RetrogeneDB ID: | retro_rnor_1833 | ||
Retrocopy location | Organism: | Rat (Rattus norvegicus) | |
| Coordinates: | 3:150215483..150216665(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Dpp3 | ||
| Ensembl ID: | ENSRNOG00000031485 | ||
| Aliases: | None | ||
| Description: | Dipeptidyl peptidase 3 [Source:UniProtKB/Swiss-Prot;Acc:O55096] |
Retrocopy-Parental alignment summary:
>retro_rnor_1833
ATGGCAGATACCCAGTACATCCTGCCCAATGACATCGGTGTGTCTAGCCTGGACTGCCGGGAGGCATTCCGCCTGCTGTC
ACCCACAGAGCGCCTCTATGCCCATCACCTGTCTAGAGCCGCTTGGTATGGAGGCCTGGCTGTGCTGCTCCAGACATCTC
CTGAAGCCCCCTACATCTATGCCCTGCTTAGCCGCCTCTTCCGTGCCCAGGACCCTGACCAGCTACGCCAACATGCCCTG
GCTGAGGGCCTGACTGAAGAAGAGTATCAGGCATTCCTGGTCTACGCTGCAGGGGTCTACTCCAACATGGGCAACTATAA
GTCCTTCGGTGACACCAAGTTTGTCCCTAACCTGCCCAAGGAAAAGCTGGAGCGTGTGATCCTTGGGAGTAAGGCTGCCC
AACAGCATCCAGAAGAAGTCAGGAGCCTTTGGCAGACCTGTGGGGAGCTTATGTTCTCCCTGGAACCAAGGCTTCGACAT
CTTGGGCTGGGGAAGGAGGGAGTCACCACCTATTTCTCTGGGGATTGTGCCATGGAAGATGCCAAGCTGGCCCAGGACTT
CCTGGACTCTCAGAACCTCAGTGCATACAACACCCGGCTCTTCAAGGTGGTCGGCCAGGAAGGGAAGTACCACTATGAGG
TGCGACTGGCTTCAGTACTCAACACAGAACCTGCTCTCGACTCTGAGTTGACTTCCAAGCTGAAGAGCTACGAGTTCCAG
GGGAATCATTTCCAGGTCACCCATGGGGACTATGCCCCCATCCTCCAGAAGGTGGTAGAACACTTGGAGAAAGCTAAGGC
TTATGCAGCCAATAGCCACCAGGAGCAAATGCTGGCCCAGTATGTGGAGAGCTTCACCCAGGGTTCCATTGAGGCCCATA
AGAGGGGCTCCCGCTTCTGGATTCAGGACAAAGGTCCCATTGTAGAGAGTTACATTGGCTTCATTAAGAGCTACCGTGAC
CCCTTTGGCTCCCGAGGAGAATTTGAAGGCTTCGTGGCCATGGTAAACAAAGACATGAGTGCAAAGTTCGAGCGGCTGGT
TGCAAGTGCTGAGCAGCTGCTGAAGGAGCTGCCTTGGCCTCCTGCCTTTGAGAAGGACAAGTTCCTCACCCCTGACTTCA
CTTCCCTGGATGTCCTTACCTTTGCCGGCTCTGGCATCCCTGCAGGCATCAACATCCCCAAC
ORF - retro_rnor_1833 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 99.49 % |
| Parental protein coverage: | 53.39 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MADTQYILPNDIGVSSLDCREAFRLLSPTERLYAHHLSRAAWYGGLAVLLQTSPEAPYIYALLSRLFRAQ |
| MADTQYILPNDIGVSSLDCREAFRLLSPTERLYAHHLSRAAWYGGLAVLLQTSPEAPYIYALLSRLFRAQ | |
| Retrocopy | MADTQYILPNDIGVSSLDCREAFRLLSPTERLYAHHLSRAAWYGGLAVLLQTSPEAPYIYALLSRLFRAQ |
| Parental | DPDQLRQHALAEGLTEEEYQAFLVYAAGVYSNMGNYKSFGDTKFVPNLPKEKLERVILGSKAAQQHPEEV |
| DPDQLRQHALAEGLTEEEYQAFLVYAAGVYSNMGNYKSFGDTKFVPNLPKEKLERVILGSKAAQQHPEEV | |
| Retrocopy | DPDQLRQHALAEGLTEEEYQAFLVYAAGVYSNMGNYKSFGDTKFVPNLPKEKLERVILGSKAAQQHPEEV |
