RetrogeneDB ID: | retro_rnor_2602 | ||
Retrocopy location | Organism: | Rat (Rattus norvegicus) | |
| Coordinates: | 8:132076834..132077375(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Cacul1 | ||
| Ensembl ID: | ENSRNOG00000009954 | ||
| Aliases: | Cacul1, RGD1308127 | ||
| Description: | CDK2-associated and cullin domain-containing protein 1 [Source:UniProtKB/Swiss-Prot;Acc:Q5XI53] |
Retrocopy-Parental alignment summary:
>retro_rnor_2602
GATGTTGCCACCTCGGTGGTCAAGGCAGCCCCTGTCCCTACCCCTAGCTCCACCATCAACATCAACATCAACAACTTCAC
CTCCAATTTCCTAATGAATGTTATAACAATTGAAGATTATAAGAGCACATACTGGCCAAAATTAGATGGTGCCATAGATC
AACCTTTAACCCTGAGTCCTGGTGACTATATGCTTATATCCTGTGAACAGATTTACAGTTGTGTGTATAAGTGTGTGTGC
CAGAAGCACTCAGAACATATGTACAGTGATCTGATTAAAAAACATAACCAGCCACTTAGAGCGAATCTCCAAGGAGTTGC
AGGCCGACCCTCCAGACCTCTATACGGAAAGATTTAATATAGCCCCAGGACAGTATGTGGGAGCATTGCAGAGCATCATG
CCTCTTTTCATATATATGAATAAGTTTTACATAGAAACTTCGCTTAACAGAGACTTTAAAAATGACCTTGTAAAACTGTT
TATGGAACACGTTGTAGAGAAACACATTTATAGCCTAATGCCCTTTACTTTTAGAAGCCCA
ORF - retro_rnor_2602 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 75.14 % |
| Parental protein coverage: | 51.3 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | DAAAAVAKAAPA--PTPSSTININTSTSKFLMNVITIEDYKSTYWPKLDGAIDQLLTQSPGDYIPISYEQ |
| D.A..V.KAAP...P...........TS.FLMNVITIEDYKSTYWPKLDGAIDQ.LT.SPGDY..IS.EQ | |
| Retrocopy | DVATSVVKAAPVPTPSSXXXXXXXXFTSNFLMNVITIEDYKSTYWPKLDGAIDQPLTLSPGDYMLISCEQ |
| Parental | IYSCVYKCVCQQHSEQMYSDLIKK-ITSHLERVSKELQASPPDLYIERFNIALGQYMGALQSIVPLFIYM |
| IYSCVYKCVCQ.HSE.MYSDLIKK.ITSHLER.SKELQA.PPDLY.ERFNIA.GQY.GALQSI.PLFIYM | |
| Retrocopy | IYSCVYKCVCQKHSEHMYSDLIKK>ITSHLERISKELQADPPDLYTERFNIAPGQYVGALQSIMPLFIYM |
| Parental | NKFYIETKLNRDLKDDLIKLFTEHVAEKHIYSLMQWVQMAP |
| NKFYIET.LNRD.K.DL.KLF.EHV.EKHIYSLM......P | |
| Retrocopy | NKFYIETSLNRDFKNDLVKLFMEHVVEKHIYSLMPFTFRSP |
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 | 39 .40 RPM |
| SRP017611_kidney | 0 .00 RPM | 48 .78 RPM |
| SRP017611_liver | 0 .00 RPM | 30 .39 RPM |
Rattus norvegicus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_rnor_2602 retrocopy.
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_2602 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_rnor_2602 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 | ENSRNOG00000009954 | 1 retrocopy |
retro_rnor_2602 ,
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