RetrogeneDB ID: | retro_mmus_3457 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | X:53844351..53844844(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000083278 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Tnfaip1 | ||
| Ensembl ID: | ENSMUSG00000017615 | ||
| Aliases: | Tnfaip1, Edp-1, Edp1, Tnfip1 | ||
| Description: | tumor necrosis factor, alpha-induced protein 1 (endothelial) [Source:MGI Symbol;Acc:MGI:104961] |
Retrocopy-Parental alignment summary:
>retro_mmus_3457
GACATGACATTAAAACCTCCCCTCAAAACATCAAAAAGCCAGGAATTGATGGCTAAAGCAAAATATTATCTCATCCAAGG
GCTTGTAAATGCATTCCAGACTACTATGCAGTACAAGAAAGATTCCCACCAGCCTATGGTCAACATTCCCATCATCATAT
TCCTGAGGGAAGAGAACAGCCTTATTGAATCTATGGCCAAGCCTGCAGCGAAGCATCTGTATAATAGAAATAATAAGTAG
TCCCACAGCAGCAGCTATGGGGACTTGATGGAAAAAATGGAGTTTTTGATAAGTGATCCCTTGATTAAGATGGGGGGTAC
TCTTTATCAAGGACACCATAGATGACCAGGTCTGCTGCTGGTCTTTCTACAGCCAGAGTCATTATTTGGCAAAAGTGTGG
TGTACCTCCATTATGTATGCCACAGATTAGTGTCAGACTACTATGTAATTCTCAGGATCTCCAATATATAAAAACTCAAT
GTCCTACTTTATA
ORF - retro_mmus_3457 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 53.85 % |
| Parental protein coverage: | 52.85 % |
| Number of stop codons detected: | 5 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | DDTITLPQSRQEIQELMAEAKYYLIQGLVSTCQTALQDKKDSYQPVCNIPIITSLREEDRLIESSTKPVV |
| D.T...P......QELMA.AKYYLIQGLV...QT..Q.KKDS.QP..NIPII..LREE..LIES..KP.. | |
| Retrocopy | DMTLKPPLKTSKSQELMAKAKYYLIQGLVNAFQTTMQYKKDSHQPMVNIPIIIFLREENSLIESMAKPAA |
| Parental | KLLYNRSNNKYSYTSNSDDHLLKNIE-LFDKLSLRFNG-RVLFIKDVIGDEICCWSFYGQGRKLAEVCCT |
| K.LYNR.NNK.S..S...D.L....E..FDK.SL...G..VLFIKD.I.D..CCWSFY.Q...LA.V.CT | |
| Retrocopy | KHLYNR-NNK*SHSSSYGD-LMEKME<VFDK*SLD*DG<GVLFIKDTIDDQVCCWSFYSQSHYLAKVWCT |
| Parental | SIVYATEKKQTKVEFPEARIYEETLNVLL |
| SI.YAT...QT...F....IY........ | |
| Retrocopy | SIMYATD*CQTTM*FSGSPIYKNSMSYFI |
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 | 47 .89 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 55 .97 RPM |
| SRP007412_heart | 0 .00 RPM | 80 .47 RPM |
| SRP007412_kidney | 0 .00 RPM | 68 .05 RPM |
| SRP007412_liver | 0 .00 RPM | 42 .87 RPM |
| SRP007412_testis | 0 .00 RPM | 20 .31 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_3457 was not detected
No EST(s) were mapped for retro_mmus_3457 retrocopy.
No TSS is located nearby retro_mmus_3457 retrocopy 5' end.
retro_mmus_3457 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_3457 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 4 parental genes, and 5 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Dasypus novemcinctus | ENSDNOG00000010870 | 1 retrocopy | |
| Monodelphis domestica | ENSMODG00000019235 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000017615 | 2 retrocopies |
retro_mmus_3457 , retro_mmus_3615,
|
| Pan troglodytes | ENSPTRG00000008912 | 1 retrocopy |