RetrogeneDB ID: | retro_cpor_755 | ||
Retrocopy location | Organism: | Guinea Pig (Cavia porcellus) | |
| Coordinates: | scaffold_26:23320290..23321157(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | HAUS6 | ||
| Ensembl ID: | ENSCPOG00000008053 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cpor_755
ATGAGCTCTGCCTGAGTCACTTCTGTTGAGAAGCAGCATTTCTGGACATATCTGTAGGTGCTCAGCTTCAAGCCAGGCCC
AGCTATCATGGTCCACAGGAAGATTTTGTTGCACACACAACTTGGAGTGAACATGTTGGATGAACTGAGCCATGATGCCT
TTCAAATAGTTTATTTTTGTTTCAAATGCTAGACCAGTCTCTCATCAAAGAAGTTTTCAAGTTTTGCTGATCTCCATTTG
ACTGAAAAGTGACACCAAATTCCAGAAACACTGTTGTGAATAGTTAAAAAATATGTCTGACAAATGTGAAAGTAGCTTTT
CTCAAGTCCTTGGCTCACTTTTTCTTTCTCTTGGTGGTTCTAAGTTTATTCATTTGATATATCATTTTGCAAGAGTTGTT
GCAATGAAATATATTGGGACCAATTTCAAAAGTTCTTCTCTACATTTTACAGAAACATTTAATATAAAGACACAAGATAT
GCACAAGTGCCTTTCCAGATATCATATAGCATGTAAGGAGTTTTATAAATTTTATAAAGAGAAGATTGTGTTGTCCAAAA
ATATCAGGAAAATGCCCAATTATCAGTTAAGCTAGTTCAGAATTTGAGACCAGTATATATAGGATTGCAAAACTAAATAA
AAAATGGAACCCTCTGATGAGTAAATATTATAAAAGAGAAAACTGAGAAGGTTCAATCTTTGTGGACCTAAGTAAATGAC
ATAAAGTTTTGGAAAGAGAAAGTGAAGTTCTTAATTTCAGTCCTTAGTCTTGTTAACCAATATGATTTAGATGGAAGTAA
TTTTGTTATTAATATTCTAAATCTCTTTCTTGACAAAACAGAGAAATAGATGTGACAGTTATTCATC
ORF - retro_cpor_755 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 64.88 % |
| Parental protein coverage: | 53.28 % |
| Number of stop codons detected: | 12 |
| Number of frameshifts detected: | 6 |
Retrocopy - Parental Gene Alignment:
| Parental | MSSACVTSFEKQHLWMYLRALGFEPGRAAVASGKIVSHTHLGVNMFDKLNRDAFHIVSYF-LFQTLDQSL |
| MSSA.VTS.EKQH.W.YL..L.F.PG.A.....KI..HT.LGVNM.D.L..DAF.IV.YF.LFQ.LDQSL | |
| Retrocopy | MSSA*VTSVEKQHFWTYL*VLSFKPGPAIMVHRKILLHTQLGVNMLDELSHDAFQIV-YF<LFQMLDQSL |
| Parental | TKEVFKFCWPPFD-QKSDTEFRKHCCEWLKKISAECD-SFPQVVGSLFLSPGGPKFIHLMYHFARYVAIK |
| .KEVFKFC..PFD..KSDT.F.KHCCE.LK..S..C..SF.QV.GSLFLS.GG.KFIHL.YHFAR.VA.K | |
| Retrocopy | IKEVFKFC*SPFD<LKSDTKFQKHCCE*LKNMSDKCESSFSQVLGSLFLSLGGSKFIHLIYHFARVVAMK |
| Parental | YIKANSKNSSLHFSETCNVKTQDMHKCLARCLIARNRF-LQILQREDCVIRKYHENAQLSVKQLRNLRSE |
| YI..N.K.SSLHF.ET.N.KTQDMHKCL.R..IA...F.L.IL.REDCV..KY.ENAQLSVK...NLR.. | |
| Retrocopy | YIGTNFKSSSLHFTETFNIKTQDMHKCLSRYHIACKEF<L*IL*REDCVVQKYQENAQLSVKLVQNLRPV |
| Parental | YIGLQNQI-KKMEP-SDDQSILKEKI-EKVRSLWTLVNETLMVLEKEREVVNSVLSLVNQYDLDGSNVVI |
| YIGLQN.I.KK..P.SD.....K.K..EKV.SLWT.VN......EK......SVLSLVNQYDLDGSN.VI | |
| Retrocopy | YIGLQN*I<KKWNP<SDE*IL*KRKL<EKVQSLWT*VNDIKFWKEKVKFLI-SVLSLVNQYDLDGSNFVI |
| Parental | NIPSLLLDKIEKQMGQLHI |
| NI..L.LDK.EK.M.QL.I | |
| Retrocopy | NILNLFLDKTEK*M*QLFI |
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 | 5 .00 RPM |
| SRP017611_kidney | 0 .00 RPM | 5 .44 RPM |
| SRP017611_liver | 0 .00 RPM | 3 .44 RPM |
| SRP040447_lung | 0 .00 RPM | 5 .42 RPM |
| SRP040447_skeletal_muscle | 0 .00 RPM | 1 .94 RPM |
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_755 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_755 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 | ENSCPOG00000008053 | 1 retrocopy |
retro_cpor_755 ,
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