RetrogeneDB ID: | retro_cpor_656 | ||
Retrocopy location | Organism: | Guinea Pig (Cavia porcellus) | |
| Coordinates: | scaffold_21:16888236..16889348(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PRKCI | ||
| Ensembl ID: | ENSCPOG00000015212 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cpor_656
CCAAGAAAAGATAAACCCATCTACTGCAGAGCTGCATGCCTCTAGAGAAAGCTTTATTATGCAAATGGGCACACTTTTCA
AGCCAAAGGTTTCATTCAGCAGTCGTGCTGATTGTACCATCTTCTCAGTCCATACAGGGTGGCTTGGATGCTAGATATAC
AAGTGTATCAACTGTAAACTTTTGGTTCATATGAAGTGCCACACACTTGTCACAATTGAATGCAAGCAGCATTTTTTGCC
ACCAGAACCCATGATGACAATGGATCGATCACCCATGTCTTTAGACCCTGCACAGATAGTAATTCTATATAATCCCAAAA
GTCATAAAGGTTTGGAAGAATTAGATGAAGGGAATGAGGCAGGGAACAACTGGGAAAAGTGTATGAAAGCTTTGTCCAGT
TTTGATCTTCATCTTTAGGACCTTTGATTTGCTTTGAGTAATAGGGAGAGGAAGTTATGCAAAAGTACTATTAACTGAAT
TTTTAAAAAGACATTGCATCTATGCAATGAAAGTTCTGAAAAAAAACCAGCCTGCTGACATTGACCAGATGTAGACAAAG
AAGCATGTTTTGGAGCAAGTATCAATTACTCTTTTCTTGTTGGATTGCAATCTTGCTCTTAGACAGAAAGCAATCTATTC
CCTGTTCTAGCCCATGTAAGTGGAGGAGATCTAATGTGTTATATGCAGCAACAAGGAATACTTCCTGAAGACCATGCCAG
GTTTTACTCTGTAAAAACCAGGTTAGCATTTGGTTTTCTTCATGTGCAAGGGATAATATACAGAAATTTTAAATTGGACA
ATTTATTTCTGGACTCAAAAATTAAACTCACTGACTATTGGTTGTGTTAGGAAGGACTACAGCCAGGAGACAAGACCAGC
ACTTTCTGTGGCACTCCTAACTACCTTGCTCTAGAAATTCTAAGAGGAGAAGATTATTGTTCCAGTGTGGACAGGTGGAC
CCTTGGAGTACTGTTTGAGATGATGGTTGGCAAGTCTCCATTTCATCTTGTTGGGAGCCCTGATAACCCTGATTACAACA
CAAAAAACAATCTCTTGCAAGTCATTTTGGAAAGAAAAAATTCACATCCCATGTTGTCTGTCTGTATATGCA
ORF - retro_cpor_656 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 57.67 % |
| Parental protein coverage: | 65.54 % |
| Number of stop codons detected: | 7 |
| Number of frameshifts detected: | 4 |
Retrocopy - Parental Gene Alignment:
| Parental | PGEDKSIYRRGARRWRKLYCANGHT-FQAK-RFNRRAHCAICTDRIWGLGRQGYKCINCKLLVHKKCHKL |
| P..DK.IY.R.A...RKLY.ANGHT.F..K..F..RA.C.I.......LG...YKCINCKLLVH.KCH.L | |
| Retrocopy | PRKDKPIYCRAACL*RKLYYANGHT>FKPKVSFSSRADCTIFSVHTGWLGC*IYKCINCKLLVHMKCHTL |
| Parental | VTIECGRHSLPPEPMMQMDQSSMHSDHAQTVIPYNPSSH---ESLDQVGEEKEAMNTRESGKASSSLGLQ |
| VTIEC..H.LPPEPMM.MD.S.M..D.AQ.VI.YNP.SH...E.LD...E.............S..L.L. | |
| Retrocopy | VTIECKQHFLPPEPMMTMDRSPMSLDPAQIVILYNPKSHKGLEELDEGNEAGNNWEKCMKALSSFDLHL* |
| Parental | D-FDLLRVIGRGSYAKVLLVRD-RIYAMKVVKKELVNDDEDIDWVQTEKHVFEQAS-NHPFLVGLHSCFQ |
| D.FDLL.VIGRGSYAKVLL............K........DID...T.KHV.EQ.S.N..FLVGL.SC.. | |
| Retrocopy | D>FDLL*VIGRGSYAKVLLTEFLKRHCIYAMKVLXXXQPADIDQM*TKKHVLEQVS<NYSFLVGLQSCS* |
| Parental | TESRLFFVIEYVNGGDLMFHMQRQRKLPEEHASFNSAEISLALNYLHERGIIYRDLKLDNVLLDSEGHIK |
| TES.LF.V...V.GGDLM..MQ.Q..LPE.HA.F.S....LA...LH..GIIYR..KLDN..LDS...IK | |
| Retrocopy | TESNLFPVLAHVSGGDLMCYMQQQGILPEDHARFYSVKTRLAFGFLHVQGIIYRNFKLDNLFLDSK--IK |
| Parental | LTDYGMCKKEGLRPGDTTSTFCGTPNYIAPEILRGEDYGFSVDWWALGVLMFEMMAGRSPFDIVGSSDNP |
| LTDY..C..EGL.PGD.TSTFCGTPNY.A.EILRGEDY..SVD.W.LGVL.FEMM.G.SPF..VGS.DNP | |
| Retrocopy | LTDYWLC*-EGLQPGDKTSTFCGTPNYLALEILRGEDYCSSVDRWTLGVL-FEMMVGKSPFHLVGSPDNP |
| Parental | DQNTEDYLFQVILEK-QIRIPRSLSVKA |
| D.NT...L.QVILE...I.IP..LSV.A | |
| Retrocopy | DYNTKNNLLQVILER>KIHIPCCLSVYA |
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 | 43 .42 RPM |
| SRP017611_kidney | 0 .00 RPM | 17 .27 RPM |
| SRP017611_liver | 0 .00 RPM | 7 .66 RPM |
| SRP040447_lung | 0 .00 RPM | 25 .93 RPM |
| SRP040447_skeletal_muscle | 0 .00 RPM | 4 .64 RPM |
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_656 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_656 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 4 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Cavia porcellus | ENSCPOG00000015212 | 1 retrocopy |
retro_cpor_656 ,
|
| Homo sapiens | ENSG00000163558 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000014289 | 1 retrocopy | |
| Pan troglodytes | ENSPTRG00000015615 | 1 retrocopy |