RetrogeneDB ID: | retro_mmus_3088 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 7:130352040..130354362(-) | ||
| Located in intron of: | ENSMUSG00000030849 | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000082988 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Rfwd3 | ||
| Ensembl ID: | ENSMUSG00000033596 | ||
| Aliases: | Rfwd3, BC027246 | ||
| Description: | ring finger and WD repeat domain 3 [Source:MGI Symbol;Acc:MGI:2384584] |
Retrocopy-Parental alignment summary:
>retro_mmus_3088
ATGGCCGAAGTCGCGGTCGGCCAGGCGTCCGACTTGGTCCCCTCAGAGATGGATCATGAAGTGATATACAGTCATCTTCA
GGGACCGTTAGAGGGTACTATAGAACCAGCTACTCCAACTGAAGTCGTCAGCAATGGGGCACCTCTCCAGCCTGCCCCTG
CTGAACTGGCCAATAGCCAAGGTGGAGCACATGTTCAGCCTGCCCCTGCTGAAGTGGTCAGCAGCCAAGATGGACTGCCC
ACTCTACAGCCTCTGCCACCAGCATCCATTGATTTGACGGAGGAAGTACAGCCCTCAGAAGAAAATATGGAGGTTGTCAA
TCCTGGAACTTCAGAGGAGCCTAGTCAGGGATCTGGTGCTAACCGAACCTCCGGAGCTGCTAGATCCGTTTCAATGAACA
ACTTCATCAGCGGGCTGCAGAGGCTTCATAACATGCTGGAATTGCTGAGACCTCCACCTGCAGACCACAGTGTGGGGCCA
ATAAGAACAAGGAGGAGGATGGCACCCATTTTGAGGGCCAGAGCTGGAGAGTCTCAGAGGCAAGACAATGGCAGGTATGT
GCCACATACACCACTATATGCCTACTTTCAGGTAAGCAGGTCTCAGCCTTACCCACTACCCGCTGCTCATGATTCAGAGA
CCAGGAATCCACCGTCAGGCACTGACTCTGACAGCGATGGCTCTGCAGAGGATGAAGAGGTTGTTGTCCAAGCAGAAGAA
CCTGAAGCCAACATTCCAGAACAAGGAGTTATCGCAACAGACCAAGAAGCTACATCTGTCACAGGAGATGATGCAGTCCC
TAAAGAGTCTCCCCAGAAGCCCAGCATGCTATCTGCTATGGAAGATGAGGAAGGTGAAACTTGCACAATATGTTTGGAAC
AGTGGACCAATGCTGGGGACCACCGGATCTCAGCGCTACGCTGTGGGCACCTCTTTGGATTTAGATGCATTTCTAAATGG
CTCAAAGGACAAACAGGAAAATGTCCTCAGTGCAACAAGAAAGCCAAGCACAGTGACATCGTTGTCATTTATGCCCGATC
CCTGCGAGCTTTGGACACTAGTGAACAGGAGCGCATGAAAAGTGACTTACTGAATGAGCAAATGCTCAGGAAGCAGGCTG
AGTTAGAGTCTGCACAGTGCCGGCTCCAGCTTCAGGTCCTTATTGATAAATGCACTAAACTCAATAGCCGTGTCCAGGAC
TTGGAAAAGTTTGTTGTGCGGCATCAGAACTCAGCTGTGCAGCAGTGCAGTCGCTCGAAAGCACTTTGTGGGAAATGCCT
GTCCTCCAGCCAGATCCCAGGCAAATACAGCTCAGAAAAGACCTTCACCATATCTCAGACGGGAAAATGCCGAATCTTGG
CCTATTGTGATGGTCTGAGCTGCCTGGTGGCCTCCCAGCCCTCCCCTCAGGCCTCCTTTCTTCCAGGCTTTGGTGTTAAG
ATGTTGAGTACTGCCAACATGAAGAGCAGTCAGTATATTCCTATGCACAACAAGCAGATTCGTGGATTATCTTTCAGCAG
TCAGTCCAAAGGCTTGCTCCTGTCTGCCTCCCTTGACTGCACTATTAAGCTGACCAGCCTAGAAACAAATACTGTGGTGC
AGACTTACAACACTGGACGTCCTGTCTGGAGCTGCTGCTGGTGTCTTGACGAAAACAATTACGTCTATGCTGGACTAGCC
