEARGIAGLKNHLEYLSTLKVKGLVLGPIHKNQKDEVNETDLKQIDPDLGSQEDFKDLL |
| Y.IG.LQAFVG.EA..I...KNHL.YL.TLKVKGLVLGPIHKNQKDEVNET.LKQIDP.LGSQEDF.DLL | |
| Retrocopy | YHIGNLQAFVGREAGSIDDVKNHLDYLRTLKVKGLVLGPIHKNQKDEVNETNLKQIDPALGSQEDF*DLL |
| Parental | QSAK-KKSIHIILDLTPNYKGQNAWFLPPQADIVATKMKEALSSWLQDGVDGFQVRDVGKLANASLYLAE |
| QSAK.KKSIHIILDLTPNYK.QN...LP.....VATKMKEALS.WLQD.VDGFQV.DVGKLANASLYL.E | |
| Retrocopy | QSAK>KKSIHIILDLTPNYKDQNV-VLPSSGWLVATKMKEALSTWLQDNVDGFQVWDVGKLANASLYLTE |
| Parental | WQNITKNFSEDRLLIAGTASSDLQQIVNILESTSDLLLTSSYLSQPVFTGEHAELLVIKYLNATGSRWCS |
| ..NITKNFSEDRLLIAGT.SS.LQQI.NILESTSDLLLTSSYLSQ..FTG.H...LV.KYLNATGS.W.S | |
| Retrocopy | -*NITKNFSEDRLLIAGTESSGLQQIGNILESTSDLLLTSSYLSQSIFTGKHTGFLVTKYLNATGSCWFS |
| Parental | WSVSQAGLLTSFIPAQFLRLYQLLLFTLPGTPVFSYGDELGLQAVALPGQPMEAPFMLWNESSNSQTSSP |
| WS..QA.LLT..IPAQFL.LYQLLLFTL.GTPVFSYGDELGLQA..L.GQPMEAPFM.WNES..S.TS.P | |
| Retrocopy | WSELQARLLTASIPAQFL*LYQLLLFTLTGTPVFSYGDELGLQAANLSGQPMEAPFMPWNESGISHTSRP |
| Parental | VSLNMTVKGQNED |
| VSLNMTVKG.NED | |
| Retrocopy | VSLNMTVKGRNED |
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 |
|---|---|---|
| SRP017611_brain | 0 .00 RPM | 98 .43 RPM |
| SRP017611_kidney | 0 .00 RPM | 210 .04 RPM |
| SRP017611_liver | 0 .00 RPM | 42 .29 RPM |
Rattus norvegicus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_rnor_2919 retrocopy.
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_2919 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_rnor_2919 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Rattus norvegicus | ENSRNOG00000018487 | 1 retrocopy |
retro_rnor_2919 ,
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