RetrogeneDB ID: | retro_sscr_244 | ||
Retrocopy location | Organism: | Pig (Sus scrofa) | |
| Coordinates: | 10:22598112..22599237(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | TPST2 | ||
| Ensembl ID: | ENSSSCG00000009963 | ||
| Aliases: | None | ||
| Description: | tyrosylprotein sulfotransferase 2 [Source:HGNC Symbol;Acc:12021] |
Retrocopy-Parental alignment summary:
>retro_sscr_244
ATGCGCCTGTTGGTGTGGAGGGCACTGCTGGCAGCCGGCCTTGCCCTGGCCCTGGTGCTGGCCATCCAGCTAGGGCAGCA
GGTGCTGGAGTGCCAGGCAGTGCTGGGGGCCCCCCAGAACCCCTGGCAGGCTATGCGGCCGGAGCAGGAGGACCTGGTGA
TGATGGGCACGGACTATGTGGAATACCATTGTGGCAAGGCTATGCCGCACATCTTCGTGGGGGGCGTGCCCCTGAGCTGC
ACTACACTGATGCACATGATGCTGGATGCCCACCTGGAAGTGCGCTGCGGTGAGGAGACCCGCATCATCCCCCAGGCCAT
GCGTCAGGCCTGGTCCAAGTCCCGTGGGGAGAAGCTGCGGCTGGATGAAGCCAGCATCACGGACCAAGCGCTGGAGGCCA
CCATGCAGGCCTTCATCCTGGAGGTGATCGCCAAGCATGGCCGGCCGGCCGGCATCCTCTGCAACAAAGACCCATTCACC
CTCAAGTCCTCTGTCTGCCTGTCACGCCTGTTCCCCAACTCTAAGTCCCTGCTGATGGTGTGAGATGGCTGGGCCTTGGT
GCACTCCATGATCACCCGCAAGGTCACCATTGCTGGCTTTGACCTCAGCAGCTACCACAACTGCCCCACCAAGTGGAACA
AGGCCATTGAGGTGATGTAGGCACAGTGTGTGGAGGTGGGCAAGGACAAGTGTCTGCCGGTGTACTACTAGCAGCTGGTG
CTGCACCCCCGTTGCTCCCTCAAGCTCATCCTCAACTTCCTTGGCATCACCTGGAGTGATGCTGTCCTGCACTACGAGGA
CCTCATTGGCAAGCCCGGAGGTGTCTCCCTGTTCAAGATTGAGCAATCCACAGTCCAGGTCATCAAGCCTGTGAACCTGG
AAGCTCTCATCAAGAAGACTGGCCACATCCCTGGGGACATGATGTGAGACATGGCCCAGATCACCCCCATGCTGGCTCGG
CTAGGCTATGACCCCTATGCAAACCCACCCAACTACAGCAACCTTGACCCCATCGTTGTCAACAACACACACGAGGTCTT
GAAAGGGGACTGTAAAACACCAGCCAATCTGAAAGGATATTTTCAGGTGAACCAGAATGGTACCTCCTCCCACCTAAGAA
GTGCA
ORF - retro_sscr_244 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 83.82 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MRLSVRRALLAAGLALALVLAVQLGQQVLECRAVLGGPRSPRRAMRPEQEDLVMMGTDHVEYRYGKAMPL |
| MRL.V.RALLAAGLALALVLA.QLGQQVLEC.AVLG.P..P..AMRPEQEDLVMMGTD.VEY..GKAMP. | |
| Retrocopy | MRLLVWRALLAAGLALALVLAIQLGQQVLECQAVLGAPQNPWQAMRPEQEDLVMMGTDYVEYHCGKAMPH |
| Parental | IFVGGVPRSGTTLMRAMLDAHPEVRCGEETRIIPRVLAMRQAWSKSGREKLRLDEAGVTDEVLDAAMQAF |
| IFVGGVP.S.TTLM..MLDAH.EVRCGEETRIIP...AMRQAWSKS..EKLRLDEA..TD..L.A.MQAF | |
| Retrocopy | IFVGGVPLSCTTLMHMMLDAHLEVRCGEETRIIPQ--AMRQAWSKSRGEKLRLDEASITDQALEATMQAF |
| Parental | ILEVIAKHGEPARVLCNKDPFTLKSSVYLSRLFPNSKFLLMVRDGRASVHSMITRKVTIAGFDLSSYRDC |
| ILEVIAKHG.PA..LCNKDPFTLKSSV.LSRLFPNSK.LLMV.DG.A.VHSMITRKVTIAGFDLSSY..C | |
| Retrocopy | ILEVIAKHGRPAGILCNKDPFTLKSSVCLSRLFPNSKSLLMV*DGWALVHSMITRKVTIAGFDLSSYHNC |
| Parental | LTKWNKAIEVMYAQCMEVGKDKCLPVYYEQLVLHPRRSLKLILDFLGIAWSDAVLHHEDLIGKPGGVSLS |
| .TKWNKAIEVM.AQC.EVGKDKCLPVYY.QLVLHPR.SLKLIL.FLGI.WSDAVLH.EDLIGKPGGVSL. | |
| Retrocopy | PTKWNKAIEVM*AQCVEVGKDKCLPVYY*QLVLHPRCSLKLILNFLGITWSDAVLHYEDLIGKPGGVSLF |
| Parental | KIERSTDQVIKPVNLEALTKWTGHIPGDVMRDMAQIAPMLARLGYDPYANPPNYGNPDPIVVNNTHRVLK |
| KIE.ST.QVIKPVNLEAL.K.TGHIPGD.M.DMAQI.PMLARLGYDPYANPPNY.N.DPIVVNNTH.VLK | |
| Retrocopy | KIEQSTVQVIKPVNLEALIKKTGHIPGDMM*DMAQITPMLARLGYDPYANPPNYSNLDPIVVNNTHEVLK |
| Parental | GDYKTPANLKGYFQVNQNSTSSHLGSA |
| GD.KTPANLKGYFQVNQN.TSSHL.SA | |
| Retrocopy | GDCKTPANLKGYFQVNQNGTSSHLRSA |
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 | 3 .85 RPM | 6 .50 RPM |
| SRP014902_testis | 22 .21 RPM | 23 .62 RPM |
| SRP018288_heart | 0 .65 RPM | 7 .26 RPM |
| SRP018288_kidney | 0 .89 RPM | 6 .11 RPM |
| SRP018288_liver | 5 .92 RPM | 4 .48 RPM |
| SRP018288_lung | 11 .00 RPM | 26 .78 RPM |
| SRP018856_adipose | 2 .30 RPM | 42 .99 RPM |
| SRP035408_brain | 1 .52 RPM | 15 .31 RPM |
| SRP035408_liver | 2 .44 RPM | 3 .87 RPM |
Sus scrofa was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_sscr_244 retrocopy.
Sus scrofa was not studied using FANTOM5 data.
retro_sscr_244 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_sscr_244 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 | ENSSSCG00000009963 | 1 retrocopy |
retro_sscr_244 ,
|
| Tursiops truncatus | ENSTTRG00000009430 | 1 retrocopy |