RetrogeneDB ID: | retro_sscr_953 | ||
Retrocopy location | Organism: | Pig (Sus scrofa) | |
| Coordinates: | 7:112747798..112748482(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | CSK | ||
| Ensembl ID: | ENSSSCG00000001900 | ||
| Aliases: | None | ||
| Description: | c-src tyrosine kinase [Source:HGNC Symbol;Acc:2444] |
Retrocopy-Parental alignment summary:
>retro_sscr_953
GTCATGCAGCAATATATCTCAGATGAAGATGGACTCTGCATTTGCCTCACTAAGCCAAAGGTAATGGAGTAACAAACTGC
CAGCTCAGGATGAGTTTTTTGGCAGCTGGTGGATACTAAACACAAAGAAACTGAATCTTCTGCAGACTCTTGGGAAGCGG
GGGGTTAGAGAGTTGATGCTGGGCGATTACCCCAGAAAGAATGTCACTGTCAAGTTCATTAATGTGATACCACTTTGCAT
ACCTTCCTGGCTGAAGTCTCTGTCATAACACAACTTAGGCATAGCAACCAGATACAGCTTCTGGATATGATCGTGGAGAG
AAAGGTGGGCTCTACATATTACTGAGTGAATGGCTGTGGGGAGTCTGTGCTGTTGGATTGTCAACAGTGGCAGAGTTTGT
ATTGGGTGGGGATCATCTCCTCACACGTTCACTAGACACATTAGGGGCCATGGAATACATGCGGGGCAAAAACATTTTGC
GCAGAGACCTGGATGCCCTCACCATGGCTGGTGTTTGAGGACAGTGTAGCCAAAATCAGTGACTTGAGCCTCATCAAGAA
GATTTCCAGCACACAGGACTCAGGCAAGCTGCTGGTCAAGTAGACAACTCCCAAGACCCTGAGAGAGAGAAAAAATTCTC
CACAAGGTTTGATGTATGAAGTTCTCTGGAAAATCTCCTCCTTT
ORF - retro_sscr_953 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 55.27 % |
| Parental protein coverage: | 51.45 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 6 |
Retrocopy - Parental Gene Alignment:
| Parental | LVEHYTSDADGLCTRLIKPKLMEGTVA-AQDEFFRSGWALNMKDLKLLQTIGKGEFGDVMLGDYRGNKVA |
| ....Y.SD.DGLC..L.KPK.ME...A.AQDEFF.S.W.LN.K.L.LLQT.GK......MLGDY....V. | |
| Retrocopy | VMQQYISDEDGLCICLTKPKVME*QTA>AQDEFFGSWWILNTKKLNLLQTLGKRGVRELMLGDYPRKNVT |
| Parental | VKCIK-NDATAQAFLAEASVMTQLRHSNLVQLLGVIVE-EKGGLYI-VTEYMAKGSLVDYLRSRGR-SVL |
| VK.I...D.T...FLAE.SV.TQLRHSN..QLL..IVE.EKGGLYI..TE.MA.GSL.......GR..VL | |
| Retrocopy | VKFIN<CDTTLHTFLAEVSVITQLRHSNQIQLLDMIVE<EKGGLYI<ITE*MAVGSLCCWIVNSGR>FVL |
| Parental | GGDCLLKFSLDVCEAMEYLEGNNFVHRDLAARNV-LVSEDNVAKVSDFGLTKEASSTQDTGKLPVKWTAP |
| GGD.LL..SLD...AMEY..G.N...RDL.A....LV.ED.VAK.SD..L.K..SSTQD.GKL.VK.T.P | |
| Retrocopy | GGDHLLTRSLDTLGAMEYMRGKNILRRDLDALTM>LVFEDSVAKISDLSLIKKISSTQDSGKLLVK*TTP |
| Parental | EALREKKFSTKSDVWSFGILLWEIYSF |
| ..LRE.K.S...........LW.I.SF | |
| Retrocopy | KTLRERKNSPQGLMYE---VLWKISSF |
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 | 57 .07 RPM |
| SRP014902_testis | 0 .00 RPM | 58 .84 RPM |
| SRP018288_heart | 0 .00 RPM | 11 .39 RPM |
| SRP018288_kidney | 0 .00 RPM | 20 .59 RPM |
| SRP018288_liver | 0 .00 RPM | 22 .55 RPM |
| SRP018288_lung | 0 .00 RPM | 96 .94 RPM |
| SRP018856_adipose | 0 .00 RPM | 43 .70 RPM |
| SRP035408_brain | 0 .00 RPM | 29 .76 RPM |
| SRP035408_liver | 0 .00 RPM | 20 .55 RPM |
Sus scrofa was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_sscr_953 retrocopy.
Sus scrofa was not studied using FANTOM5 data.
retro_sscr_953 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_sscr_953 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Equus caballus | ENSECAG00000013581 | 1 retrocopy | |
| Myotis lucifugus | ENSMLUG00000013625 | 1 retrocopy | |
| Sus scrofa | ENSSSCG00000001900 | 1 retrocopy |
retro_sscr_953 ,
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