RetrogeneDB ID: | retro_mmus_3518 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | X:122100932..122102480(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000082840 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Hltf | ||
| Ensembl ID: | ENSMUSG00000002428 | ||
| Aliases: | Hltf, AF010600, BC057116, P113, Smarca3, Snf2l3 | ||
| Description: | helicase-like transcription factor [Source:MGI Symbol;Acc:MGI:1196437] |
Retrocopy-Parental alignment summary:
>retro_mmus_3518
TTTGGACAACATGTAAAATCAGAAGTGCACTTGAACTTTTATGTTTATTATGGTCCTGATCGTATTAGAGATTCAGCCTG
GCTTTCAAAACAGGATATTATTTTGACTACTTACAATATTTTAACTCATGATTAAGGAACTAAAGATGATAGTCCATTGC
ATAGCATCAAGTGGTTCAGGGTGATCCTGGATGAAGACCATGCTATTTGAAATTCAAACGCTCAGCAGACAAAAGCTGTA
CTTGAGTTAGAGGCAGAAAGAAGATGGGTATTGACAGGTACTCCGATCCAGAATTCTTTAAAGGACTTGTGGTCTCTTCT
GTCGTTCTTAAAACTTAAGCCATTTATTGATAGAGAGTGGTGGTATAGGATCATACAGCATCCTGTCACTACAGGAGATG
AGGGCGGACTTAGGCGTTTACAGTCCTTAATAAAAAATATCACGCTTAGAAGAACAAAGACAAGCAAAATTAAAGGGAAA
CCTGTTTTGGAGTTGCCAGAAAGGAAAGTATTTATTCCGCACATTACTCTGTCAGAAGAAGAGAGAAAGATTTATCAGTC
TGTTAAAAATGAAGGTAAAGCTGCTATTGGAGGGTATTTTACTGAAGGGACTGTCCTTGCACACTATGCAGATGTCTTGG
GTCTTCTGCTTAGATTGCGGCAGATTTGTTGCCATACCTATCTTCTTACAAACGGAATGTCTTCAAGTGGCCCCTCCAGA
AGTGACATGCCTGAAGAGCTGAGAAAGATGTTAATAGAGAAGATGAAGATAATTCTGAGCTCTGGTTCAGATGAGGAATG
TGCAATCTGCCTGGATTCCTTAACATTTCCTGTGATAACCCATTGTGCACACATGCTCTGTAAACCTTGTATCTGTCAGG
TCATCCAGAGTGAGCAGCTACCTGCAGAGTGTCCTTTGTGCAGAAATGAGATATATGGAGATAATCTATTAAAATGTCCT
CCAGAAGAATTGGCATGTGACAGTGACAAAGAGTCCAGTATGGAATGGACATCCAGCTCAAAGATTAATGCTCTAATGCA
TGCTTTGATTGAATTATGGACAAAGGAACCCAACATAAAAAGTTTAGTTGTTTCTCAGTTTACCACATACTTGTCTTTAA
TAGAAACGCCTCTTAAAGCCTCAGGATTTGTATTTACTCCTTTAGATGGTTCCATGGCTCAAAAGAAAAGAGTTGAATCA
ATTCAGCGTTTTCAAAACACAGAAGCAGGATCTACCATTATAATGCTACTGTCCTTAAAAGCAGGTGGAGTTTGCTTGAA
TCTCTGTGCAGCTTCGTGAATGTTCTTAATGGATCCGGCCTGGAATCCTGCTGCAGAAGATCAGTGCTTTGACCGGTGCC
ATCGACTTCTCCAGAAGCAAGAGATGATCATCACAAAATTAATTGTGAAGGACTCTGTGGAAGAAAATATGTTGAAAATA
CAGAACACGAAGTGAGACCTTGCAGCTGGAGCCTTTGGCACCAAGAAAACAGACGCCAATGAAATGAAACAAGTGAAAAT
CAACGAAATCAGAACTTTAATAGACTTA
ORF - retro_mmus_3518 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 93.41 % |
| Parental protein coverage: | 51.45 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | FGQHVKSEVHLNFYVYYGPDRIRDSAWLSKQDIILTTYNILTHDYGTKDDSPLHSIKWLRVILDEGHAIR |
| FGQHVKSEVHLNFYVYYGPDRIRDSAWLSKQDIILTTYNILTHD.GTKDDSPLHSIKW.RVILDE.HAI. | |
| Retrocopy | FGQHVKSEVHLNFYVYYGPDRIRDSAWLSKQDIILTTYNILTHD*GTKDDSPLHSIKWFRVILDEDHAI* |
