RetrogeneDB ID: | retro_sscr_869 | ||
Retrocopy location | Organism: | Pig (Sus scrofa) | |
| Coordinates: | 6:55080122..55080843(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSSSCG00000003311 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PMM1 | ||
| Ensembl ID: | ENSSSCG00000000061 | ||
| Aliases: | None | ||
| Description: | phosphomannomutase 1 [Source:HGNC Symbol;Acc:9114] |
Retrocopy-Parental alignment summary:
>retro_sscr_869
GTGCTCTGCTTCTTTGATGTGGACAGGACTCTGACCGCCCCAAGGCAGAAAATTACCAAAGACATGGGTTGCTTTCTACA
AGAACTGAGGCCAGAAGATCAAAACTGGGGTCATGGATGGGTCAGACTTTGAGAAAGGACAGAAGCAACTGGAAAAAGAT
GTGGTTGAAAAATACAACTACGTGTTTCCAGAGAATAGATTGGTGGCATACAAAGATGGGAAACTCCTGTGTAAACCGCA
TATCCAAAGTCACTCGGGGGAAGCCCCGATTCAAGATTTAATCAACCAGTGTCTGAGCTACATTGTGAAAATTAAGCTGT
GGAAGAAGGGGGGTACTTTCATTGAATTCCAAAATGAGATGTTGAATGTGTCCCTATCAGAAGGAGCTGCACACAAGAAG
AATGCATTGAGCTCTACGAACGTGATACAAAAAGAAAATATCAGACAAAAATTCATGGAGGATCTGTGGAAAGAGTTTTC
ACAGAAAGAACTCACGTTTTCCATAGGAGGTCAGATCAACTTTGAAGTTTTCCCTGAGGGAGGGGACAAGAGGTGTTTCC
TGGAACACGTGGAAAAGGACAGCTTCAAGACCATTTATTTCTTTGGAGACAAAACCATGCCAGGCGGGAACGACCCTGAG
ATCGTCTGGGACCCAAGGGTGGTGGGCTACACTCTAACAGTGCCCAAGGACACATGCAGGATCTGCCAGGGTCTCTTCTA
C
ORF - retro_sscr_869 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 54.69 % |
| Parental protein coverage: | 92.37 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | VLCLFDVDGTLTPARQKIDPEVAAFLQKLR-SRVQIGVVGGSDYSKIAEQLGEGDEVVEKFDYVFAENGT |
| VLC.FDVD.TLT..RQKI......FLQ.LR......GV..GSD..K...QL.....VVEK..YVF.EN.. | |
| Retrocopy | VLCFFDVDRTLTAPRQKITKDMGCFLQELR>QKIKTGVMDGSDFEKGQKQLEK--DVVEKYNYVFPENRL |
| Parental | VQYKHGRLLSKQTIQNHLGEELLQDLINFCLHYMALLRLPKKRGTFIEFRNGMLNIS-PIGRSCTLEERI |
| V.YK.G.LL.K..IQ.H.GE...QDLIN.CL.Y.....L.KK.GTFIEF.N.MLN.S.PI.RSCT.EE.I | |
| Retrocopy | VAYKDGKLLCKPHIQSHSGEAPIQDLINQCLSYIVKIKLWKKGGTFIEFQNEMLNVS<PIRRSCTQEECI |
| Parental | EFSELD-KKEKIREKFVEALKTEFAGKGLRFSRGGMISFDVFPEGWDKRYCLDCLDQDCFDTIHFFGNET |
| E..E.D..KE.IR.KF.E.L..EF..K.L.FS.GG.I.F.VFPEG.DKR..L.....D.F.TI.FFG..T | |
| Retrocopy | ELYERD>QKENIRQKFMEDLWKEFSQKELTFSIGGQINFEVFPEGGDKRCFLEHVEKDSFKTIYFFGDKT |
| Parental | SPGGNDFEIYTDPRTVGHSVVSPQDTVQRCREIFF |
| .PGGND.EI..DPR.VG.....P.DT...C...F. | |
| Retrocopy | MPGGNDPEIVWDPRVVGYTLTVPKDTCRICQGLFY |
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 |
|---|---|---|
| SRP014902_placenta | 0 .00 RPM | 25 .88 RPM |
| SRP014902_testis | 0 .00 RPM | 18 .39 RPM |
| SRP018288_heart | 0 .00 RPM | 2 .80 RPM |
| SRP018288_kidney | 0 .00 RPM | 191 .00 RPM |
| SRP018288_liver | 0 .00 RPM | 12 .47 RPM |
| SRP018288_lung | 0 .00 RPM | 7 .54 RPM |
| SRP018856_adipose | 0 .12 RPM | 13 .02 RPM |
| SRP035408_brain | 0 .00 RPM | 34 .46 RPM |
| SRP035408_liver | 0 .00 RPM | 30 .15 RPM |
Sus scrofa was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_sscr_869 retrocopy.
Sus scrofa was not studied using FANTOM5 data.
retro_sscr_869 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_sscr_869 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Sus scrofa | ENSSSCG00000000061 | 1 retrocopy |
retro_sscr_869 ,
|
| Sus scrofa | ENSSSCG00000021236 | 1 retrocopy |