RetrogeneDB ID: | retro_ocun_1564 | ||
Retrocopy location | Organism: | Rabbit (Oryctolagus cuniculus) | |
| Coordinates: | GL018700:1309550..1310381(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | SLC35A3 | ||
| Ensembl ID: | ENSOCUG00000015538 | ||
| Aliases: | None | ||
| Description: | solute carrier family 35 (UDP-N-acetylglucosamine (UDP-GlcNAc) transporter), member A3 [Source:HGNC Symbol;Acc:11023] |
Retrocopy-Parental alignment summary:
>retro_ocun_1564
AAGATAATGGCCTGTATTTTATTAGTTTACAAAGACAACAAGTGTAGTCTAAGAGCACTGAGCTGAGTACGACACGAAGA
GATTCTTAATAAACCCATGGAAACACTTAAACTTGCTATTTCAACAGGGATATATACTCTTCAGAATAATTTGCTCTATG
TGGCTCTGTCAGATCTAGATGCAGCTGCTTATCAGGTCATGTATCAGTTGAAAATTCTTACAACAGCGTTATATTCTGTG
TCTATGCTTAGTAAAAAATTAGATGTGTACCAGTGGCTTTCCCTATTAATTTTGATGACAGGAGTTGCTTTTGTTCAGTG
GCCCTCAGATTCTCAAGAACTTGAATCTAAGGAACTTTCGGTTGGCTCTCAGTTTGTAGGCCTCATGGCAATTCTCACAG
CATGTTTTTTAAGTGGCTTTGCTGGTGTTTATTTTGAGAAAATATTAAAAGAAACTAAATAATCAGTATGGATAAGAAAC
ATTCAGCTTGGTTTCTTTGGGAGTATATTTGGATTAATGGCTATATATATTTATGATGGAGAATTGGTATCCAAGAATGG
ATTCTTTCAGGGATATAACCAATTGACCTGGATAGTTGTTGCTCTTCAGGCACTTGGAGGCCATGTAGTGGCTGCTGTTA
TTAAGTATGTGGATAATATTTTAAAAGGATTCGCAACGTCTTTGTCTATAATATTATCAACACTGATATCCTATTTTTGG
CTACAAGATTTTGTGCCAATGAGTGTCTTTTTCCTTGGAGCCATCCTTGTAATAACAGCTACTTTCTTATATGGTTATGA
TCCCAAGACTGCAGGAAACCTCACTAAAGCA
ORF - retro_ocun_1564 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 92.42 % |
| Parental protein coverage: | 78.03 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | KIMACILLVYKDNKCSLRALNRVLHDEILNKPMETLKLAIPSGIYTLQNNLLYVALSNLDAATYQVTYQL |
| KIMACILLVYKDNKCSLRAL..V.H.EILNKPMETLKLAI..GIYTLQNNLLYVALS.LDAA.YQV.YQL | |
| Retrocopy | KIMACILLVYKDNKCSLRALS*VRHEEILNKPMETLKLAISTGIYTLQNNLLYVALSDLDAAAYQVMYQL |
| Parental | KILTTALFSVSMLSKKLGVYQWLSLLILMTGVAFVQWPSDSQELDSKELSAGSQFVGLMAVLTACFSSGF |
| KILTTAL.SVSMLSKKL.VYQWLSLLILMTGVAFVQWPSDSQEL.SKELS.GSQFVGLMA.LTACF.SGF | |
| Retrocopy | KILTTALYSVSMLSKKLDVYQWLSLLILMTGVAFVQWPSDSQELESKELSVGSQFVGLMAILTACFLSGF |
| Parental | AGVYFEKILKETKQSVWIRNIQLGFFGSIFGLMAVYIYDGELVSKNGFFQGYNQLTWIVVALQALGGLVV |
| AGVYFEKILKETK.SVWIRNIQLGFFGSIFGLMA.YIYDGELVSKNGFFQGYNQLTWIVVALQALGG.VV | |
| Retrocopy | AGVYFEKILKETK*SVWIRNIQLGFFGSIFGLMAIYIYDGELVSKNGFFQGYNQLTWIVVALQALGGHVV |
| Parental | AAVIKYADNILKGFATSLSIILSTLISYFWLQDFVPTSVFFLGAILVITATFLYGYDPKPAGNLTKA |
| AAVIKY.DNILKGFATSLSIILSTLISYFWLQDFVP.SVFFLGAILVITATFLYGYDPK.AGNLTKA | |
| Retrocopy | AAVIKYVDNILKGFATSLSIILSTLISYFWLQDFVPMSVFFLGAILVITATFLYGYDPKTAGNLTKA |
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 | 1 .60 RPM |
| SRP017611_kidney | 0 .00 RPM | 8 .11 RPM |
| SRP017611_liver | 0 .00 RPM | 18 .88 RPM |
Oryctolagus cuniculus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ocun_1564 retrocopy.
Oryctolagus cuniculus was not studied using FANTOM5 data.
retro_ocun_1564 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ocun_1564 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 4 parental genes, and 5 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Choloepus hoffmanni | ENSCHOG00000000695 | 1 retrocopy | |
| Oryctolagus cuniculus | ENSOCUG00000015538 | 2 retrocopies |
retro_ocun_1564 , retro_ocun_436,
|
| Tupaia belangeri | ENSTBEG00000004128 | 1 retrocopy | |
| Vicugna pacos | ENSVPAG00000001029 | 1 retrocopy |