RetrogeneDB ID: | retro_ocun_1669 | ||
Retrocopy location | Organism: | Rabbit (Oryctolagus cuniculus) | |
| Coordinates: | GL018752:598277..599469(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | GFPT1 | ||
| Ensembl ID: | ENSOCUG00000029568 | ||
| Aliases: | None | ||
| Description: | glutamine--fructose-6-phosphate transaminase 1 [Source:HGNC Symbol;Acc:4241] |
Retrocopy-Parental alignment summary:
>retro_ocun_1669
CTTCAGGGACTGGAATATAGAGGATACGATTCTGCTGGTGTGGGAGTTGATGGAGGCAATGACAAAGAACTGGGAAGCCA
ATGCCTGCAAAATCCAGCTCATTAAGAAGAAAGGAAAAGTTAAGGCACTGGATGAAGAAGTCTACAAACAACAGGCTATG
GATTTGGATATAGAATTTGATGTCCACCTTGGAATGGCTCATACCTGTTGGGCAACACATGGAGAACCCAATCCTGTCAA
TAGCCACCCGCAGCGCTCTGATAAAAATAGCGAATTTATTGTCATTCACAATGGAATCATCACTAACTACAAAGACTTGA
AAAAGTTTTTGGAGAGCAAAGGCTATGGCTTTGAAACTGAAACAGACACAGAGACAATCGCCAAGCTTGTTTAGTATATG
TATGACAATCGGGAAAGTCAAGATATCAGTTCTACAACCTTGGTGGAGACAGTTATCCAACAACTGGAAGGTTCTTTTGC
ACTTGTGTTTAAGAGCGTTCATTTCCCTGGTCAAGCAGTTGGCACAAGGTGAGGTAGCCCTCTGCTGACTGGTGTACAGA
GTGAACATAAAATTTCTATTGATCACATTCTGATACTGTACAGAAGAGGCAAAGACAAGAAGGGGAGCTGCAATCTCTCA
TGTGGACAGCACAACTTGCCTTTTCCCTGTTGAAGAAAAAGCAGTGGAATATTACTTTGCTTCTGATGCAAGTGCTGCCA
TAGAACATACCAACCACGTCATCTTTCTAGAAGATGATGATGTTGCAGCAGTGGTGGATGGCCGTTTTTCTATCCATCGA
ATTAAATGGACTGCAGGAGATCACCCTGGATGAGCTGTGCAAACCCTGCAGATGGAACTCCTACAGATCATAAAGGGCAA
TTTCAGTTCATTTATGCAGAAGGAAATTTTTGAGCAGCCAGAGTCCATGATGAACACAATGAAAGGAAGAATCAACTTTA
ATGACTATGCTGTGAATCTGGGTGGTATGAAGGATCACATTAAGGAGATCCAGAGGTGTCAGTTCTGATCCCTGTTGCCT
GTGGAACGAGTTACCATGCTGGAGTAGCAACACATCCAGTTCTGGAGGAGCTGACAGAGTTGCCTGTGATGGTGGAAGTA
GCCAGTGACTTCTTGGAGAGAAACACGCCAGTCTTTCAAGATGACATTTGCTTTTTCATCAGTCAGTCAGGT
ORF - retro_ocun_1669 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 86.78 % |
| Parental protein coverage: | 78.04 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | LQRLEYRGYDSAGVGVDGGNDKD-WEANACKIQLIKKKGKVKALDEEVHKQQDMDLDIEFDVHLGIAHTR |
| LQ.LEYRGYDSAGVGVDGGNDK..WEANACKIQLIKKKGKVKALDEEV.KQQ.MDLDIEFDVHLG.AHT. | |
| Retrocopy | LQGLEYRGYDSAGVGVDGGNDKE>WEANACKIQLIKKKGKVKALDEEVYKQQAMDLDIEFDVHLGMAHTC |
| Parental | WATHGEPNPVNSHPQRSDKNNEFIVIHNGIITNYKDLKKFLESKGYDFESETDTETIAKLVKYMYDNRES |
| WATHGEPNPVNSHPQRSDKN.EFIVIHNGIITNYKDLKKFLESKGY.FE.ETDTETIAKLV.YMYDNRES | |
| Retrocopy | WATHGEPNPVNSHPQRSDKNSEFIVIHNGIITNYKDLKKFLESKGYGFETETDTETIAKLV*YMYDNRES |
| Parental | QDISFTTLVERVIQQLEGAFALVFKSVHFPGQAVGTRRGSPLLIGVRSEHKLSTDHIPILYRTGKDK-KG |
| QDIS.TTLVE.VIQQLEG.FALVFKSVHFPGQAVGTR.GSPLL.GV.SEHK.S.DHI.ILYR.GKDK..G | |
| Retrocopy | QDISSTTLVETVIQQLEGSFALVFKSVHFPGQAVGTR*GSPLLTGVQSEHKISIDHILILYRRGKDK>RG |
| Parental | SCNLSRVDSTTCLFPVEEKAVEYYFASDASAVIEHTNRVIFLEDDDVAAVVDGRLSIHRIKRTAGDHPGR |
| ....S.VDSTTCLFPVEEKAVEYYFASDASA.IEHTN.VIFLEDDDVAAVVDGR.SIHRIK.TAGDHPG. | |
| Retrocopy | AA-ISHVDSTTCLFPVEEKAVEYYFASDASAAIEHTNHVIFLEDDDVAAVVDGRFSIHRIKWTAGDHPG* |
| Parental | AVQTLQMELQQIMKGNFSSFMQKEIFEQPESVVNTMRGRVNFDDYTVNLGGLKDHIKEIQRCR-RLILIA |
| AVQTLQMEL.QI.KGNFSSFMQKEIFEQPES..NTM.GR.NF.DY.VNLGG.KDHIKEIQRC...LI..A | |
| Retrocopy | AVQTLQMELLQIIKGNFSSFMQKEIFEQPESMMNTMKGRINFNDYAVNLGGMKDHIKEIQRCQ<VLIPVA |
| Parental | CGTSYHAGVATRQVLEELTELPVMVELASDFLDRNTPVFRDDVCFFISQSG |
| CGTSYHAGVAT..VLEELTELPVMVE.ASDFL.RNTPVF.DD.CFFISQSG | |
| Retrocopy | CGTSYHAGVATHPVLEELTELPVMVEVASDFLERNTPVFQDDICFFISQSG |
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 .33 RPM | 12 .14 RPM |
| SRP017611_kidney | 0 .41 RPM | 20 .17 RPM |
| SRP017611_liver | 0 .23 RPM | 2 .70 RPM |
Oryctolagus cuniculus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ocun_1669 retrocopy.
Oryctolagus cuniculus was not studied using FANTOM5 data.
retro_ocun_1669 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ocun_1669 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 | |
|---|---|---|---|
| Oryctolagus cuniculus | ENSOCUG00000029568 | 1 retrocopy |
retro_ocun_1669 ,
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