RetrogeneDB ID: | retro_cpor_569 | ||
Retrocopy location | Organism: | Guinea Pig (Cavia porcellus) | |
| Coordinates: | scaffold_2:12876249..12877285(+) | ||
| Located in intron of: | ENSCPOG00000007869 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | RAB11FIP2 | ||
| Ensembl ID: | ENSCPOG00000000453 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cpor_569
ATAATACTGTCAGAGCAAGCCCTAAAGTCATTCCTACTCTATTGCACAGGTCACAGTGCTTCACGGCAAAGATCTGAAGC
CAGAAGGCAAAAGTGGCACCAGTGTATATACACTATAATTCATTTGGGCAAGAAAAAGTATCCTACCTTGTAGCTGACAA
AACCCTTAAGCCAATTTGGAAGGAAGAGGCCTCCTCTGAGCCACTAGATTGCTAATGGAGGGAAATCCAGAGAAATAATT
CTTGTCTTTAGTTATACACAGATCACTAGTAGGTCTGGATAAATTTCTAGGGCAGGTGGCAGTTAAGCTCAGTGACACCT
TTGAGGACAAACAAAGAAGGAAAACAGTAGTTTGGATTAGAATCCAAACAAGGAAAAAGAGTCAAAAACAGGGATGCAAT
AAAGGTCAATATTCAGTTTATGAGGAAAAAGATGACAGCAACTATGTTTGACTTATCAAAGAAGGACAAAACAAGGTCTG
CAAAATTAAAAGATAAGATGAAAGGTAGAAAAAATGGTGGGGTATTTTCTGATATGTCTTCTGCATTCATTCCAAGTACT
CACATGCCTGATGCCAGCGTTGAGTTTCAAGTGGTGAAGTACAAATGAAATCCAAACTGAAAAAGCCTTTTCTTTTGGGT
CCTCAGAATTTCTCTTTTGCACATTCATTGTCTGATTTAACTGAGTCCCACGCATCTTCTGAGAAACTAACGTGTGGTGC
TGTAGGTGAAACACATCTTCTTGGATGCCAGATAGATTCCTTTGGAGCAGTTTCCAGAGAGTAGAAGTCTCAAATCTCCA
CACAGAAGGATTTTGAGCTTTTGCACTTTTAAAATGAACCAACCTGACAGCATTGTGGATGAAGGTAAATTGTCTTTTGG
AAGACAAAATGACCTATTTGCAAACATGACTGCTTCATTACCCCCAAATTTGCAACATTGCCAAGAAAGGAAAATTTATT
TGAAGAAAACTGTGAGTCATGAGACAATAATATGAATTTGTTTTCAAAATCAATTGAAGTAAGAAAAGGGAGCAAG
ORF - retro_cpor_569 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 73.46 % |
| Parental protein coverage: | 68.36 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 8 |
Retrocopy - Parental Gene Alignment:
| Parental | MMLSEQAQKWFPTH-VQVTVLQAKDLKPKGKSGTND-TYTIIQLGKEKYSTS-VAEKTLEPVWKEEASFE |
| ..LSEQA.K.F.....QVTVL..KDLKP.GKSGT....YTII.LGK.KY.T..VA.KTL.P.WKEEAS.E | |
| Retrocopy | IILSEQALKSFLLY>AQVTVLHGKDLKPEGKSGTSV<IYTIIHLGKKKYPTL<VADKTLKPIWKEEASSE |
| Parental | -LPGLLMQGNPEKYILFLIVMHRSLVGLDKFLGQVAINLNDIFEDKQRRRT-EWFRLESKQGKSIKNRGE |
| ....LLM.GNPEK..L.L...HRSLVGLDKFLGQVA..L.D.FEDK..RR....F.LESKQGK..KNR.. | |
| Retrocopy | <ATRLLMEGNPEK*FLSLVI-HRSLVGLDKFLGQVAVKLSDTFEDK-QRRK>Q*FGLESKQGKRVKNRDA |
| Parental | IKVNIQFMRNNMTASMFDLSMKDKTRSPFAKLKDKMKGRKNDGTFSDTSSAIIPSTHMPDANTEF-SSGE |
| IKVNIQFMR..MTA.MFDLS.KDKTRS..AKLKDKMKGRKN.G.FSD.SSA.IPSTHMPDA..EF.SSGE | |
| Retrocopy | IKVNIQFMRKKMTATMFDLSKKDKTRS--AKLKDKMKGRKNGGVFSDMSSAFIPSTHMPDASVEF<SSGE |
| Parental | ILMKSKPKKPFLLGPQRLSSAHSMSDLTGSHASSEKLKSGAVGQTHLLGCRIDSFGAV-PESGSLKSPHR |
| ..MKSK.KKPFLLGPQ..S.AHS.SDLT.SHASSEKL..GAVG.THLLGC.IDSFGAV.PES.SLKSPHR | |
| Retrocopy | VQMKSKLKKPFLLGPQNFSFAHSLSDLTESHASSEKLTCGAVGETHLLGCQIDSFGAV>PESRSLKSPHR |
| Parental | RTLSFDTSKMNQPDSIVDEGELSFGRQNDLFTNVTASLP-QKFATLPRKKNPFEESSESWDSSMNLFSKS |
| R.LSF.T.KMNQPDSIVDEG.LSFGRQNDLF.N.TASLP..KFATLPRK.N.FEE..ES.D..MNLFSKS | |
| Retrocopy | RILSFCTFKMNQPDSIVDEGKLSFGRQNDLFANMTASLP<PKFATLPRKENLFEENCES*DNNMNLFSKS |
| Parental | IEVRKENK |
| IEVRK..K | |
| Retrocopy | IEVRKGSK |
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 .29 RPM | 24 .67 RPM |
| SRP017611_kidney | 0 .10 RPM | 11 .10 RPM |
| SRP017611_liver | 0 .00 RPM | 4 .18 RPM |
| SRP040447_lung | 0 .13 RPM | 7 .36 RPM |
| SRP040447_skeletal_muscle | 0 .01 RPM | 6 .56 RPM |
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_569 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_569 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 | ENSCPOG00000000453 | 1 retrocopy |
retro_cpor_569 ,
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