RetrogeneDB ID: | retro_rnor_2414 | ||
Retrocopy location | Organism: | Rat (Rattus norvegicus) | |
| Coordinates: | 7:5720881..5722130(+) | ||
| Located in intron of: | ENSRNOG00000047228 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Psmc4 | ||
| Ensembl ID: | ENSRNOG00000018994 | ||
| Aliases: | Psmc4, Tbp7 | ||
| Description: | 26S protease regulatory subunit 6B [Source:UniProtKB/Swiss-Prot;Acc:Q63570] |
Retrocopy-Parental alignment summary:
>retro_rnor_2414
GAGATAGGCATTTTGGTGGAGAAAATTCAGGATGAGATGCCAGCACTGTCCGTGTCTCGGCTGCAGACTGGTCTGTCCTT
TCTGCAACCTGAACCTGAAGACCTGGAGGACGTATACAGCCTCTACAAGAAGCTGTAGCAAGAGCTGGAGTTCCTGGAGG
TGCAGGAGGAATATATCAAGGATGAACAGAAGAACCTGAAGAAGGAGTTCCTCCATGCCCAGGAGGAGGTAAAGCAAATC
CAGAGCATTCCGTTGGTCATTGGTCAGTTTTTGGAAGTTGTGGATCAGAACACAACCATTGTGGGCTCTACCACAGGCTC
TAACTGTTATGTGTGCATCCTGAGTACCATTGATCGGGAGCTGCTCAAACCCAATGCCTCAGTGACCCTCCACAAGCACA
GCAACGCACTGGTGAATGTGCTGCCTCCCGAGGCCGAAAGCAGCATCATGATGCTCACCTCAGACCAGAAGCCCAACGTG
ATGTACGCTGATACAGGAAGCATGGACATCCAGAAACAGGAGGTGCGGGAGGCAATGGAACTCCCACTTACACACTTCGA
GCTCTACAAGCAGGTTGGCATCGATCCTCCCTGAGGGGTCCTCATGTATGGCCCACCTGGCTGTGGAAAGACCATGTTAG
AAAAGGCAGTGGCACATCACATGACAGCTGCATTTATCCGTGTGGTGGGTTCAGAGTTTGTTCATAAGTACCTGGGTGAG
GGCCCCCGAATGATCTGGGATGTGTTCCTCCTGGACAAGGAGAATGCACCTGCCATCATCTTCATAGATGAAATTGATGC
CATTGCCACCAAGAGATTCGATGCCCAGACCGGAGCTGACAGGGAGGTTCAGAGGATCCTGCTGGAGCTACTGAATCAAA
TGGATGGATTTGACCAAAACATCAGTGTGAAGGCAATCATGGCCACAAACAGAACAGACACCTTGGATCCAACTCTACTT
CGGCCAGGACGCCTAGACCACAAAATTGAATTCCCACTCCCTGATCGTCACCAAAAAGAGGTTGATTTTCTCCACCATCA
CCAGCAAGATGAACCTTTCTGAGGAGGTCGACCTAGAAGACTATGTGGCCTGCCCAGATAAGATTTCAGGAGCCGATATC
AACTCCATCTGTCAGGAGACTGGAATGTTGACTGTCTGTGAGAACCGCTACATTGTCCTGGCCAAAGACTTCGAGAAAGC
ATACAAGACCGTGATCAAGAAAGATGAGCAGGAACATGAGTTTTACAAG
ORF - retro_rnor_2414 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 90.65 % |
| Parental protein coverage: | 99.52 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | EIGILVEKIQDEIPALSVSRPQTGLSFLGPEPEDLEDLYSRYKKLQQELEFLEVQEEYIKDEQKNLKKEF |
| EIGILVEKIQDE.PALSVSR.QTGLSFL.PEPEDLED.YS.YKKL.QELEFLEVQEEYIKDEQKNLKKEF | |
| Retrocopy | EIGILVEKIQDEMPALSVSRLQTGLSFLQPEPEDLEDVYSLYKKL*QELEFLEVQEEYIKDEQKNLKKEF |
| Parental | LHAQEEVKRIQSIPLVIGQFLEAVDQNTAIVGSTTGSNYYVRILSTIDRELLKPNASVALHKHSNALVDV |
| LHAQEEVK.IQSIPLVIGQFLE.VDQNT.IVGSTTGSN.YV.ILSTIDRELLKPNASV.LHKHSNALV.V | |
| Retrocopy | LHAQEEVKQIQSIPLVIGQFLEVVDQNTTIVGSTTGSNCYVCILSTIDRELLKPNASVTLHKHSNALVNV |
| Parental | LPPEADSSIMMLTSDQKPDVMYADIGGMDIQKQEVREAVELPLTHFELYKQIGIDPPRGVLMYGPPGCGK |
| LPPEA.SSIMMLTSDQKP.VMYAD.G.MDIQKQEVREA.ELPLTHFELYKQ.GIDPP.GVLMYGPPGCGK | |
| Retrocopy | LPPEAESSIMMLTSDQKPNVMYADTGSMDIQKQEVREAMELPLTHFELYKQVGIDPP*GVLMYGPPGCGK |
| Parental | TMLAKAVAHHTTAAFIRVVGSEFVQKYLGEGPRMVRDVFRLAKENAPAIIFIDEIDAIATKRFDAQTGAD |
| TML.KAVAHH.TAAFIRVVGSEFV.KYLGEGPRM..DVF.L.KENAPAIIFIDEIDAIATKRFDAQTGAD | |
| Retrocopy | TMLEKAVAHHMTAAFIRVVGSEFVHKYLGEGPRMIWDVFLLDKENAPAIIFIDEIDAIATKRFDAQTGAD |
| Parental | REVQRILLELLNQMDGFDQNVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQ-KRLIFSTITSK |
| REVQRILLELLNQMDGFDQN..VK.IMATNR.DTLDP.LLRPGRLD.KIEFPLPDR.Q.KRLIFSTITSK | |
| Retrocopy | REVQRILLELLNQMDGFDQNISVKAIMATNRTDTLDPTLLRPGRLDHKIEFPLPDRHQ>KRLIFSTITSK |
| Parental | MNLSEEVDLEDYVARPDKISGADINSICQESGMLAVRENRYIVLAKDFEKAYKTVIKKDEQEHEFYK |
| MNLSEEVDLEDYVA.PDKISGADINSICQE.GML.V.ENRYIVLAKDFEKAYKTVIKKDEQEHEFYK | |
| Retrocopy | MNLSEEVDLEDYVACPDKISGADINSICQETGMLTVCENRYIVLAKDFEKAYKTVIKKDEQEHEFYK |
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 | 51 .98 RPM |
| SRP017611_kidney | 0 .07 RPM | 62 .32 RPM |
| SRP017611_liver | 0 .00 RPM | 43 .23 RPM |
Rattus norvegicus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_rnor_2414 retrocopy.
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_2414 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_rnor_2414 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 | |
|---|---|---|---|
| Pteropus vampyrus | ENSPVAG00000004372 | 1 retrocopy | |
| Rattus norvegicus | ENSRNOG00000018994 | 2 retrocopies |
retro_rnor_1952, retro_rnor_2414 ,
|