RetrogeneDB ID: | retro_mmus_3253 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 9:23904058..23904707(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Smap1 | ||
| Ensembl ID: | ENSMUSG00000026155 | ||
| Aliases: | Smap1, 1700056O10Rik, 4921514B13Rik, 4921525H11Rik, AI462175 | ||
| Description: | stromal membrane-associated protein 1 [Source:MGI Symbol;Acc:MGI:2138261] |
Retrocopy-Parental alignment summary:
>retro_mmus_3253
TGGACACAAGAACAGATACAGTGCATGCAAGATATGGGAGATACTAAATCAGGAGTACTCCATGAAGCCAGTCTTCCAAA
GAACTTTCAAGGACCAGACAGAGCAAGCAATAGAATTGTTTAGCAGAGATAAATAAAAAAGTGAAAACATTATGGTAAAA
ATAGCTATCACTATTACAAATAAAGAAAGTGGGCAGGGTAGGGGGAAGGAGCCAGAGAAGCCTGTAAAGCCACTGAGAGC
TGAAAAGCTGCAGAGGGCAGAAGATCAATCATTTGAGACTAAGAAAAATGCCAGCCTGAACAAAGCTGCAGAATCCATAA
TTGATCTTTTGGGACTTGATGGCCCTGCCAAGATCCAGTGGCCAATGGGAACACAACCACAACGCCATGTCTGAATGGTG
ACTTGCATATTTTAGTTTCTAATCCCTTGTCTCCACTGTCCTGTCTCCACTTAGGGGAGTGACTTGTTAGCAGCAGCTGT
TACCCTGTCTGTCATAACATGTGAGACATCTGGATCTGTTCACTAAGATCCAAACTAAGTCAGAAGAAATAGGAAAGATG
GACACTCCAAAGAATCGATCTTATCCTTCTATGGAACAGGAACCATACATCAACAAAGTATTCCTGGTGTGTTAATGGAA
TCCACAAAT
ORF - retro_mmus_3253 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 51.07 % |
| Parental protein coverage: | 50.91 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 6 |
Retrocopy - Parental Gene Alignment:
| Parental | WTPEQIQCMQDMGNTKARLLYEANLPENFRRPQTDQAVEFFIRDKYEKK-KYYDKN-AIAITNKEKEKKK |
| WT.EQIQCMQDMG.TK...L.EA.LP.NF..P..D.A..........KK.K.Y.KN.AI.ITNKE..... | |
| Retrocopy | WTQEQIQCMQDMGDTKSGVLHEASLPKNFQGP--DRASNRIV*QR*IKK*KHYGKN>AITITNKESGQGR |
| Parental | DEKKREKEPEKPAKPLTTEKLPKKEEQQLEPKKSTSPKNAAEPTIDLLGLDGPA-EAPVTNGNPATAPAL |
| ..K..EK....P.KPL..EKL...E.Q..E.KK..S...AAE..IDLLGLDGPA...PV.NGN..T.P.L | |
| Retrocopy | G-KEPEK----PVKPLRAEKLQRAEDQSFETKKNASLNKAAESIIDLLGLDGPA<QDPVANGNTTTTPCL |
| Parental | SDDLDIFGPMISNPLP-AAVMPPAQGTAS-VPAPATLSTVTS-GDLDLFTEQTTKSEEVAKKQL-SKDSI |
| ..DL.I.....SNPL....V..P..G......A..TLS..T....LDLFT...TKSEE..K....SK.SI | |
| Retrocopy | NGDLHI---LVSNPLS<STVLSPLRGVTC<LAAAVTLSVITC>RHLDLFTKIQTKSEEIGKMDT<SKESI |
| Parental | LSLYGTGA--QQSTPGVFMGPTN |
| LS.YGTG...QQS.PGV.M..TN | |
| Retrocopy | LSFYGTGTIHQQSIPGVLMESTN |
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 | 30 .68 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 24 .45 RPM |
| SRP007412_heart | 0 .00 RPM | 5 .29 RPM |
| SRP007412_kidney | 0 .00 RPM | 17 .13 RPM |
| SRP007412_liver | 0 .00 RPM | 10 .62 RPM |
| SRP007412_testis | 0 .00 RPM | 97 .97 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_3253 was not detected
No EST(s) were mapped for retro_mmus_3253 retrocopy.
No TSS is located nearby retro_mmus_3253 retrocopy 5' end.
retro_mmus_3253 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_3253 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 4 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Echinops telfairi | ENSETEG00000001865 | 1 retrocopy | |
| Felis catus | ENSFCAG00000007247 | 1 retrocopy | |
| Loxodonta africana | ENSLAFG00000007948 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000026155 | 1 retrocopy |
retro_mmus_3253 ,
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