RetrogeneDB ID: | retro_mmus_3684 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | X:106641383..106642734(-) | ||
| Located in intron of: | ENSMUSG00000073010 | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000083595 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Zfp277 | ||
| Ensembl ID: | ENSMUSG00000055917 | ||
| Aliases: | Zfp277, 2410017E24Rik, NIRF4 | ||
| Description: | zinc finger protein 277 [Source:MGI Symbol;Acc:MGI:1890393] |
Retrocopy-Parental alignment summary:
>retro_mmus_3684
GGGCTTCCTGTGGATCCCCAGGAGGCTGGGGTCCGCGGTGGAATCGAGCACAAGTATTATGAAGACAGTAAAGACTATAT
CCTAGAGCCGCTTTCCCTGCCAGAGAGTCCAGGTGGCACCGCCGCTTTAGAGGGGTCTTTACCTGTGCCTTGTATTTTCT
GTGAAGAACATTTTTCCATGGCTGAACAATACAAACGTTTGAAGCCCATGATTATCGAGCATAAGATTGTCATAGCTGAT
GTATAGCTCGTTGCAGGTTTCCGAAGGTACATTTTATACTGGAGGAAATGGTTCACTGAACAGTCCATCACTAATTTTTG
CAGTGTGATAAGAATCAATGCCAAGGTTCCATTTGAAGAACAAGACAACTATTATTTGTTATACGATGCATTACCAGAAT
ATAGAATCCCCAGAGAAGAGCTTCAAACACAGAAACTGAAAGAAGTTCTGGATCAGCAACAGGGAGAGGGAAATGATACA
AGCTTTCATGGCGTGTGCATGTTTTGCAGTGAGGAATTTCGCTGAAACAGATCTGTTCTGTTGAACCACATGGTCAGACA
GCATGCTTTCAACATTGGTTTGCCAGACAACATTGTAAATTGCACTGAATTCCTATGCACATTACAAAAGAAACTGGACA
ATTTACAGTGTTTGTACTGTGAGAAGACCTTCAGAGACAAAAACACCCTTAAAGATCACATGAGAAAAAAAGCAGCATTG
TAGGATCAATCCAAAAAAAAAAAAAGAGAGAGAATATGACTGATTCTATGCCATCAATTACTTGGAACTTGGGAAGTAAT
GGGAAGAGGTGCAGTCAGAAGATGGCCTCAAGCTTCTGGACCTTCAGGAAGATGACTGGTCTGATTGGCAGGAGTACCCA
GTCTCTGCTGTCTGTCTATTTTGTGAAAAGCAAGAGGAAGACGATAGATAAACTGTATGTGCACATGAAGGACACACATG
AGTTTGATCTCCTCAGAATAAAGTCAGAGCTTGGATTAAATTTCTATCAGCAAGTGAAGCTGATCAATTTCATTAGAAGG
CAAGTTCACCAATGCAAGTGCTTCAGTTGCCATGTAAAGTTCAAATCCAAAGCAGATTTAAGGACTCACACGGAAGACAC
TAAACACACTTCACTGCTTCCTGACAGGAGACATGGGATCAACTGGAGTATTATTTCCCCACCTATGAGAATGACACTCT
CCTGTGTACACTGTCTGACAGTGAAAGTGACCTAACAGCTCAAGAGCAAACTTTAAATGTTCCCACCATCAGTGAAGACA
CGTCCAGACTGTGTGCTTTAAAACAGAGCAGTGTCCTCAACCAATTGCTACTCCAGGGATACCTGGAAAAC
ORF - retro_mmus_3684 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 87.28 % |
| Parental protein coverage: | 98.47 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | GLPVDPREAGVRGVRGGIGHTDHEDSKDCILEPLSLPESPGGTTALEGSPSVPCIFCEEHFPMAEQDKLL |
| GLPVDP.EA...GVRGGI.H...EDSKD.ILEPLSLPESPGGT.ALEGS..VPCIFCEEHF.MAEQ.K.L | |