AGTGGTTCAATTCTGATCTATGACTTACGGAACACAAACACCTATATTCAGGAATTAGTTCCTCAGAAAGCCAGATGTCC
TCTGGTATCCCTGTCATATTTACCCAAAGCTGCAGTGGCTGCATTTCCTTATGGTGGGGTGCTGGCTGGAACATTGGAGA
ATGCCTCCTTCTGGGAGCTAAAATCAGACTTTTCTCATAAGCCTCATGTGCTGTCCTTGGAGCCAGGGGACTTTGTAGAC
TTTCAGACAGAGAGCAGCACCCGACACTGTCTTGTGACTTACAGACCTGATAAAAGCCATAACACTGTCCGAACTGTGCT
ATTGGAGATGTCTTACAAACTGGACGATGCTGGAGAGCCGGTCTGTTCCTGTCTTCCTGTACAAACATTCCTTGGGGGAC
CCACTTGCAAACTGTTGACCAAAAGTGCCATCTTCCAAAGCCCAGAGAATAATGGCAATGTCCTAGTATGTACTGGGGAT
GAAGCATCACAGTCTACGCTGTTGTGGAATGCTGGCAGTGGCTTGTTGCTGCAGAACCTGAAGGCTGGTGAACCTGTCCT
GGACATCTGCCCATTTGAAACGAGTCAGAACAGCTATCTGGCCACCTTGACAGAGAAGACTGTCCATATGTACAAGTGGG
AG
ORF - retro_mmus_3088 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 98.97 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MAEVAVGQASDLVPSEMDHEVIYSHLQGPLEGTIEPATPTEVVSNGAPLQPAPAELANSQGGAHVQPAPA |
| MAEVAVGQASDLVPSEMDHEVIYSHLQGPLEGTIEPATPTEVVSNGAPLQPAPAELANSQGGAHVQPAPA | |
| Retrocopy | MAEVAVGQASDLVPSEMDHEVIYSHLQGPLEGTIEPATPTEVVSNGAPLQPAPAELANSQGGAHVQPAPA |
| Parental | EVVSSQDGLPTLQPLPPASIDLTEEVQPSEENMEVVNPGTSEEPSQGSGANPTAGAARSVSMNNFISGLQ |
| EVVSSQDGLPTLQPLPPASIDLTEEVQPSEENMEVVNPGTSEEPSQGSGAN.T.GAARSVSMNNFISGLQ | |
| Retrocopy | EVVSSQDGLPTLQPLPPASIDLTEEVQPSEENMEVVNPGTSEEPSQGSGANRTSGAARSVSMNNFISGLQ |
| Parental | RLHNMLELLRPPPADHSVGPIRTRRRMAPILRARAGESQRQDNGRYVPHTPLYAYFQVSRSQPYPLPAAH |
| RLHNMLELLRPPPADHSVGPIRTRRRMAPILRARAGESQRQDNGRYVPHTPLYAYFQVSRSQPYPLPAAH | |
| Retrocopy | RLHNMLELLRPPPADHSVGPIRTRRRMAPILRARAGESQRQDNGRYVPHTPLYAYFQVSRSQPYPLPAAH |
| Parental | DSETRNPPSGTDSDSDGSAEDEEVVVQAEEPEANIPEQGVIATDQEATSVTGDDAVPKESPQKPNMLSAM |
| DSETRNPPSGTDSDSDGSAEDEEVVVQAEEPEANIPEQGVIATDQEATSVTGDDAVPKESPQKP.MLSAM | |
| Retrocopy | DSETRNPPSGTDSDSDGSAEDEEVVVQAEEPEANIPEQGVIATDQEATSVTGDDAVPKESPQKPSMLSAM |
| Parental | EDEEGETCTICLEQWTNAGDHRISALRCGHLFGFRCISKWLKGQTRKCPQCNKKAKHSDIVVIYARSLRA |
| EDEEGETCTICLEQWTNAGDHRISALRCGHLFGFRCISKWLKGQT.KCPQCNKKAKHSDIVVIYARSLRA | |
| Retrocopy | EDEEGETCTICLEQWTNAGDHRISALRCGHLFGFRCISKWLKGQTGKCPQCNKKAKHSDIVVIYARSLRA |
| Parental | LDTSEQERMKSDLLNEQMLRKQAELESAQCRLQLQVLIDKCTKLNSRVQDLEKFVVRHQNSAAQQCSRSK |
| LDTSEQERMKSDLLNEQMLRKQAELESAQCRLQLQVLIDKCTKLNSRVQDLEKFVVRHQNSA.QQCSRSK | |
| Retrocopy | LDTSEQERMKSDLLNEQMLRKQAELESAQCRLQLQVLIDKCTKLNSRVQDLEKFVVRHQNSAVQQCSRSK |
