RetrogeneDB ID: | retro_rnor_2689 | ||
Retrocopy location | Organism: | Rat (Rattus norvegicus) | |
| Coordinates: | 9:57045259..57045833(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Cyb5d1 | ||
| Ensembl ID: | ENSRNOG00000045742 | ||
| Aliases: | Cyb5d1, RGD1559567 | ||
| Description: | cytochrome b5 domain containing 1 [Source:RefSeq peptide;Acc:NP_001178819] |
Retrocopy-Parental alignment summary:
>retro_rnor_2689
AACAACCAGCCAGAAGACCTATGGTGTCTTACCTTGGATTTGTTTGCAATCTAACACTGCTTCTACAGGAATTCAAATTT
GACCTCCTGTTGAAACCCATCCTGGAGGTTGCAGGCCAGGACATTAGTCAGTGTTTTGATCCAAAGACTAAAGACATTCA
CAAGCACATAGATCCACTGACCGGTTGCATGAGATACTGCACTCGGCGGGGCTGCTTTGTGCATATCCCGCCTTCTGGTC
CCTGTTCAGACTGGGCCAATGATTTCAGAACACCCTGGTGGAAGGGGCTAAATTACCAGGTGGGAAGTCTGCCCAGACCC
AGAACATCCATATTATCAACTCTCTTACATCACAGGAGCACATACTATAGGTGGGGCCTCTGAAGTCAATGTGGGAAATC
CTACACTGCTATCTCCCCTATAATGTACATGCTGCCAGCCACACATGGAAATACAATGGGAAGAATTTGAACATGGATCA
AACCCTGGATGAAAATGGGATCCGTGATGAAGAAGAGGATTTGGAATGTGAGCTTGTCCTAGGATTGTTGCATGATGGGG
AAATGTAAGTCTAT
ORF - retro_rnor_2689 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 75.38 % |
| Parental protein coverage: | 84.65 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | HNQPEDLW-VSYLGFVYNLTPLVQEFKGDLLLKPILEVAGQDISHWFDPKTKDIRKHIDPLTGCVRYRTP |
| .NQPEDLW.VSYLGFV.NLT.L.QEFK.DLLLKPILEVAGQDIS..FDPKTKDI.KHIDPLTGC.RY.T. | |
| Retrocopy | NNQPEDLW<VSYLGFVCNLTLLLQEFKFDLLLKPILEVAGQDISQCFDPKTKDIHKHIDPLTGCMRYCTR |
| Parental | RGRFVHIPPPLPRSDWANDFGIPWWKGLNYQV-GRLSAQTRNIRIINTLTSQEHTLEVGALDSMWEILHR |
| RG.FVHIPP..P.SDWANDF..PWWKGLNYQV.G..SAQT.NI.IIN.LTSQEH.L.VG.L.SMWEILH. | |
| Retrocopy | RGCFVHIPPSGPCSDWANDFRTPWWKGLNYQV<GK-SAQTQNIHIINSLTSQEHIL*VGPLKSMWEILHC |
| Parental | YLPYNAHAASYTWKYDGKNLNMDQTLEENGIRDEEEEFDFLNMDGTLHTPAILLY |
| YLPYN.HAAS.TWKY.GKNLNMDQTL.ENGIRDEEE........G.LH......Y | |
| Retrocopy | YLPYNVHAASHTWKYNGKNLNMDQTLDENGIRDEEEDLECELVLGLLHDGEM*VY |
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 | 14 .74 RPM |
| SRP017611_kidney | 0 .00 RPM | 19 .96 RPM |
| SRP017611_liver | 0 .00 RPM | 6 .99 RPM |
Rattus norvegicus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_rnor_2689 retrocopy.
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_2689 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_rnor_2689 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Mus musculus | ENSMUSG00000044795 | 1 retrocopy | |
| Rattus norvegicus | ENSRNOG00000045742 | 1 retrocopy |
retro_rnor_2689 ,
|
| Tursiops truncatus | ENSTTRG00000010293 | 1 retrocopy |