RetrogeneDB ID: | retro_mmus_1722 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 18:50134794..50135508(+) | ||
| Located in intron of: | ENSMUSG00000024507 | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000085939 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Cd63 | ||
| Ensembl ID: | ENSMUSG00000025351 | ||
| Aliases: | Cd63, C75951, ME491, Tspan30 | ||
| Description: | CD63 antigen [Source:MGI Symbol;Acc:MGI:99529] |
Retrocopy-Parental alignment summary:
>retro_mmus_1722
ATGGCGGTGGAAGGAGGAATGAAGTGTGTCAAGTTTTTGCTCTACGTTCTCCTGCTGGCCTTCTGCACCTGTGCAGTGGG
ATTGATCGCCATTGGTGTAGCGGTTCAGGTTGTCTTGAAGCAGGCTATTACCTATGAGACTACTGCTGGCTCGCTGTTGC
CTGTGGTCATCATTGCAGTGGGTGCCTTCCTCTTCCTGGTGGCCTTTGTGGGCTGCTGTGGCGCCTGCAAGGAGAACTAC
TGTCTCATGATTACATTTGCCATCTTCCTGTCTCTTATCATGCTTGTGGAGGTGGCTGTGGCCATTGCTGGCTATGTGTT
TAGAGACCAGGTGAAGTCAGAGTTTAATAAAAGCTTCCAGCAGCAGATGCAGAATTACCTTAAAGACAACAAAACAGCCA
CTATTTTGGACAAATTGCAGAAAGAAAATAACTGCTGTGGAGCTTCTAACTACACAGACTGGGAAAACATCCCCGTCATG
GCCAAGGACAGAGTCCCCGATTCTTGCTGCATCAACATAACTGTGGGCTGTGGGAATGATTTCAAGGAATCCACTATCCA
TACCCAGGGCTGCGTGGAGACTATAGCAATATGGCTAAGGAAGAACATACTGCTGGTGGCTGCAGTGGCCCTGGGCATTG
CTTTTGTGGAGGTCTTGGGAATTATCTTCTCCTGCTGTCTGGTGAAAAGTATTCGAAGTGGCCATGAAGTAATG
ORF - retro_mmus_1722 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 97.9 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MAVEGGMKCVKFLLYVLLLAFCACAVGLIAIGVAVQVVLKQAITHETTAGSLLPVVIIAVGAFLFLVAFV |
| MAVEGGMKCVKFLLYVLLLAFC.CAVGLIAIGVAVQVVLKQAIT.ETTAGSLLPVVIIAVGAFLFLVAFV | |
| Retrocopy | MAVEGGMKCVKFLLYVLLLAFCTCAVGLIAIGVAVQVVLKQAITYETTAGSLLPVVIIAVGAFLFLVAFV |
| Parental | GCCGACKENYCLMITFAIFLSLIMLVEVAVAIAGYVFRDQVKSEFNKSFQQQMQNYLKDNKTATILDKLQ |
| GCCGACKENYCLMITFAIFLSLIMLVEVAVAIAGYVFRDQVKSEFNKSFQQQMQNYLKDNKTATILDKLQ | |
| Retrocopy | GCCGACKENYCLMITFAIFLSLIMLVEVAVAIAGYVFRDQVKSEFNKSFQQQMQNYLKDNKTATILDKLQ |
| Parental | KENNCCGASNYTDWENIPGMAKDRVPDSCCINITVGCGNDFKESTIHTQGCVETIAIWLRKNILLVAAAA |
| KENNCCGASNYTDWENIP.MAKDRVPDSCCINITVGCGNDFKESTIHTQGCVETIAIWLRKNILLVAA.A | |
| Retrocopy | KENNCCGASNYTDWENIPVMAKDRVPDSCCINITVGCGNDFKESTIHTQGCVETIAIWLRKNILLVAAVA |
| Parental | LGIAFVEVLGIIFSCCLVKSIRSGYEVM |
| LGIAFVEVLGIIFSCCLVKSIRSG.EVM | |
| Retrocopy | LGIAFVEVLGIIFSCCLVKSIRSGHEVM |
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 .19 RPM | 24 .86 RPM |
| SRP007412_cerebellum | 0 .04 RPM | 31 .78 RPM |
| SRP007412_heart | 0 .50 RPM | 80 .41 RPM |
| SRP007412_kidney | 3 .70 RPM | 479 .91 RPM |
| SRP007412_liver | 0 .00 RPM | 4 .64 RPM |
| SRP007412_testis | 0 .05 RPM | 10 .98 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_1722 was not detected
No EST(s) were mapped for retro_mmus_1722 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_59717 | 85 libraries | 26 libraries | 116 libraries | 126 libraries | 719 libraries |
| TSS #2 | TSS_59718 | 524 libraries | 358 libraries | 183 libraries | 6 libraries | 1 library |
| TSS #3 | TSS_59719 | 401 libraries | 309 libraries | 302 libraries | 56 libraries | 4 libraries |
The graphical summary, for retro_mmus_1722 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_1722 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_1722 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 | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000011931 | 1 retrocopy | |
| Callithrix jacchus | ENSCJAG00000007935 | 1 retrocopy | |
| Cavia porcellus | ENSCPOG00000009142 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000025351 | 1 retrocopy |
retro_mmus_1722 ,
|
| Mus musculus | ENSMUSG00000058254 | 1 retrocopy |