RetrogeneDB ID: | retro_mmus_45 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 18:52331613..52332327(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000024510 | |
| Aliases: | Ftmt, 4930447C24Rik, FerH, Fth3, MtF | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Fth1 | ||
| Ensembl ID: | ENSMUSG00000024661 | ||
| Aliases: | Fth1, FHC, Fth, HFt, MFH | ||
| Description: | ferritin heavy chain 1 [Source:MGI Symbol;Acc:MGI:95588] |
Retrocopy-Parental alignment summary:
>retro_mmus_45
ATGCTGTCCTGCTTTTGGTTCTTCTCCAAGCACATCAGCTCTGCACTGATGTCCCTGCCCCGTGTGTTACACAGATTCAC
TGCCCCACAGTGCTTGGCCTCCAGGTATCCTTTAGGTCCCCTACTGGCCTCCCCTCGACGCCTCCTGGCCTCGGTGGCTT
CCTCTCAGGACTCCACTAGACCTTCCAGGGTCCGCCAGAACTTTCACCCGGACTCGGAGGCTGCTATCAACCGCCAAATC
AACCTGGAGCTTTACGCATCCTACGTGTACCTGTCCATGGCTTACTACTTCTCCAGGGATGATGTGGCCTTGTATAACTT
CTCCAAGTATTTCCTTCGCCAGTCCCTGGAAGAGAGGGAACATGCAGAGAAGCTAATGAAACTGCAGAACCAGCGAGGAG
GCCGGATCTGCCTCCAGGACATCAAGAAGCCAGATAAAGATGACTGGGAATGCGGACTGCGGGCCATGGAATGTGCCCTG
CTCCTGGAAAAGAATGTAAACCAGTCGCTGCTGGACTTACATACTCTGGCCTCAGAAAAAGGAGATCCTCATTTGTGTGA
CTTTCTGGAAACTCACTACCTGCATGAGCAAGTGAAGTCTATCAAAGAATTAGGTGACCACGTGCACAACTTAGTCACCA
TGGGGGCTCCAGCCGCGGGCTTAGCGGAATATCTTTTCGACAAGCACACGCTTGGAAGCGAGAGCAAGCACTAA
ORF - retro_mmus_45 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 82.56 % |
| Parental protein coverage: | 94.51 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | PSQVRQNYHQDAEAAINRQINLELYASYVYLSMSCYFDRDDVALKNFAKYFLHQSHEEREHAEKLMKLQN |
| PS.VRQN.H.D.EAAINRQINLELYASYVYLSM..YF.RDDVAL.NF.KYFL.QS.EEREHAEKLMKLQN | |
| Retrocopy | PSRVRQNFHPDSEAAINRQINLELYASYVYLSMAYYFSRDDVALYNFSKYFLRQSLEEREHAEKLMKLQN |
| Parental | QRGGRIFLQDIKKPDRDDWESGLNAMECALHLEKSVNQSLLELHKLATDKNDPHLCDFIETYYLSEQVKS |
| QRGGRI.LQDIKKPD.DDWE.GL.AMECAL.LEK.VNQSLL.LH.LA..K.DPHLCDF.ET.YL.EQVKS | |
| Retrocopy | QRGGRICLQDIKKPDKDDWECGLRAMECALLLEKNVNQSLLDLHTLASEKGDPHLCDFLETHYLHEQVKS |
| Parental | IKELGDHVTNLRKMGAPEAGMAEYLFDKHTLG |
| IKELGDHV.NL..MGAP.AG.AEYLFDKHTLG | |
| Retrocopy | IKELGDHVHNLVTMGAPAAGLAEYLFDKHTLG |
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 | 1220 .31 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 1340 .29 RPM |
| SRP007412_heart | 0 .00 RPM | 1076 .05 RPM |
| SRP007412_kidney | 0 .00 RPM | 2397 .51 RPM |
| SRP007412_liver | 0 .03 RPM | 1186 .06 RPM |
| SRP007412_testis | 25 .98 RPM | 144 .99 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_45 was not detected
No EST(s) were mapped for retro_mmus_45 retrocopy.
| TSS No. | TSS Name | TSS expression level (Expr) in TPM range: | ||||
|---|---|---|---|---|---|---|
| no expression | 0 < Expr ≤ 1 | 1 < Expr ≤ 5 | 5 < Expr ≤ 10 | Expr > 10 | ||
| TSS #1 | TSS_59743 | 1060 libraries | 6 libraries | 1 library | 1 library | 4 libraries |
The graphical summary, for retro_mmus_45 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)
retro_mmus_45 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_45 has 4 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_87 |
| Pongo abelii | retro_pabe_35 |
| Bos taurus | retro_btau_121 |
| Sus scrofa | retro_sscr_78 |