RetrogeneDB ID: | retro_rnor_1382 | ||
Retrocopy location | Organism: | Rat (Rattus norvegicus) | |
| Coordinates: | 18:3357438..3358197(-) | ||
| Located in intron of: | ENSRNOG00000012795 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Slc25a19 | ||
| Ensembl ID: | ENSRNOG00000003918 | ||
| Aliases: | None | ||
| Description: | mitochondrial thiamine pyrophosphate carrier [Source:RefSeq peptide;Acc:NP_001007675] |
Retrocopy-Parental alignment summary:
>retro_rnor_1382
GTGGAGGTGGTGGCGGCAGGATCAGTGTCAGGATTTGTCACTTGTGTCCTGATCAGCCTTTCGAACGTCATCGAGATCTG
TTTCCAGCTCCAGATTGAACACCTGTGTCCAAGTGACCCCAATGCCAAATACCACAGAATCTTCCAGGCGGCCAAGCATA
TTTTGTAAGAGGAGGGTCCAAGAGCGTCCTGGAAAGGACATGTTCCAGCCCAGATTCTGTCCATAGGCTACGGAGAGGTC
CAATTTTTGGCCTTTGAAGAACTGACTGAACTGCTTTACCGAGCCAACTTGTAATCAAACCCACCAATTCTCAGTGCACT
TTGTACATGGTGGCCTGTCTGCCGGTACAGCCACCCTCACCGTGCACCCTGTGGATGTGCTACACACCTGCCTAGCAGCT
CGGATCTATAACAATCTGCAAGAGGCCATACGGACCATGTATAGGACCAAGGGCCCCTTCATCTTCTACAAAGGCTTGAC
CCCCACCATGATCACCATCTTCCCCTCTATGGGCCTGCAGTTCTCCTGCTGCCACTCATTATTGAACCATGCCTATGACT
GGGTCATACCTACAGACAGAAGCAAACAGGGAACCTTAAAAACCTGCTTTGTAGCTGTGGATCTGGAGTCATCAGCAAGA
TCCTTACATATCCCCTGGACCTCTTCAAGAAGCCCCTACAGGTGGGTGGGTTTGAACATATCCTATCTGCCTTTCGCTGG
CTGCAGAGCTATGGGGACCTCCTAGACATCTCCACACAG
ORF - retro_rnor_1382 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 75.29 % |
| Parental protein coverage: | 80.5 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | LEVAVAGSVSGFVTRALISPLDVIKIRFQLQLERVCPSDPNAKYHGILQAAKQILQEEGPRAFWKGHVPA |
| .EV..AGSVSGFVT..LIS...VI.I.FQLQ.E..CPSDPNAKYH.I.QAAK.IL.EEGPRA.WKGHVPA | |
| Retrocopy | VEVVAAGSVSGFVTCVLISLSNVIEICFQLQIEHLCPSDPNAKYHRIFQAAKHIL*EEGPRASWKGHVPA |
| Parental | QILSIGYGAVQFLAFEELTELLYQANL-YQTHQFSAHFVCGGLSAGTATLTVHPVDVLRTRLAAQGEPKI |
| QILSIGYG.VQFLAFEELTELLY.ANL..QTHQFS.HFV.GGLSAGTATLTVHPVDVL.T.LAA.....I | |
| Retrocopy | QILSIGYGEVQFLAFEELTELLYRANL>NQTHQFSVHFVHGGLSAGTATLTVHPVDVLHTCLAA----RI |
| Parental | YSNLREAIRTMYRTEGPFVFYKGLTPTVIAIFPYAGLQFSCYRS-LKRAYDWIMPPD-GKQTGNLKNLLC |
| Y.NL.EAIRTMYRT.GPF.FYKGLTPT.I.IFP..GLQFSC..S.L..AYDW..P.D..KQTGNLKNLLC | |
| Retrocopy | YNNLQEAIRTMYRTKGPFIFYKGLTPTMITIFPSMGLQFSCCHSLLNHAYDWVIPTD<QKQTGNLKNLLC |
| Parental | GCGSGVISKTLTYPLDLFKKRLQVRGFEHARSAFGQVRSYRGLLDLAQQ |
| .CGSGVISK.LTYPLDLFKK.LQV.GFEH..SAF....SY..LLD...Q | |
| Retrocopy | SCGSGVISKILTYPLDLFKKPLQVGGFEHILSAFRWLQSYGDLLDISTQ |
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 | 10 .64 RPM |
| SRP017611_kidney | 0 .00 RPM | 11 .93 RPM |
| SRP017611_liver | 0 .00 RPM | 3 .50 RPM |
Rattus norvegicus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_rnor_1382 retrocopy.
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_1382 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_rnor_1382 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Macropus eugenii | ENSMEUG00000008772 | 1 retrocopy | |
| Rattus norvegicus | ENSRNOG00000003918 | 2 retrocopies |
retro_rnor_12, retro_rnor_1382 ,
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