RetrogeneDB ID: | retro_rnor_1002 | ||
Retrocopy location | Organism: | Rat (Rattus norvegicus) | |
| Coordinates: | 14:46100948..46102768(+) | ||
| Located in intron of: | ENSRNOG00000002190 | ||
Retrocopy information | Ensembl ID: | ENSRNOG00000024704 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Trim28 | ||
| Ensembl ID: | ENSRNOG00000027487 | ||
| Aliases: | Trim28, Kap1, Krip1, Tif1b | ||
| Description: | Transcription intermediary factor 1-beta [Source:UniProtKB/Swiss-Prot;Acc:O08629] |
Retrocopy-Parental alignment summary:
>retro_rnor_1002
CTGTTCTGTGAGAGCTGTGACATGCTCACTTGCCGGGACTGCCAACTCAGTGCTCACAAGAACTTGGAAGATGCAGTGAG
GAACCAACATAAACTCTTGGCTTCACTGGTGAATCGTCTTGGGGACAAACATGCCACACTGCAGAAAAACACCAAGGAGG
TTCGAAGCTCCATCCGCCAGGTGTCTGATGTGCAGAAGCGAGTGGAGGTTGATGTCAAGATGGCCATTCTGCAGATCATG
AAGGAGATGAATAAGCAAGGGGAGTTCTGGTCAATGATGCCCAGAAGGTGACTGAGGGTCAGCAGGAACATCTGGAGTGC
CAGCACTGGACCATGACCAAAATCCAGAAGCACCAGGAACACATTTTGCACTTTGCCTCTTGGGCTTTGGAGAGTAATAA
CAATACAGCCCTCTTGCTTTCTAAGAAGCTGATTTATTTCCTGCTGCATCAAGCCCTCAAAATGATTGTGGATCCTGTGG
AGCCTCATGGTGAGATGAAGTTTCAGTGGGATCTCAATACCTGGACCAAGAGTGCTGAAGCCTTTGGAAAGATTGTGGCT
AAGCGTCCTGGTACAAACTCCACGGATCCTGGGCCCATGGCTCCTCCAAGAGCCCCAGGCCCCCTAAGCAAGCAAGGTTC
TGGCAGTAGCCAGCCCATGGAAGGACAAGAGGGCTATGGCTTTGGGTCAGATGATCCATACTCAAGTGCAGAGCCACATG
TATGAGGCATGAAGCGGTCCCACTCTGGTGAGGGAGAAGTAAGTGGCCTCATGAGGAAGGTGCCACGTGTGAGCCTTGAA
CGCCTAGATCTGGATCTCACCTCTGATAGCCAGCCACCAGTCTTCCAGGTCTTCCCTGGAAGCACCACTGAGGACTACAA
TCTGATTGTTATTGAACGTGGTGCTGCTACAGCAGCCGCTGGCCAGGCTGGGTCTGTGCCACTAAGAGCCCCTCGTGCCC
CACCCCTGCCTGGCATGGCCATAGTCAAGGAAGGAGACAGAAGCTGCTATTGGAGCCCCTCCTGTGCCCCTGAGGGGCCT
GAAACCAAGCCTGTGTTGATGGCTCTGACTGAAGGCCCTGGTGCTCAGAGACCTCGTCTAACTTCACCTAGTGGCAGTAC
CAGCTCAGGCTTGGAGATGGTAGCTCCTGAGGTTACCTCAGCCCCAGTAAGTAGGCCAGGTATCCTGGATGACAGTGACA
CTATCTGCCGTGTCTGCCAGAAGCAAGGTGACCTGGTCATGTGCAACCAGTGCGAGTTTTGCTTCCACCTGGATTGTCAC
CTCCCTTTCCTGCAGGATGTTCCAGGGGAGGAATAGAGTTGCTCACTCTGCCACGTGCTCCCTGACCTAAAGGAGGAAGA
TGGAAGCCTTAGCCTGGATGGAGCAGATAGCACTGGTATGGTAGCTAAACTCTCATCAGCCAACCAGCGGAAATGTGAAC
GTGTTCTGCTGGCCTTTTTCTGCCATGAACCGTGCGGCCCCTTGCATCAGCTGGCTACCAACTCTACATTCTCCATGGAG
CAGCCTGGTGGTACCCTAGACCTGACCTTGATTCGTGCTTGTCTCCAAGAGAAGCTGTCACCTCCTTATAGCTCCCCCCA
GGAGTTTGCCCAGGATGTGGGCCACATGTTCAAAGAGTTCAATAAGCTGACTGAGGACAAGGCAGATGTTCAGTCCATCA
TCGGCCTGCAGTGCTTGAGACACATGAATGATGCCTTTGGTGACACCAAACTTTCTGCTGTGCTGGTAGAACCACCACCA
CTGAACCTTCCCAGTGCTGGCCTAAGTTCTCAGAAGCTGTCTGGTCCTGGTGATGGACCC
ORF - retro_rnor_1002 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 87.23 % |
| Parental protein coverage: | 72.69 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | LTCRDCQLNAHKDHQ---YQFLEDAVRNQRKLLASLVKRLGDKHATLQKNTKEVRSSIRQVSDVQKRVQV |
