RetrogeneDB ID: | retro_sscr_1023 | ||
Retrocopy location | Organism: | Pig (Sus scrofa) | |
| Coordinates: | 9:37580915..37581658(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSSSCG00000002722 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_sscr_1023
CCACGCAAGCAGATACCCCAGTGTCTGTGCTTCTCCCAAACTTAAGAGCTTGTCCTTCAAACAGGAAAAGTGATTTAGTG
GATGGGAAAATCTTACCCTGAACTTAAGCCAGCTTATGGTGTTCAAGTCAATAAACTGGAAAAAAGATCAGAAGGTCAGT
GAGCATGTTTTCATTGGCACCCCCTGGGGCCATTCTGGACTGCTGCTCCAAGCTTACGTTCATTGACTCCAAGAAGATCA
AGATTTGACCTGGATGAAACTGACATGGTGATAGCTACTCACCACCACCAAGATCAGAATATCTCCATCTAGAGGCTGCT
ACCCAGGAACTGCCAGATGCTGTTTTCCCCCGCCACCTTTGAAGACTGTGTGGAAATTTGCCCAGACAGTGGTCCCAGAC
CCAAATATTATTAAACTGAGATTAAACAGGAAACAGTGAACAACAAGAAGCACTACTACATCCTGTGCAATAATAGAAAT
GAGAAGTTCCAGGCCTTGAATAGCCTCTATGAGACCATCGCCATTGCTTAAGCAATGATCTTCTGCCATACTCCTAAAAC
ACCTGGCTGGCTGGCAGTTGATCTCTCAAAAGAAGGCCACCAGGTGGCTCTGCTGACTGGTGAAATGAGGTGGAGCAGAG
GGCTGTAGTGATTGAGAACTCCAGAGAGAACAAAGAGAAAGTTCTGGTGACCACCAACATACATGCCCAAATTGTTGATT
TTGAACACATGTCTCTCATACTT
ORF - retro_sscr_1023 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 63.92 % |
| Parental protein coverage: | 51.77 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 6 |
Retrocopy - Parental Gene Alignment:
| Parental | PANRYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLER-GQKISEHIVIGTP-GTVLDWC |
| P....PQCLC.S.T.EL.LQTGKVI..MGK.YPELK.AY.V..NKLE...QK.SEH..IGTP.G..LD.C | |
| Retrocopy | PRKQIPQCLCFSQT*ELVLQTGKVI*WMGKSYPELKPAYGVQVNKLEK>DQKVSEHVFIGTP>GAILDCC |
| Parental | SKLKFID-PKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFED-SVWKFAQKVVPDPN |
| SKL.FID.P.....F.LDE.D..IAT..HQDQ.I.I.R.LPRNCQM.LFS.......VWKFAQ.VVPDPN | |
| Retrocopy | SKLTFID>PRRSR-FDLDETDMVIATHHHQDQNISI*RLLPRNCQM-LFSPATFE>TVWKFAQTVVPDPN |
| Parental | IIKLKR-EEETLDTIKQYYVLCNNRDEKFQALCNLYGAITIAQAMIFCHTRKTASWLAAELSKEGHQVAL |
| IIKL.....ET....K.YY.LCNNR.EKFQAL..LY..I.IA.AMIFCHT.KT..WLA..LSKEGHQVAL | |
| Retrocopy | IIKLRL<KQETVNNKKHYYILCNNRNEKFQALNSLYETIAIA*AMIFCHTPKTPGWLAVDLSKEGHQVAL |
| Parental | LSGEM-VVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVI |
| L.GEM..VEQRA.VIE..RE.KEKVLVTTN..A...D.E..S... | |
| Retrocopy | LTGEM<EVEQRAVVIENSRENKEKVLVTTNIHAQIVDFEHMSLIL |
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 | 3 .45 RPM |
| SRP014902_testis | 0 .00 RPM | 2 .69 RPM |
| SRP018288_heart | 0 .00 RPM | 3 .69 RPM |
| SRP018288_kidney | 0 .00 RPM | 5 .91 RPM |
| SRP018288_liver | 0 .00 RPM | 3 .36 RPM |
| SRP018288_lung | 0 .10 RPM | 7 .54 RPM |
| SRP018856_adipose | 0 .00 RPM | 5 .34 RPM |
| SRP035408_brain | 0 .00 RPM | 5 .18 RPM |
| SRP035408_liver | 0 .00 RPM | 6 .02 RPM |
Sus scrofa was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_sscr_1023 retrocopy.
Sus scrofa was not studied using FANTOM5 data.
retro_sscr_1023 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_sscr_1023 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 | |
|---|---|---|---|
| Choloepus hoffmanni | ENSCHOG00000010216 | 1 retrocopy | |
| Sus scrofa | ENSSSCG00000002722 | 1 retrocopy |
retro_sscr_1023 ,
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