| Parental | RSLWQTCGELMFSLEPRLRHLGLGKEGVTTYFSGDCAMEDAKLAQDFLDSQNLSAYNTRLFKVVGQEGKY |
| RSLWQTCGELMFSLEPRLRHLGLGKEGVTTYFSGDCAMEDAKLAQDFLDSQNLSAYNTRLFKVVGQEGKY | |
| Retrocopy | RSLWQTCGELMFSLEPRLRHLGLGKEGVTTYFSGDCAMEDAKLAQDFLDSQNLSAYNTRLFKVVGQEGKY |
| Parental | HYEVRLASVLNTEPALDSELTSKLKSYEFQGNHFQVTRGDYAPILQKVVEHLEKAKAYAANSHQEQMLAQ |
| HYEVRLASVLNTEPALDSELTSKLKSYEFQGNHFQVT.GDYAPILQKVVEHLEKAKAYAANSHQEQMLAQ | |
| Retrocopy | HYEVRLASVLNTEPALDSELTSKLKSYEFQGNHFQVTHGDYAPILQKVVEHLEKAKAYAANSHQEQMLAQ |
| Parental | YVESFTQGSIEAHKRGSRFWIQDKGPIVESYIGFIESYRDPFGSRGEFEGFVAMVNKDMSAKFERLVASA |
| YVESFTQGSIEAHKRGSRFWIQDKGPIVESYIGFI.SYRDPFGSRGEFEGFVAMVNKDMSAKFERLVASA | |
| Retrocopy | YVESFTQGSIEAHKRGSRFWIQDKGPIVESYIGFIKSYRDPFGSRGEFEGFVAMVNKDMSAKFERLVASA |
| Parental | EQLLKELPWPPAFEKDKFLTPDFTSLDVLTFAGSGIPAGINIPN |
| EQLLKELPWPPAFEKDKFLTPDFTSLDVLTFAGSGIPAGINIPN | |
| Retrocopy | EQLLKELPWPPAFEKDKFLTPDFTSLDVLTFAGSGIPAGINIPN |
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 .14 RPM | 16 .68 RPM |
| SRP017611_kidney | 0 .07 RPM | 28 .47 RPM |
| SRP017611_liver | 0 .07 RPM | 26 .36 RPM |
Rattus norvegicus was not studied using ChIP-Seq data.
12 EST(s) were mapped to retro_rnor_1833 retrocopy
| EST ID | Start | End | Identity | Match | Mis-match | Score |
|---|---|---|---|---|---|---|
| CB611308 | 150215462 | 150215977 | 100 | 515 | 0 | 515 |
| CB696092 | 150215484 | 150215853 | 100 | 369 | 0 | 369 |
| CB712899 | 150215465 | 150215949 | 100 | 484 | 0 | 484 |
| CB733266 | 150215462 | 150215883 | 100 | 421 | 0 | 421 |
| CB738427 | 150215462 | 150215870 | 99.8 | 404 | 1 | 403 |
| CB743938 | 150215463 | 150215870 | 100 | 407 | 0 | 407 |
| CB747746 | 150215462 | 150215864 | 100 | 400 | 0 | 399 |
| CB773888 | 150215462 | 150215843 | 100 | 381 | 0 | 381 |
| CB800213 | 150215462 | 150215860 | 100 | 398 | 0 | 398 |
| CB804726 | 150215462 | 150215835 | 99.5 | 368 | 2 | 366 |
| CB809168 | 150215462 | 150215830 | 100 | 368 | 0 | 368 |
| DY315155 | 150215464 | 150216063 | 99.9 | 597 | 1 | 595 |
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_1833 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_rnor_1833 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 | |
|---|---|---|---|
| Pongo abelii | ENSPPYG00000003023 | 1 retrocopy | |
| Rattus norvegicus | ENSRNOG00000031485 | 2 retrocopies |
retro_rnor_1833 , retro_rnor_2611,
|