RetrogeneDB ID: | retro_cpor_851 | ||
Retrocopy location | Organism: | Guinea Pig (Cavia porcellus) | |
| Coordinates: | scaffold_3:19930902..19932524(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PIAS1 | ||
| Ensembl ID: | ENSCPOG00000007278 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cpor_851
CCCCTGCATCCCGTTTCTCTTCTGGGACCTAAACCTGAACTGGAACTCCCACATCTTACATCAGCTCTTTACCCAGTCCC
TCCGACTACAAAACCTCAAAAACTACCATTTTAGGACTCACTGGATGAACAGACAAAACCCACTAGTCTAGCATCAGACA
ACAGCATTTTCAAGAAACCTGTTTTGCATTTACCTTGATCCCACAACAAGTGCAGCAGATCAGTAGCTCCGTGGATAATT
CTGGGACCAAATGTGACTTCACAGTACAGGTCCAGTTAAGGGTTTGTTTATCTGAAACCAGCTGGCCCCAGGAAGATCAC
TTCCCACCCGGTCTTTGCGTGAAAGCGAATACAAAACCTCGCAGCCTTCCAGGTTACCTTCCACCTACTAAAAATGGTGT
GGAACCAAAGAGACCCAGCAGACCAATTAATATCACCTCGCTTATCCGATTGTCCACAACAGTACCCAAATACCATTGCT
GTTTCTTGGACTGCGAAAATTGGAAGAGCCTATTCCATGGAAGTATATCTTATAAAACAGTTGTCCTCAACAGTTCTTCA
GAGGTTATGAACAAAGAGAATAAGGAATCCAGATCACTCTAGAACTTTAATTAAAGAGAAATTGACTGGGGATCCAGCCA
ATGAAATAGCTACAACCACCTAAGGGTTTCCCTTCTATGTCCACTTGGTAAAATGCGGTTGACAATTCCATACCAGGCCC
TTACATGCTCTCATCTGCAGTGTTTTGATGCAACTCTTTATATTCAGATGAATGAGAAAAAGCCAACCTGGGTCTGTCCT
GTCTGTGATAAGTAGGCTCCATAGGAACACATTATTGATGGCTTGTTTATGGAAATCCTAAAGTACTGTATAGACTGTGA
TGAAATACAGCTTAAGGAGGGCGGCTTTTGGGCACCAATGCGGTCAAAAAAGGAAGTTCAGGAAGTTTCTGCCTCTCACA
GTGCAGCTGATGGATGCTTGAGTTCCACTTTGGAGCATCAGGTGGCTTCTCAGAACCAGTCCTCCAGTAAAAACAACGAA
GTCAAGGTGATTGACCTAACTGTAAATAGCTCATCTGATGAAGAGGAAGAAACTTCTGCCAAGAGAACCTGTCCTGTCCT
TTCTCCCACCTCACTACTAAACCATAAAGACATTTTAAGTCTTCCACACCAAGCATCTCCAGTATCCTGTACCCCAAGCC
TTCCTGCTGTAGACACAAACTACATCAAAACCTCCCAGTCCAAGACTGCAGGCATCCTTTCCATGTGACACTTAACCACC
TATGACTTACAAAGATTAGATTTCTTTCCTTTCTTGTCAGGAGACAGTCAACATTACAACACCTCCCTGCTCGGAGCCAT
GACCGCTGCAGTCTCAGATGACCAGGACCTGCTGCACTCATCAAGCTTTTTCCTGTATATCTCCTCCCAGATGTTCCTCG
ACCAGCTAAGTGCAGGAGACAGCACGACCCTGCCTGCCACCAGTGGGAGCAGCAGTGGCAGCAACAGCAGCCTCCTGTCT
TCCAACAGCCTGAGGGAGGGCCACAGCCACACGGAAGCCAACAGGAGCAGCGTAGATGCAGTGTCTGTCTTCAACATCAT
AGTGGACATTATCTCCCTGGAC
ORF - retro_cpor_851 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 80.0 % |
| Parental protein coverage: | 79.91 % |
| Number of stop codons detected: | 5 |
| Number of frameshifts detected: | 5 |
Retrocopy - Parental Gene Alignment:
| Parental | PLLPVSLLGPKHELELPHLTSALHPVHP-DIKLQKLPFYDLLDELIKPTSLASDNSQRFRETCFAFALTP |
| PL.PVSLLGPK.ELELPHLTSAL.PV.P.D.K..K.....L.....K.T...S...Q.F.ETCFAF.L.P | |
| Retrocopy | PLHPVSLLGPKPELELPHLTSALYPVPP<DYKTSKTTILGLTG*TDK-TH*SSIRQQHFQETCFAFTLIP |