| L.C..C......D.Q......LEDAVRNQ.KLLASLV.RLGDKHATLQKNTKEVRSSIRQVSDVQKRV.V | |
| Retrocopy | LFCESCDMLTCRDCQLSAHKNLEDAVRNQHKLLASLVNRLGDKHATLQKNTKEVRSSIRQVSDVQKRVEV |
| Parental | DVKMAILQIMKELNKRGR-VLVNDAQKVTEGQQERLERQHWTMTKIQKHQEHILRFASWALESDNNTALL |
| DVKMAILQIMKE.NK.G..VLVNDAQKVTEGQQE.LE.QHWTMTKIQKHQEHIL.FASWALES.NNTALL | |
| Retrocopy | DVKMAILQIMKEMNKQGE<VLVNDAQKVTEGQQEHLECQHWTMTKIQKHQEHILHFASWALESNNNTALL |
| Parental | LSKKLIYFQLHRALKMIVDPVEPHGEMKFQWDLNAWTKSAEAFGKIVAERPGTNSTGPGPMAPPRAPGPL |
| LSKKLIYF.LH.ALKMIVDPVEPHGEMKFQWDLN.WTKSAEAFGKIVA.RPGTNST.PGPMAPPRAPGPL | |
| Retrocopy | LSKKLIYFLLHQALKMIVDPVEPHGEMKFQWDLNTWTKSAEAFGKIVAKRPGTNSTDPGPMAPPRAPGPL |
| Parental | SKQGSGSSQPMEVQEGYGFGTDDPYSSAEPHVSGMKRSRSGEGEVSGLMRKVPRVSLERLDLDLTSDSQP |
| SKQGSGSSQPME.QEGYGFG.DDPYSSAEPHV.GMKRS.SGEGEVSGLMRKVPRVSLERLDLDLTSDSQP | |
| Retrocopy | SKQGSGSSQPMEGQEGYGFGSDDPYSSAEPHV*GMKRSHSGEGEVSGLMRKVPRVSLERLDLDLTSDSQP |
| Parental | PVFKVFPGSTTEDYNLIVIERGAAAAAAGQAGTVPPGAPGAPPLPGMAIVKEEETEAAIGAPPAAPEGPE |
| PVF.VFPGSTTEDYNLIVIERGAA.AAAGQAG.VP..AP.APPLPGMAIVKE.........P..APEGPE | |
| Retrocopy | PVFQVFPGSTTEDYNLIVIERGAATAAAGQAGSVPLRAPRAPPLPGMAIVKEGD-RSCYWSPSCAPEGPE |
| Parental | TKPVLMALTEGPGAEGPRLASPSGSTSSGLEVVAPEVTSAPVSGPGILDDSATICRVCQKPGDLVMCNQC |
| TKPVLMALTEGPGA..PRL.SPSGSTSSGLE.VAPEVTSAPVS.PGILDDS.TICRVCQK.GDLVMCNQC | |
| Retrocopy | TKPVLMALTEGPGAQRPRLTSPSGSTSSGLEMVAPEVTSAPVSRPGILDDSDTICRVCQKQGDLVMCNQC |
| Parental | EFCFHLDCHLPSLQDVPGEEWSCSLCHVLPDLKEEDGSLSLDGADSTGVVAKLSPANQRKCERVLLALFC |
| EFCFHLDCHLP.LQDVPGEE.SCSLCHVLPDLKEEDGSLSLDGADSTG.VAKLS.ANQRKCERVLLA.FC | |
| Retrocopy | EFCFHLDCHLPFLQDVPGEE*SCSLCHVLPDLKEEDGSLSLDGADSTGMVAKLSSANQRKCERVLLAFFC |
| Parental | HEPCRPLHQLATDSTFSMEQPGGTLDLTLIRARLQEKLSPPYSSPQEFAQDVGRMFKQFNKLTEDKADVQ |
| HEPC.PLHQLAT.STFSMEQPGGTLDLTLIRA.LQEKLSPPYSSPQEFAQDVG.MFK.FNKLTEDKADVQ | |
| Retrocopy | HEPCGPLHQLATNSTFSMEQPGGTLDLTLIRACLQEKLSPPYSSPQEFAQDVGHMFKEFNKLTEDKADVQ |
| Parental | SIIGLQRFFETRMNDAFGDTKFSAVLVEPPPLNLPSAGLSSQELSGPGDGP |
| SIIGLQ......MNDAFGDTK.SAVLVEPPPLNLPSAGLSSQ.LSGPGDGP | |
| Retrocopy | SIIGLQCL--RHMNDAFGDTKLSAVLVEPPPLNLPSAGLSSQKLSGPGDGP |
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 | 98 .79 RPM |
| SRP017611_kidney | 0 .00 RPM | 96 .02 RPM |
| SRP017611_liver | 0 .00 RPM | 51 .91 RPM |
Rattus norvegicus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_rnor_1002 retrocopy.
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_1002 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_rnor_1002 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Procavia capensis | ENSPCAG00000007149 | 1 retrocopy | |
| Rattus norvegicus | ENSRNOG00000027487 | 1 retrocopy |
retro_rnor_1002 ,
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