RetrogeneDB ID: | retro_mmus_2136 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 3:8327500..8329707(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Usp1 | ||
| Ensembl ID: | ENSMUSG00000028560 | ||
| Aliases: | None | ||
| Description: | ubiquitin specific peptidase 1 [Source:MGI Symbol;Acc:MGI:2385198] |
Retrocopy-Parental alignment summary:
>retro_mmus_2136
ACGGACTCTCGAAGGGCCATGACTGGTAACCAAGTTGTTCCTGCTGCACAGTCCTCCCAAGTAAGCTGCGAGAAGACAGA
GAACTTGTTACCATTTGTGAGATTGAATAACCTTGGCAATACTTGTTATCTGAATAGTATTCTTCAGGTGTTATACTTTT
GTCCTGGCTTTAAGACTGGAGTTAAGCACTTATTTAATATTATTTCAAGGAAGAAAGAAGCTCTAAAGGATGACTCTAAT
CAGAAGGATAAGGGAAGCTGCAAAGAAGAGTCTTTGGCAAGTTATGAGCTTATATGCAGTTTACAGTCCTTAATAATTTC
AGTTGAACAGCTTCAGGCTAGTTTTCTCTTAAATCCAGAGAAATATACAGATGAACTTGCTACACAGCCAAGGCGACTGC
TGAACACACTCAGGGAACTCAACCCTATGTATGAAGGATTTCTACAGCATGATGCACAGGAAGTGCTACAATGTATTCTG
GGAAACATTCAAGAAACATGCCAACTCCTAAAAAAAGAAGAAATAAAAAACCTGGCTGAATTATCCAGCAAGGTTGAAGA
ACAATCTCTTCAGAAAGAGGAAACAGGTGGAATTACCAGCACAAAGATTGACAGTATGAGGAATACGGAGGACGTCAAAG
AGCAGCTCCCCAAAGGGAACTGGAAAAGAAAAAGTGACACTGAGTCGAGTAACGTGAAGAAAAAGGTTAAACTGTCCAGG
GAATCCCAACCATTGGAAGAAAACCAGAGACAAACCAGATCCAAGAGAAAAGCTATCAGAGACACACTAGAGGCTGCTCC
TAAGATCATCCCCAAGTGTGTTTCTGAAAGTGAGAGTGCAAAGCCCTCACAGAAGAAATCAAAAGTTAAAATAAATTGGT
TAAAGCCATCCACTAAGCAACCCAGCATTCTTTCCAAGTTCTGTAGTCTTGGAAAATTAACAACTAACCAGCGCTCCAGA
GGACAACCTAAGGAAAAGGAGGGTGACGTTGAAGAGGACTTGGAGAAGTATGGAAGTGACCACACAGCTAATGGTGGACC
CGAATCTCCAGGAAGTAGCGTCACACCTGTAGACAGCAGTGAAGCCAAGTCCAGAAACAAAGGTGCTGAGCAGATTGGCT
TTGAGCTAGTAGAGAAACTGTTTCAAGGTCAGCTCGTGTTAAGGACTCGGTGTTTGGAATGTGAAAGCTTAACAGAAAGA
AGAGAAGATTTCCAGGATATTAGTCTTCCAGTGTAAGAAGATGAGCTTTCCAAGGTCGAGGAGAGCTCTGAAATTTCTCC
AGATCCAAAAACAGAAATGAAGACCTTGAGATGGGCAATTTCACAGTTTGCTTCAGTGGAGAGAATTGTAGGAGAGGATA
AATACTTCTGTGAAAATTGCCATCATTATACGGAAGCAGAGCGAAGTCTCCTGTTTGATAAAATGCCTGAAGTTATCACT
ATTCATCTGAAGTGCTTTGCTGCTAGTGGCTTGGAGTTTGATTGCTACGGTGGTGGACTTTCCAAGATCAACACTCCTTT
ATTGACACCTCTTAAACTGTCACTAGAAGAATGGAGCACAAAGCCGACGAATGACAGCTATGGATTATTTGCTGTTGTGA
TGCACAGTGGCATTACTATTAGTAGTGGGCACTATACCGCATCTGTTAAAGTCACTGACCTTAACAGTCTAGAACTCGAT
AAGGGGAATTTTGTGGTTGACCAGATGTGTGAAATAGGTAAGCCAGAGCCACTGAATGAGAAGGAAGCAAGGGGGACGGC