| Parental | NPNAQQTKAVLELEAERRWVLTGTPIQNSLKDLWSLLSFLKLKPFIDREWWYRIIQRPVTTGDEGGLRRL |
| N.NAQQTKAVLELEAERRWVLTGTPIQNSLKDLWSLLSFLKLKPFIDREWWYRIIQ.PVTTGDEGGLRRL | |
| Retrocopy | NSNAQQTKAVLELEAERRWVLTGTPIQNSLKDLWSLLSFLKLKPFIDREWWYRIIQHPVTTGDEGGLRRL |
| Parental | QSLIKNITLRRTKTSKIKGKPVLELPERKVFIQHITLSEEERKIYQSVKNEGKAAIGRYFTEGTVLAHYA |
| QSLIKNITLRRTKTSKIKGKPVLELPERKVFI.HITLSEEERKIYQSVKNEGKAAIG.YFTEGTVLAHYA | |
| Retrocopy | QSLIKNITLRRTKTSKIKGKPVLELPERKVFIPHITLSEEERKIYQSVKNEGKAAIGGYFTEGTVLAHYA |
| Parental | DVLGLLLRLRQICCHTHLLTNGMSSSGPSRSDTPEELRKMLIEKMKIILSSGSDEECAICLDSLTFPVIT |
| DVLGLLLRLRQICCHT.LLTNGMSSSGPSRSD.PEELRKMLIEKMKIILSSGSDEECAICLDSLTFPVIT | |
| Retrocopy | DVLGLLLRLRQICCHTYLLTNGMSSSGPSRSDMPEELRKMLIEKMKIILSSGSDEECAICLDSLTFPVIT |
| Parental | HCAHVFCKPCICQVIHSEQPHAKCPLCRNEIHGDNLLECPPEELACDSDKESSMEWKSSSKINALMHALI |
| HCAH..CKPCICQVI.SEQ..A.CPLCRNEI.GDNLL.CPPEELACDSDKESSMEW.SSSKINALMHALI | |
| Retrocopy | HCAHMLCKPCICQVIQSEQLPAECPLCRNEIYGDNLLKCPPEELACDSDKESSMEWTSSSKINALMHALI |
| Parental | ELRTKDPNIKSLVVSQFTTFLSLIETPLKASGFVFTRLDGSMAQKKRVESIQRFQNTEAGSPTIMLLSLK |
| EL.TK.PNIKSLVVSQFTT.LSLIETPLKASGFVFT.LDGSMAQKKRVESIQRFQNTEAGS..IMLLSLK | |
| Retrocopy | ELWTKEPNIKSLVVSQFTTYLSLIETPLKASGFVFTPLDGSMAQKKRVESIQRFQNTEAGSTIIMLLSLK |
| Parental | AGGVGLNLCAASRVFLMDPAWNPAAEDQCFDRCHRLGQKQEVIITKFIVKDSVEENMLKIQNTKRDLAAG |
| AGGV.LNLCAAS..FLMDPAWNPAAEDQCFDRCHRL.QKQE.IITK.IVKDSVEENMLKIQNTK.DLAAG | |
| Retrocopy | AGGVCLNLCAAS*MFLMDPAWNPAAEDQCFDRCHRLLQKQEMIITKLIVKDSVEENMLKIQNTK*DLAAG |
| Parental | AFGTKKTDANDMKQAKINEIRTLIDL |
| AFGTKKTDAN.MKQ.KINEIRTLIDL | |
| Retrocopy | AFGTKKTDANEMKQVKINEIRTLIDL |
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 | 21 .14 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 22 .49 RPM |
| SRP007412_heart | 0 .00 RPM | 13 .64 RPM |
| SRP007412_kidney | 0 .02 RPM | 22 .06 RPM |
| SRP007412_liver | 0 .00 RPM | 9 .53 RPM |
| SRP007412_testis | 0 .00 RPM | 4 .16 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_3518 was not detected
1 EST(s) were mapped to retro_mmus_3518 retrocopy
| EST ID | Start | End | Identity | Match | Mis-match | Score |
|---|---|---|---|---|---|---|
| D77731 | 122101352 | 122101491 | 97.8 | 133 | 2 | 129 |
No TSS is located nearby retro_mmus_3518 retrocopy 5' end.
retro_mmus_3518 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_3518 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Mus musculus | ENSMUSG00000002428 | 1 retrocopy |
retro_mmus_3518 ,
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