RetrogeneDB ID: | retro_mmus_1307 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 14:105199978..105201101(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Lcp1 | ||
| Ensembl ID: | ENSMUSG00000021998 | ||
| Aliases: | Lcp1, AW536232, D14Ertd310e, LCP-1, Pls2, pp65 | ||
| Description: | lymphocyte cytosolic protein 1 [Source:MGI Symbol;Acc:MGI:104808] |
Retrocopy-Parental alignment summary:
>retro_mmus_1307
GCAGAGACAGATACCGATGGCAACGGATACATCAGCTACAATGAGCTGCGTCACTTGTTCAAGGCCGCCTGCTGGCCTCT
GCCTGGGTACCGAGTGAGAGAAATTGCAGAAACCTGATGGCCACAGGTGATCTGGACCAAGATAGAAAGATAAAGCTTTG
ATGAGTTTATCAAGGTCTTCCATGGCTTAAAAAGCACCGAGGTTGCCAAAACCTTCCAAAAAAGCTATCAACAAGAAAAA
AGATCTGTGCAATTGGCGGCACCTCTGAGCAGTCTAGTGTTGGTACCCAGCACTCTTATTCAGAGGAAGAAAAGTATGCC
TTAGTCAACTGGATAAACAAAGCCCTGGAGAATGATCTCGACTGCCGGCACGTCATCCCCATGAACCCCAACACCGACGA
TCTCTTCAATGCTGTAGGCGTTGGCATAGTTCTTTGTAAAATGATCAACCTGTCCGTGCCAGACACAATTGACGAGAGAA
CGATCAACAAGAAAAAGCTCACACCGTTCACCATTCGGGAAAACTTGAACTTGACTCTGAACTCTGCCTTGGCCATCGGG
TGCCACGTGGTTAATATAGGGGCCGAGGACCTGAAGGAGGGCAAGCCTTACCTGGTCCTGGGACTTCTGTGGCAAGTCAT
CAAGATTGGGTTGTTTGTTGACATTGAACTCAGCAGAAATGAAGCTCTGATTGCTCTTTTGAGAGAAGGAGAGAGCCTAG
AGGATTTGATGAAGTTGTCTCCTGAAGAATTCCTGCTGCAGTGGGCTAACTACCACCTAGAAAACGCAGGCTGCACCAAA
ATCACCAACTTCAGCACGACATCAAGGACTCCAAAGCTTATTACCACCTGCTCGAGCAAGTGGCTCCAAAAGGAGATGAA
GAAGGGATCCCGGCTGTTGTGATTGACACATCAGGACTGAAGAAGGATGACATCCAGAGTGCAGAGCGCATGCTGCAACA
GGCGGAGAGGCTGGGCTGCCGGCAGTTTGTCACAGCTACTGATGTTGTCCGAGGGAACCCCAAGTTGAACCTGGTCTTCA
TTGCCAACCTCTTTAACAAATACCCTGCCTTACATAAACCAGAGAACCAGGACATTGACTGGGGGGCTCTCGAAGAGCGG
ACG
ORF - retro_mmus_1307 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 90.26 % |
| Parental protein coverage: | 59.97 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 4 |
Retrocopy - Parental Gene Alignment:
| Parental | AKVDTDGNGYISCNELNDLFKAACLPLPGYRVREITE-NLMATGDLDQDGKI-SFDEFIKVFHGLKSTEV |
| A..DTDGNGYIS.NEL..LFKAAC.PLPGYRVREI.E.NLMATGDLDQD.KI.SFDEFIKVFHGLKSTEV | |
| Retrocopy | AETDTDGNGYISYNELRHLFKAACWPLPGYRVREIAE<NLMATGDLDQDRKI>SFDEFIKVFHGLKSTEV |
| Parental | AKTFRKA-INKKEGICAIGGTSEQSSVGTQHSYSEEEKYAFVNWINKALENDPDCRHVIPMNPNTDDLFN |
| AKTF.K........ICAIGGTSEQSSVGTQHSYSEEEKYA.VNWINKALEND.DCRHVIPMNPNTDDLFN | |
| Retrocopy | AKTFQKS<LSTRKKICAIGGTSEQSSVGTQHSYSEEEKYALVNWINKALENDLDCRHVIPMNPNTDDLFN |
| Parental | AVGDGIVLCKMINLSVPDTIDERTINKKKLTPFTIQENLNLALNSASAIGCHVVNIGAEDLKEGKPYLVL |
| AVG.GIVLCKMINLSVPDTIDERTINKKKLTPFTI.ENLNL.LNSA.AIGCHVVNIGAEDLKEGKPYLVL | |
| Retrocopy | AVGVGIVLCKMINLSVPDTIDERTINKKKLTPFTIRENLNLTLNSALAIGCHVVNIGAEDLKEGKPYLVL |
| Parental | GLLWQVIKIGLFADIELSRNEALIALLREGESLEDLMKLSPEELLLRWANYHLENAGCTKITNFST-DIK |
| GLLWQVIKIGLF.DIELSRNEALIALLREGESLEDLMKLSPEE.LL.WANYHLENAGCTKITNFST.DIK | |
| Retrocopy | GLLWQVIKIGLFVDIELSRNEALIALLREGESLEDLMKLSPEEFLLQWANYHLENAGCTKITNFST<DIK |
| Parental | DSKAYYHLLEQVAPKGDEEGIPAVVIDMSGLREKDDIQRAECMLQQAERLGCRQFVTATDVVRGNPKLNL |
| DSKAYYHLLEQVAPKGDEEGIPAVVID.SGL..KDDIQ.AE.MLQQAERLGCRQFVTATDVVRGNPKLNL | |
| Retrocopy | DSKAYYHLLEQVAPKGDEEGIPAVVIDTSGLK-KDDIQSAERMLQQAERLGCRQFVTATDVVRGNPKLNL |
| Parental | AFIANLFNKYPALHKPENQDIDWGALEGET |
| .FIANLFNKYPALHKPENQDIDWGALE..T | |
| Retrocopy | VFIANLFNKYPALHKPENQDIDWGALEERT |
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 | 7 .85 RPM |
| SRP007412_cerebellum | 0 .04 RPM | 10 .64 RPM |
| SRP007412_heart | 0 .00 RPM | 26 .31 RPM |
| SRP007412_kidney | 0 .06 RPM | 49 .03 RPM |
| SRP007412_liver | 0 .00 RPM | 88 .45 RPM |
| SRP007412_testis | 0 .05 RPM | 2 .65 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_1307 was not detected
No EST(s) were mapped for retro_mmus_1307 retrocopy.
No TSS is located nearby retro_mmus_1307 retrocopy 5' end.
retro_mmus_1307 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_1307 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 | |
|---|---|---|---|
| Choloepus hoffmanni | ENSCHOG00000012037 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000021998 | 2 retrocopies |
retro_mmus_1307 , retro_mmus_3697,
|