RetrogeneDB ID: | retro_mmus_2310 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 3:140116624..140117830(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Dgcr14 | ||
| Ensembl ID: | ENSMUSG00000003527 | ||
| Aliases: | Dgcr14, AI462402, D16H22S1269E, Dgcr1, Dgsi, ES2, Es2el | ||
| Description: | DiGeorge syndrome critical region gene 14 [Source:MGI Symbol;Acc:MGI:107854] |
Retrocopy-Parental alignment summary:
>retro_mmus_2310
GCTGAGGAAAATGGAGATTTGGAGCGCATGTGCCAGATTGCCATCAAGTTTGACTCTGCCCTGGACAAGATATCTCGGAA
ACCTACACCACCCTATGTTACTCCAGCCACCTTTGAAACTCCTGAGGTATACCTGGGCTCTGGTGTGCTGGGTAGCAAGC
CCCAGCCCCAGGGCCGAGACCTAGATGACAGATCAGCTGGAGATGAGAAGCAGGAGCCACTGCCCACCCTGGATGTCTAC
TTGAGCCACTACACAAGCGAGGACAACGCCGTATTCCAGAAGATCATGGAAGTGGCTAAGGGAAAAAGCCATGCCCACCA
TATTTGGCTCTACCAGGCTGAGGAGGAATTTGAGAAGCGACAGAAAGATAATCTTGAAAACCCATCAGCAGAAACTAAGC
CATTGAGAATAGTCGGGCTGGAGTGGAATCCTGGAAGTACAAGGCCAAGAATTCTCTCATGTACTATCCCAAGGGTGTGC
CTGATATCAAACAGTTGTTCAAGGAGCCGCTTCAGGTAGTACATAAGAACACACGTTTCCTCCAGGACCCCTTCAGTCAG
GTTCTGAGCAAATCCCAGCTTCAGCAAGCAGCTGCCCTCAATGCTCAGCACAAACTGGGCAATGTTGGCCCAGATGGCAA
GGAACTCATTCCCCAGGAGTCCCCCAGAGTGAATGGCTTTGGATTCGTTGCCACTCCTTCCCCTGCTCCTGGTATGAATG
AGTCCCCACTGATGGTGTGGGGACAGGTTGAGAACACACCCCTGCTAATCGAAGGGTCCGAGAGCCCCTATGTGGACAGG
ACACTGGGACCCGTGTTCAAGATCTCAGAGCCAGGACCCAGGGAGCGTCTGGGACTGAAGATAGCCAATGAAGCAGCTGC
CAAAAACCGGGCCATGAAGCATAAAGCATTGCAGAGAGTTACAGGGAACTTGACCAGTCTTACTCGCAAAGGCCTGAGCC
CAGCCATGTCCCCAGCCCTACATCGCCCCGTAAGCAGGACAGCAAGCAGGTATACAGATCTTGCCCTGTGGGCCAGCCAT
ACACCATCCCCAGCATGCTCTACCCACCTCAAGAACCCAACTGCTGGGCCGCAGACACCCACAAGCATCCCAGCCCTAAC
AGGTACACCCCTCACACAGGATCCAGCCTCTATCACAGACAACCTGCTGCAGTTTCCCCGCCCGGCACAAAGCTTCAGAC
TTCTTT
ORF - retro_mmus_2310 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 80.2 % |
| Parental protein coverage: | 84.79 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | AEENGDLERMRQIAIKFGSALGKISREPPPPYVTPATFETPEVHPGSAVLGNKPRPQGRDLDDAGEAGEE |
| AEENGDLERM.QIAIKF.SAL.KISR.P.PPYVTPATFETPEV..GS.VLG.KP.PQGRDLDD...AG.E | |
| Retrocopy | AEENGDLERMCQIAIKFDSALDKISRKPTPPYVTPATFETPEVYLGSGVLGSKPQPQGRDLDDRS-AGDE |
| Parental | EEKEPLPSLDVFLSQYTSEDNASFQEIMEVAKEKSHARHAWLYQAEEEFEKRQKDNLELPSAEHQ-AIES |
| ...EPLP.LDV.LS.YTSEDNA.FQ.IMEVAK.KSHA.H.WLYQAEEEFEKRQKDNLE.PSAE...AIE. | |
| Retrocopy | KQ-EPLPTLDVYLSHYTSEDNAVFQKIMEVAKGKSHAHHIWLYQAEEEFEKRQKDNLENPSAETK<AIEN |
| Parental | SQAGVETWKYKAKNSLMYYPEGVPDEEQLFKKPRQIVHKNTRFLRDPFSQALSRSQLQQAAALNAQHKQG |
| S.AGVE.WKYKAKNSLMYYP.GVPD..QLFK.P.Q.VHKNTRFL.DPFSQ.LS.SQLQQAAALNAQHK.G | |
| Retrocopy | SRAGVESWKYKAKNSLMYYPKGVPDIKQLFKEPLQVVHKNTRFLQDPFSQVLSKSQLQQAAALNAQHKLG |
| Parental | KVGPDGKELIPQESPRVGGFGFVATPSPAPGVNESPLMTWGEVENTPLRVEGSESPYVDRTPGPTFKILE |
| .VGPDGKELIPQESPRV.GFGFVATPSPAPG.NESPLM.WG.VENTPL..EGSESPYVDRT.GP.FKI.E | |
| Retrocopy | NVGPDGKELIPQESPRVNGFGFVATPSPAPGMNESPLMVWGQVENTPLLIEGSESPYVDRTLGPVFKISE |
| Parental | PGRRERLGLKMANEAAAKNRAKKQEALRRVTENLASLTPKGLSPAMSPALQRLVSRTASKYTDRALRASY |
| PG.RERLGLK.ANEAAAKNRA.K..AL.RVT.NL.SLT.KGLSPAMSPAL.R.VSRTAS.YTD.AL.AS. | |
| Retrocopy | PGPRERLGLKIANEAAAKNRAMKHKALQRVTGNLTSLTRKGLSPAMSPALHRPVSRTASRYTDLALWASH |
| Parental | TPSPARSSHLKTPAGGPQTPTSTPAPGSATRTPLTQDPASITDNLLQ-LPARRKASDFF |
| TPSPA.S.HLK.P..GPQTPTS.PA....T.TPLTQDPASITDNLLQ..PAR.KASDFF | |
| Retrocopy | TPSPACSTHLKNPTAGPQTPTSIPA---LTGTPLTQDPASITDNLLQ>FPARHKASDFF |
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 .00 RPM | 22 .38 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 23 .84 RPM |
| SRP007412_heart | 0 .00 RPM | 12 .36 RPM |
| SRP007412_kidney | 0 .00 RPM | 12 .70 RPM |
| SRP007412_liver | 0 .00 RPM | 5 .08 RPM |
| SRP007412_testis | 0 .05 RPM | 39 .47 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_2310 was not detected
No EST(s) were mapped for retro_mmus_2310 retrocopy.
No TSS is located nearby retro_mmus_2310 retrocopy 5' end.
retro_mmus_2310 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_2310 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 | |
|---|---|---|---|
| Macropus eugenii | ENSMEUG00000007959 | 2 retrocopies | |
| Mus musculus | ENSMUSG00000003527 | 1 retrocopy |
retro_mmus_2310 ,
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