RetrogeneDB ID: | retro_mmus_2372 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 4:84697862..84698910(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000081775 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Serinc3 | ||
| Ensembl ID: | ENSMUSG00000017707 | ||
| Aliases: | Serinc3, AA959945, AA960047, AIGP1, DIFF33, TMS-1, Tde1 | ||
| Description: | serine incorporator 3 [Source:MGI Symbol;Acc:MGI:1349457] |
Retrocopy-Parental alignment summary:
>retro_mmus_2372
GCTGTGGCCATCTTTTTCTTTGCCTTCCTTTTGCTCGTGTTAAAAGTTAAAGCAAGCAAAGATCCCAGAGCAGCCGTACA
CAATGGGTTTTGGTTCTTCAAAAGTGCTGCCCTTATTGGTACCATGGACGGATCTTTCTACATCCCTGGGGGCCATTTCA
CTGAAGTCTGGATTAGTGCTGGAATGTTGGGGGCCACTTTCTTCATTTTCATCCAGCTGGTGCTCTTAGTAGATGAGGCT
TATTCTTGGAATGAATCATGGGTAAATCGAGTGGAGGAGGGAAGCCCAAGGCTCTGGTATGCTGCCTTGCTGTCCTTCAC
AAGCCTCGTTTACATCCTTCCGATCGTCTCTGTTGTGCCGCTCCACATCTTCTACACCAAACCCGACAACTGCACAGAAA
ACAAGGTCTTCATCAGCCCGAACCTGACTTTTTGTATTGCAGTTTCTATTGTATCCATCCTCCCCAAAGTTCAGGAACAT
CAGACTGCTCTGGCCTCCTGCAGTCCTCCATCACCGCTCTGTACACCCTTTACCTCACGTGGTCGCCCATGACCAATGAG
CTTGAGCGGTCCTGCAACCCCTCCCTTCTGAGCATCGTCACACACTTAACTTCACCAAATGTGTGTCCTGCAAAGTCAGC
TACTCTTGCTCCTGCCTATGCTCCGCCATCACAGAGTGGACACTTTATGAATTTGGATGATGTTGGGGACCAACTATCTT
TGTTATCTGCCTTATATATTCTAGCATCGGTACTTTGAGCAACAGCCAAGTTAACAAGCTGACCTTGTCTGGGAGTGACA
GTGATATCCTTGGCGATACCACCAATGGAGCCAGTGATTAAGAAGGCTGACAGCCTCAGCGGGCTGTAGACAATGAGAAG
GAGGAGGTGCAGTATAGCTACTCCTTTTTCCACCTGATGCTCTGCTGTGCCTCCTTGTACACCATGATGACCATAACCAG
CTGGTACAGCCCTGATGCCAAATTCCAGAAGGTATCCAGCGACTGGGTAGCTGTGTGGGTCAAAATGAGCTCCAGCTGGG
TATGTCTT
ORF - retro_mmus_2372 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 82.1 % |
| Parental protein coverage: | 74.15 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | AVAIFFFAFFLLMLKVKTSKDPRAAVHNGFWFFKIAAIIGIMIGSFYIPGGSFTEVWFVAGMLGASFFII |
| AVAIFFFAF.LL.LKVK.SKDPRAAVHNGFWFFK.AA.IG.M.GSFYIPGG.FTEVW..AGMLGA.FFI. | |
| Retrocopy | AVAIFFFAFLLLVLKVKASKDPRAAVHNGFWFFKSAALIGTMDGSFYIPGGHFTEVWISAGMLGATFFIF |
| Parental | IQLVLLVDMAHSWNELWVNRMEEGNPRLWYAALLSFTSLFYILSIVFAALLYVFYTKPDDCTENKVFISL |
| IQLVLLVD.A.SWNE.WVNR.EEG.PRLWYAALLSFTSL.YIL.IV....L..FYTKPD.CTENKVFIS. | |
| Retrocopy | IQLVLLVDEAYSWNESWVNRVEEGSPRLWYAALLSFTSLVYILPIVSVVPLHIFYTKPDNCTENKVFISP |
| Parental | NLIFCVAVSIVSILPKVQEHQPR-SGLLQSSIITLYTLYLTWSAMTNEPERSCNPSLMSIITHLTSPTVS |
| NL.FC.AVSIVSILPKVQEHQ...SGLLQSSI..LYTLYLTWS.MTNE.ERSCNPSL.SI.THLTSP.V. | |
| Retrocopy | NLTFCIAVSIVSILPKVQEHQTA<SGLLQSSITALYTLYLTWSPMTNELERSCNPSLLSIVTHLTSPNVC |
| Parental | PANSTTLAPAYAPPSQSGHFMNLDDI-WGLIIFVFCLIYSSFRTSSNSQVNKLTLSGSDSVILGDTTNGA |
| PA.S.TLAPAYAPPSQSGHFMNLDD..WG..IFV.CLIYSS..T.SNSQVNKLTLSGSDS.ILGDTTNGA | |
| Retrocopy | PAKSATLAPAYAPPSQSGHFMNLDDV<WGPTIFVICLIYSSIGTLSNSQVNKLTLSGSDSDILGDTTNGA |
| Parental | NDEEDGQPRRAVDNEKEGVQYSYSFFHLMLCCASLYIMMTITSWYSPDAKFQKVSSKWLAVWFKMGSSWL |
| .D.E..QP.RAVDNEKE.VQYSYSFFHLMLCCASLY.MMTITSWYSPDAKFQKVSS.W.AVW.KM.SSW. | |
| Retrocopy | SD*EG*QPQRAVDNEKEEVQYSYSFFHLMLCCASLYTMMTITSWYSPDAKFQKVSSDWVAVWVKMSSSWV |
| Parental | CL |
| CL | |
| Retrocopy | CL |
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 | 256 .64 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 172 .04 RPM |
| SRP007412_heart | 0 .00 RPM | 286 .99 RPM |
| SRP007412_kidney | 0 .00 RPM | 403 .40 RPM |
| SRP007412_liver | 0 .00 RPM | 240 .45 RPM |
| SRP007412_testis | 0 .00 RPM | 209 .58 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_2372 was not detected
No EST(s) were mapped for retro_mmus_2372 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_106646 | 820 libraries | 214 libraries | 38 libraries | 0 libraries | 0 libraries |
| TSS #2 | TSS_106647 | 173 libraries | 398 libraries | 396 libraries | 87 libraries | 18 libraries |
The graphical summary, for retro_mmus_2372 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_2372 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_2372 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 | |
|---|---|---|---|
| Mus musculus | ENSMUSG00000017707 | 1 retrocopy |
retro_mmus_2372 ,
|
| Ictidomys tridecemlineatus | ENSSTOG00000015682 | 1 retrocopy |