RetrogeneDB ID: | retro_cpor_701 | ||
Retrocopy location | Organism: | Guinea Pig (Cavia porcellus) | |
| Coordinates: | scaffold_24:26955583..26956360(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | DUS4L | ||
| Ensembl ID: | ENSCPOG00000002384 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cpor_701
GTTATAGCCACTGATTTTATCAGATCCATAAAAGCCAGAGACAGTGAATTTACTACCACTAACCAAGGTGATTGCCCATT
GATTGTGCAGTTTGCTGCTAATGATGCAAGACTTTTATCTGATGCTGCTCACAAACTGTGTCCTTATGCGAATGGAATAG
GCATGAACTGTGGTTGCTCGCAGAGGTGGCTGATCATGGAAGGTTATGGACTTGCTTAATAAACAGGCCAAACTTTGTTT
GAGGTACAGTGAAACAAGTAAGAAATCAAGTGGAAAACCCCAGATTTTCAGTTCCTATTAAAATAAGGTCCATGATGACC
TTACAAAGAACTGTAAACTTTTGTCAACAGTCTGAAGCAGCAAGAGTTAACTGGATTACAGGCCATGGAAGAACTGCTGA
AGGAAGACATCAGCCAGTCCAGAATGATGCCATTAGAATACTAAAGGAAACATGTCCTTATCTGTGATTGTTAATGGAGA
CATCATAAGATTTAAAAAAACAGAAAATGTGTGGCAAGTTATGGGACAGATGGCATGATGGTTGCAAGGGGACTCTTGGT
GAACCCTGCCGTGCTTGCTGGATGTGAGGGAAACCCACTGAAATGCGTCTGGGACCGGGTGGACATCACTCTTGAACTTG
GGACTTCTTTTGTTTGTTTCCATCAACATTTAATGCACCTGATGGAAAAAATAACTTCAAGGTAAGAAAAAAGAATATTT
AAGTGTCTGTTAAGCACATCAGCAGGTTTAGATTACCTTATAGACCATTATGACATT
ORF - retro_cpor_701 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 72.45 % |
| Parental protein coverage: | 81.7 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 5 |
Retrocopy - Parental Gene Alignment:
| Parental | IVAADFVRSIKARDSEFTT-NQGDCPLIVQFAANDARLLSDAARIVCPYANGIDINCGCPQRWAMAEGYG |
| ..A.DF.RSIKARDSEFTT.NQGDCPLIVQFAANDARLLSDAA...CPYANGI..NCGC.QRW...EGYG | |
| Retrocopy | VIATDFIRSIKARDSEFTTTNQGDCPLIVQFAANDARLLSDAAHKLCPYANGIGMNCGCSQRWLIMEGYG |
| Parental | -ACLINKPELVRDMVKQVRNQVENPRFSVSIKIR-IHDDLT-RTVDFCRKAEATGVNWITVHGRTVEERH |
| ..CLIN.P..V...VKQVRNQVENPRFSV.IKIR..HDDLT.RTV.FC...EA..VNWIT.HGRT.E.RH | |
| Retrocopy | <TCLINRPNFV*GTVKQVRNQVENPRFSVPIKIR<VHDDLT>RTVNFCQQSEAARVNWITGHGRTAEGRH |
| Parental | QPVHYDAIKIIKE-NMSIPVIANGDIRSLKEAENVWQITG-TDGVMVARGLLANPAMFAGYEETPLKCIW |
| QPV..DAI.I.KE.NMS..VI.NGDI...K..ENVWQ..G.TDG.MVARGLL.NPA..AG.E..PLKC.W | |
| Retrocopy | QPVQNDAIRILKE<NMSLSVIVNGDIIRFKKTENVWQVMG<TDGMMVARGLLVNPAVLAGCEGNPLKCVW |
| Parental | DWVDIALELGTPFMCFHQHLMYMMEKITSKQEKRIFNALSSTSAVLDYLTDHYGI |
| D.VDI.LELGT.F.CFHQHLM..MEKITS..EKRIF..L.STSA.LDYL.DHY.I | |
| Retrocopy | DRVDITLELGTSFVCFHQHLMHLMEKITSR*EKRIFKCLLSTSAGLDYLIDHYDI |
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 .12 RPM | 2 .24 RPM |
| SRP017611_kidney | 0 .00 RPM | 1 .99 RPM |
| SRP017611_liver | 0 .00 RPM | 2 .48 RPM |
| SRP040447_lung | 0 .00 RPM | 3 .51 RPM |
| SRP040447_skeletal_muscle | 0 .00 RPM | 1 .48 RPM |
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_701 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_701 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 3 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Choloepus hoffmanni | ENSCHOG00000006848 | 1 retrocopy | |
| Cavia porcellus | ENSCPOG00000002384 | 1 retrocopy |
retro_cpor_701 ,
|
| Otolemur garnettii | ENSOGAG00000013113 | 2 retrocopies |