TGAAAATTATGACGATGAAGTATCAATTAGAGTTGGTGGAAATGCCCAGCCAAGTAAAGTTTTGAACAAAATAAATGTAG
AAGGTATTGGACTTCTTGGTGGACAAAAGAGCAAAGCAGATTATGAGCTGTACAACAAAGCATCTAATCCTGATAAGGTG
GTGGGACACCATTCACCGACAATAGAAATTCTGAAACTAATGATACTACTAATGGGAACCATGAATCTGACAGGAACAAG
GAATCCAGTGACCCAACAGGCATTACCATGAACGGACTTGAGAACAAAATTTCCTATGTAGTGCAAAGCTTAAAGGAGTA
CGAGGGGAAGTGGTTGCTCTTTGACGATTCTGAGGTAAAAGTGACAGAAGAGAAAGACTTTCTGAATTCTCTCTCCCCTT
CTACATCCCCTACGTCTACTCCCTACTTGCTATTCTATAAAAAATTA
ORF - retro_mmus_2136 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 94.44 % |
| Parental protein coverage: | 93.88 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | TSEYRGSEIDQVVPAAQSSPVSCEKRENLLPFVGLNNLGNTCYLNSILQVLYFCPGFKTGVKHLFNIISR |
| T...R.....QVVPAAQSS.VSCEK.ENLLPFV.LNNLGNTCYLNSILQVLYFCPGFKTGVKHLFNIISR | |
| Retrocopy | TDSRRAMTGNQVVPAAQSSQVSCEKTENLLPFVRLNNLGNTCYLNSILQVLYFCPGFKTGVKHLFNIISR |
| Parental | KKEALKDDSNQKDKGSCKEESLASYELICSLQSLIISVEQLQASFLLNPEKYTDELATQPRRLLNTLREL |
| KKEALKDDSNQKDKGSCKEESLASYELICSLQSLIISVEQLQASFLLNPEKYTDELATQPRRLLNTLREL | |
| Retrocopy | KKEALKDDSNQKDKGSCKEESLASYELICSLQSLIISVEQLQASFLLNPEKYTDELATQPRRLLNTLREL |
| Parental | NPMYEGFLQHDAQEVLQCILGNIQETCQLLKKEEIKNLAELSGKVEEQSLQKEETGGITSTEIDSMRNTE |
| NPMYEGFLQHDAQEVLQCILGNIQETCQL........LAELS.KVEEQSLQKEETGGITST.IDSMRNTE | |
| Retrocopy | NPMYEGFLQHDAQEVLQCILGNIQETCQLXXXXXXXXLAELSSKVEEQSLQKEETGGITSTKIDSMRNTE |
| Parental | DVKEQLPKGNWKRKSDSESSNVKKKVKLSRESQPLEENQRQTRSKRKAIGDTLEAAPKIIPKCVSESESA |
| DVKEQLPKGNWKRKSD.ESSNVKKKVKLSRESQPLEENQRQTRSKRKAI.DTLEAAPKIIPKCVSESESA | |
| Retrocopy | DVKEQLPKGNWKRKSDTESSNVKKKVKLSRESQPLEENQRQTRSKRKAIRDTLEAAPKIIPKCVSESESA |
| Parental | KPSQKKSKVKINWLKPSTKQPSILSKFCSLGKITTNQRSKGQPKEKEGDVEEDLEKYGSDHTANGGPESP |
| KPSQKKSKVKINWLKPSTKQPSILSKFCSLGK.TTNQRS.GQPKEKEGDVEEDLEKYGSDHTANGGPESP | |
| Retrocopy | KPSQKKSKVKINWLKPSTKQPSILSKFCSLGKLTTNQRSRGQPKEKEGDVEEDLEKYGSDHTANGGPESP |
| Parental | GSSVTPVDSSEAKSGNKGAEQIGFELVEKLFQGQLVLRTRCLECESLTERREDFQDISVPVQEDELSKVE |
| GSSVTPVDSSEAKS.NKGAEQIGFELVEKLFQGQLVLRTRCLECESLTERREDFQDIS.PV.EDELSKVE | |
| Retrocopy | GSSVTPVDSSEAKSRNKGAEQIGFELVEKLFQGQLVLRTRCLECESLTERREDFQDISLPV*EDELSKVE |
