RetrogeneDB ID: | retro_cpor_128 | ||
Retrocopy location | Organism: | Guinea Pig (Cavia porcellus) | |
| Coordinates: | scaffold_58:9359706..9360894(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCPOG00000025958 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSCPOG00000007879 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cpor_128
ATGCTAGGCCCATGTCACCTCATCGTTGTCCTCCTGGCCATGACCATCTCCTGCACTGGGGCACGCCATGCGTCACTGTG
GGCGGAAAACTGCAGAAAATCAACATATCCTCCTTCCGGACCAACCTACAAAGGACCGGTTACATGGTATGTCATAAATC
TTGATTTACCACCCTATAATAGATGGCATGAATTAATGGCTGATAAGCGACCAGTGCTAAAGATCATAGTGAAGTCCATG
AAGAATATAGTAAATACACTTGTACCGAGTGGAAAAGTTATGCAGATGGTGGATCACAAGTTGCCTAAACTACTTGGCAG
ATTTCCTAGTCCTTATGAAGAGGAAATGAAGGGAATTGCAACTGTTACTAACATACCTTTAGGAGAGATCATTTTATTCA
ATATTTTTTATGAATTGTTTACTATGTGTACCTCAATAATAACCGAAGACAAGAACGGTCATCTACTACATGTTAGAAAC
TTGGATTTTGGAATATTTCTCAAGCAGAACAAAAATAATAGTAAGTCAATAATAACTGAGCAACTAAAACTTTTAACAGT
GAATTTGGACTTCCAAAGGAACAATAAAACTGTCTTTAAGGCTACAAGCTTTGCTGGCTATGTAGGCACCCTAACGGGTT
TCAAACCAAGACTATTTAGTCTCACACTAAACCAACGTTTCAGCCTACATGGTGGCTATCTGGGTATTCTTGAGTGGATT
TTAGGAAAGAAAGATGCTGCGTGGATAGGATTTATCATTAGATCAGTGCTGGAAAATGGTATAAGCTATGAAGAAGCCCA
GAAAATACTGATGAAAACCAAGTTATTGGTCCCAGTGTACTTTATTCTGGGCGGTAGCAAGTCTGGAGAAGGATGTGTGA
TTACACGAGACAGAAAAGACTCTTTGGATGTATATGAACTCAGTCCTAAACAGGGTAGATGGTTTTTGGTGCAAACAAAT
TATGATCGATGGAGAACCCCGCTATTGCATGATCATCGCAGAACACCTGCAGAGGTGTGTCTAAAACACACAACCCAAGA
GAGGCTGTCATTTGCAAGCTTATATGACGTTCTATCAACAAAACCCATTCTCAACAAGCTGACTGTGTTCACAACCTTGA
TTGATGTTACAAACAATCGATATGAAACTTACCTCCGGAATTGCCCACACCCTTGTATGGGCTGGTAA
ORF - retro_cpor_128 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 79.4 % |
| Parental protein coverage: | 92.48 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | WTEDCRKSTYPPSGPTYRGPIPWYTINLDLPPYKRWHELMADKGPMLKIIVNSMKNMVNTFAPSGKVMQM |
| W.E.CRKSTYPPSGPTY.GP..WY.INLDLPPY.RWHELMADK.P.LKIIV.SMKN.VNT..PSGKVMQM | |
| Retrocopy | WAENCRKSTYPPSGPTYKGPVTWYVINLDLPPYNRWHELMADKRPVLKIIVKSMKNIVNTLVPSGKVMQM |
| Parental | VDQKLPDLLGQFSSPYEEEMKGIADITEIPLGEIIAFNIFYELFTMCTSIITEDKKGHLLHARNMDFGIF |
| VD.KLP.LLG.F.SPYEEEMKGIA..T.IPLGEII.FNIFYELFTMCTSIITEDK.GHLLH.RN.DFGIF | |
| Retrocopy | VDHKLPKLLGRFPSPYEEEMKGIATVTNIPLGEIILFNIFYELFTMCTSIITEDKNGHLLHVRNLDFGIF |
| Parental | LGWNINNNTWVITEQLKPLSVNLDFQRNNKTVFKATSFAGYVGMLTGFKPGKFSVTLNERFSLNGGYLGL |
| L..N.NN....ITEQLK.L.VNLDFQRNNKTVFKATSFAGYVG.LTGFKP..FS.TLN.RFSL.GGYLG. | |
| Retrocopy | LKQNKNNSKSIITEQLKLLTVNLDFQRNNKTVFKATSFAGYVGTLTGFKPRLFSLTLNQRFSLHGGYLGI |
| Parental | LEWILGKKDAMWIGFITRSVLENSTSYEDAKNILANTKLLAPVYFILGGNQSGEGCVITRERKDSLDIYE |
| LEWILGKKDA.WIGFI.RSVLEN..SYE.A..IL..TKLL.PVYFILGG..SGEGCVITR.RKDSLD.YE | |
| Retrocopy | LEWILGKKDAAWIGFIIRSVLENGISYEEAQKILMKTKLLVPVYFILGGSKSGEGCVITRDRKDSLDVYE |
| Parental | LDPKQGRWYLVQTNYDHWKKPLFIDDRRTPAQTCLKRTTQENLSFATLYDILSTKPVLNKLTVFTTLMDV |
| L.PKQGRW.LVQTNYD.W..PL..D.RRTPA..CLK.TTQE.LSFA.LYD.LSTKP.LNKLTVFTTL.DV | |
| Retrocopy | LSPKQGRWFLVQTNYDRWRTPLLHDHRRTPAEVCLKHTTQERLSFASLYDVLSTKPILNKLTVFTTLIDV |
| Parental | TKNHFEAYLRDCPDPCMGW |
| T.N..E.YLR.CP.PCMGW | |
| Retrocopy | TNNRYETYLRNCPHPCMGW |
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 | 29 .74 RPM |
| SRP017611_kidney | 0 .00 RPM | 44 .81 RPM |
| SRP017611_liver | 0 .00 RPM | 24 .59 RPM |
| SRP040447_lung | 0 .00 RPM | 59 .40 RPM |
| SRP040447_skeletal_muscle | 0 .00 RPM | 4 .41 RPM |
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_128 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_128 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 | ENSCPOG00000007879 | 1 retrocopy |
retro_cpor_128 ,
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