| Parental | QQVQQISSSMDISGTKCDFTVQVQLRFCLSETSCPQEDHFPPNLCVKVNTKPCSLPGYLPPTKNGVEPKR |
| QQVQQISSS.D.SGTKCDFTVQVQLR.CLSETS.PQEDHFPP.LCVK.NTKP.SLPGYLPPTKNGVEPKR | |
| Retrocopy | QQVQQISSSVDNSGTKCDFTVQVQLRVCLSETSWPQEDHFPPGLCVKANTKPRSLPGYLPPTKNGVEPKR |
| Parental | PSRPINITSLVRLSTTV-PNTIVVSWTAEIGRTYSMAVYLVKQLSSTVLLQRLRAKGIRNPDHSKALIKE |
| PSRPINITSL.RLSTTV.PNTI.VSWTA.IGR.YSM.VYL.KQLSSTV.LQRL..K.IRNPDHS..LIKE | |
| Retrocopy | PSRPINITSLIRLSTTV>PNTIAVSWTAKIGRAYSMEVYLIKQLSSTV-LQRL*TKRIRNPDHSRTLIKE |
| Parental | KLTADPDSEIATTS-LRVSLLCPLGKMRLTIPCRALTCSHLQCFDATLYIQMNEKKPTWVCPVCDKKAPY |
| KLT.DP..EIATT..LRVSLLCPLGKMRLTIP..ALTCSHLQCFDATLYIQMNEKKPTWVCPVCDK.AP. | |
| Retrocopy | KLTGDPANEIATTT<LRVSLLCPLGKMRLTIPYQALTCSHLQCFDATLYIQMNEKKPTWVCPVCDK*AP* |
| Parental | EHLIIDGLFMEILKYCTDCDEIQFKEDGSWAPMRSKKEVQEVSASYNGVDGCLSSTLEHQVASHNQSSSK |
| EH.IIDGLFMEILKYC.DCDEIQ.KE.G.WAPMRSKKEVQEVSAS....DGCLSSTLEHQVAS.NQSSSK | |
| Retrocopy | EH-IIDGLFMEILKYCIDCDEIQLKEGGFWAPMRSKKEVQEVSASHSAADGCLSSTLEHQVASQNQSSSK |
| Parental | NKKVEVIDLTIDSSSDEEEEEPSAKRTCPSLSPTSPLNNKGILSLPHQASPVSRTPSLPAVDTSYINTSL |
| N..V.VIDLT..SSSD.EEEE.SAKRTCP.LSPTS.LN.K.ILSLPHQASPVS.TPSLPAVDT.YI.TS. | |
| Retrocopy | NNEVKVIDLTVNSSSD-EEEETSAKRTCPVLSPTSLLNHKDILSLPHQASPVSCTPSLPAVDTNYIKTSQ |
| Parental | -IQDYRHPFHMT-PMPYDLQGLDFFPFLSGDNQHYNTSLLAAAAAAVSDDQDLLHSSRFFPYTSSQMFLD |
| ..QD.RHPFH.T....YDLQ.LDFFPFLSGD.QHYNTSLL.A..AAVSDDQDLLHSS.FF.Y.SSQMFLD | |
| Retrocopy | <VQDCRHPFHVT>LTTYDLQRLDFFPFLSGDSQHYNTSLLGAMTAAVSDDQDLLHSSSFFLYISSQMFLD |
| Parental | QLSAGGSTSLPATNGSSSGSNSSLVSSNSLRENHSHTVASRSSTDAASVFGIIPDIISLD |
| QLSAG.ST.LPAT.GSSSGSNSSL.SSNSLRE.HSHT.A.RSS.DA.SVF.II.DIISLD | |
| Retrocopy | QLSAGDSTTLPATSGSSSGSNSSLLSSNSLREGHSHTEANRSSVDAVSVFNIIVDIISLD |
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 |
|---|---|---|
| SRP017611_brain | 0 .00 RPM | 25 .59 RPM |
| SRP017611_kidney | 0 .00 RPM | 17 .38 RPM |
| SRP017611_liver | 0 .00 RPM | 9 .53 RPM |
| SRP040447_lung | 0 .00 RPM | 31 .83 RPM |
| SRP040447_skeletal_muscle | 0 .00 RPM | 7 .45 RPM |
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_851 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_851 was not experimentally validated.
Retrocopy orthology:
Cavia porcellus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Cavia porcellus | ENSCPOG00000007278 | 1 retrocopy |
retro_cpor_851 ,
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