| Parental | ESSEISPEPKTEMKTLRWAISQFASVERIVGEDKYFCENCHHYTEAERSLLFDKMPEVITIHLKCFAASG |
| ESSEISP.PKTEMKTLRWAISQFASVERIVGEDKYFCENCHHYTEAERSLLFDKMPEVITIHLKCFAASG | |
| Retrocopy | ESSEISPDPKTEMKTLRWAISQFASVERIVGEDKYFCENCHHYTEAERSLLFDKMPEVITIHLKCFAASG |
| Parental | LEFDCYGGGLSKINTPLLTPLKLSLEEWSTKPTNDSYGLFAVVMHSGITISSGHYTASVKVTDLNSLELD |
| LEFDCYGGGLSKINTPLLTPLKLSLEEWSTKPTNDSYGLFAVVMHSGITISSGHYTASVKVTDLNSLELD | |
| Retrocopy | LEFDCYGGGLSKINTPLLTPLKLSLEEWSTKPTNDSYGLFAVVMHSGITISSGHYTASVKVTDLNSLELD |
| Parental | EGNFVVDQMCELGKPEPLTEEQARGTAGNYDDEVSIRVGGNAQPSKVLNKKNVEGIGLLGGQKSKADYEL |
| .GNFVVDQMCE.GKPEPL.E..ARGTA.NYDDEVSIRVGGNAQPSKVLNK.NVEGIGLLGGQKSKADYEL | |
| Retrocopy | KGNFVVDQMCEIGKPEPLNEKEARGTAENYDDEVSIRVGGNAQPSKVLNKINVEGIGLLGGQKSKADYEL |
| Parental | YNKASNPDKVV-GTPFTDNRNSETNDTTNGTHESDRNKESSDQTGVNMNGLENKISYVVQSLKEYEGKWL |
| YNKASNPDKVV.GTPFTDNRNSETNDTTNG.HESDRNKESSD.TG..MNGLENKISYVVQSLKEYEGKWL | |
| Retrocopy | YNKASNPDKVV<GTPFTDNRNSETNDTTNGNHESDRNKESSDPTGITMNGLENKISYVVQSLKEYEGKWL |
| Parental | LFDDSEVKVTEEKDFLNSLSPSTSPTSTPYLLFYKKL |
| LFDDSEVKVTEEKDFLNSLSPSTSPTSTPYLLFYKKL | |
| Retrocopy | LFDDSEVKVTEEKDFLNSLSPSTSPTSTPYLLFYKKL |
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 .02 RPM | 16 .35 RPM |
| SRP007412_cerebellum | 0 .09 RPM | 16 .20 RPM |
| SRP007412_heart | 0 .03 RPM | 10 .27 RPM |
| SRP007412_kidney | 0 .02 RPM | 16 .44 RPM |
| SRP007412_liver | 0 .08 RPM | 14 .12 RPM |
| SRP007412_testis | 0 .96 RPM | 261 .12 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_2136 was not detected
No EST(s) were mapped for retro_mmus_2136 retrocopy.
No TSS is located nearby retro_mmus_2136 retrocopy 5' end.
retro_mmus_2136 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_2136 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 5 parental genes, and 5 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Myotis lucifugus | ENSMLUG00000012439 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000028560 | 1 retrocopy |
retro_mmus_2136 ,
|
| Mus musculus | ENSMUSG00000054814 | 1 retrocopy | |
| Otolemur garnettii | ENSOGAG00000009357 | 1 retrocopy | |
| Tursiops truncatus | ENSTTRG00000013871 | 1 retrocopy |