| Parental | ALCGKCLSSSQSPGKYSSEKTFTISQTGKCRILAYCDGLSCLVASQPSPQASFLPGFGVKMLSTANMKSS |
| ALCGKCLSSSQ.PGKYSSEKTFTISQTGKCRILAYCDGLSCLVASQPSPQASFLPGFGVKMLSTANMKSS | |
| Retrocopy | ALCGKCLSSSQIPGKYSSEKTFTISQTGKCRILAYCDGLSCLVASQPSPQASFLPGFGVKMLSTANMKSS |
| Parental | QYIPMHNKQIRGLSFSSQSKGLLLSASLDCTIKLTSLETNTVVQTYNTGRPVWSCCWCLDENNYVYAGLA |
| QYIPMHNKQIRGLSFSSQSKGLLLSASLDCTIKLTSLETNTVVQTYNTGRPVWSCCWCLDENNYVYAGLA | |
| Retrocopy | QYIPMHNKQIRGLSFSSQSKGLLLSASLDCTIKLTSLETNTVVQTYNTGRPVWSCCWCLDENNYVYAGLA |
| Parental | SGSILIYDLRNTNTYIQELVPQKARCPLVSLSYLPKAAVAAFPYGGVLAGTLENASFWELKSDFSHKPHV |
| SGSILIYDLRNTNTYIQELVPQKARCPLVSLSYLPKAAVAAFPYGGVLAGTLENASFWELKSDFSHKPHV | |
| Retrocopy | SGSILIYDLRNTNTYIQELVPQKARCPLVSLSYLPKAAVAAFPYGGVLAGTLENASFWELKSDFSHKPHV |
| Parental | LSLEPGGFVDFQTESSTRHCLVTYRPDKSHNTVRTVLLEMSYKLDDAGEPVCSCLPVQTFLGGPTCKLLT |
| LSLEPG.FVDFQTESSTRHCLVTYRPDKSHNTVRTVLLEMSYKLDDAGEPVCSCLPVQTFLGGPTCKLLT | |
| Retrocopy | LSLEPGDFVDFQTESSTRHCLVTYRPDKSHNTVRTVLLEMSYKLDDAGEPVCSCLPVQTFLGGPTCKLLT |
| Parental | KSAIFQSPENNGNVLVCTGDEASQSTLLWNAGSGLLLQNLKAGEPVLDICPFETNQNSYLATLTEKTVHM |
| KSAIFQSPENNGNVLVCTGDEASQSTLLWNAGSGLLLQNLKAGEPVLDICPFET.QNSYLATLTEKTVHM | |
| Retrocopy | KSAIFQSPENNGNVLVCTGDEASQSTLLWNAGSGLLLQNLKAGEPVLDICPFETSQNSYLATLTEKTVHM |
| Parental | YKWE |
| YKWE | |
| Retrocopy | YKWE |
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 .05 RPM | 16 .05 RPM |
| SRP007412_cerebellum | 0 .09 RPM | 21 .36 RPM |
| SRP007412_heart | 0 .06 RPM | 14 .60 RPM |
| SRP007412_kidney | 0 .08 RPM | 25 .06 RPM |
| SRP007412_liver | 0 .03 RPM | 11 .66 RPM |
| SRP007412_testis | 0 .27 RPM | 42 .45 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_3088 was not detected
No EST(s) were mapped for retro_mmus_3088 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_129653 | 675 libraries | 350 libraries | 46 libraries | 1 library | 0 libraries |
The graphical summary, for retro_mmus_3088 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_3088 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_3088 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 | ENSMUSG00000033596 | 1 retrocopy |
retro_mmus_3088 ,
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