| Retrocopy | GLPVDPQEA---GVRGGIEHKYYEDSKDYILEPLSLPESPGGTAALEGSLPVPCIFCEEHFSMAEQYKRL |
| Parental | KHMIIEHKIVIADVKLVADFRRYILYWRKRFTEQPITDFCSVIRINSTAPFEEQDNYYLLCDALPEDRIL |
| K.MIIEHKIVIADV.LVA.FRRYILYWRK.FTEQ.IT.FCSVIRIN...PFEEQDNYYLL.DALPE.RI. | |
| Retrocopy | KPMIIEHKIVIADV*LVAGFRRYILYWRKWFTEQSITNFCSVIRINAKVPFEEQDNYYLLYDALPEYRIP |
| Parental | REELQKHKLKEVLDQQQRERNDTSFHGVCMFCSEEFRGNRSVLLNHMAREHAFNIGLPDNIVNCAEFLCT |
| REELQ..KLKEVLDQQQ.E.NDTSFHGVCMFCSEEFR.NRSVLLNHM.R.HAFNIGLPDNIVNC.EFLCT | |
| Retrocopy | REELQTQKLKEVLDQQQGEGNDTSFHGVCMFCSEEFR*NRSVLLNHMVRQHAFNIGLPDNIVNCTEFLCT |
| Parental | LQKKLDNLQCLYCEKTFRDKNTLKDHMRKK-QHRRIN---PKNREYDRFYVINYLELGKSWEEVQSEDDR |
| LQKKLDNLQCLYCEKTFRDKNTLKDHMRKK.QH.RIN......REYD.FY.INYLELGK.WEEVQSED.. | |
| Retrocopy | LQKKLDNLQCLYCEKTFRDKNTLKDHMRKK>QHCRINXXXXXEREYD*FYAINYLELGK*WEEVQSEDGL |
| Parental | ELLDLQEDDWSDWQEYPVSAVCLFCEKQEE-TIDKLYVHMKDTHEFDLLRIKSELGLNFYQQVKLVNFIR |
| .LLDLQEDDWSDWQEYPVSAVCLFCEKQEE.TIDKLYVHMKDTHEFDLLRIKSELGLNFYQQVKL.NFIR | |
| Retrocopy | KLLDLQEDDWSDWQEYPVSAVCLFCEKQEE>TIDKLYVHMKDTHEFDLLRIKSELGLNFYQQVKLINFIR |
| Parental | RQVHQCKCYSCHVKFKSKADLRTHMEDTKHTSLLPDRK-TWDQLEYYFPTYENDTLLCTLSDSESDLTAQ |
| RQVHQCKC.SCHVKFKSKADLRTH.EDTKHTSLLPDR..TWDQLEYYFPTYENDTLLCTLSDSESDLTAQ | |
| Retrocopy | RQVHQCKCFSCHVKFKSKADLRTHTEDTKHTSLLPDRR<TWDQLEYYFPTYENDTLLCTLSDSESDLTAQ |
| Parental | EQTENVPVISEDTSRLCALKQSSVLNQLLLQGCLEN |
| EQT.NVP.ISEDTSRLCALKQSSVLNQLLLQG.LEN | |
| Retrocopy | EQTLNVPTISEDTSRLCALKQSSVLNQLLLQGYLEN |
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 |
|---|---|---|
| SRP007412_brain | 0 .05 RPM | 15 .23 RPM |
| SRP007412_cerebellum | 0 .04 RPM | 7 .95 RPM |
| SRP007412_heart | 0 .00 RPM | 7 .16 RPM |
| SRP007412_kidney | 0 .06 RPM | 11 .67 RPM |
| SRP007412_liver | 0 .03 RPM | 6 .39 RPM |
| SRP007412_testis | 0 .05 RPM | 4 .07 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_3684 was not detected
No EST(s) were mapped for retro_mmus_3684 retrocopy.
No TSS is located nearby retro_mmus_3684 retrocopy 5' end.
retro_mmus_3684 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_3684 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000016891 | 2 retrocopies | |
| Mus musculus | ENSMUSG00000055917 | 1 retrocopy |
retro_mmus_3684 ,
|
| Otolemur garnettii | ENSOGAG00000005326 | 1 retrocopy |