RetrogeneDB ID: | retro_cpor_657 | ||
Retrocopy location | Organism: | Guinea Pig (Cavia porcellus) | |
| Coordinates: | scaffold_21:18520422..18521809(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | UTP18 | ||
| Ensembl ID: | ENSCPOG00000001477 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cpor_657
AGGCTGGGCATCTCTGGGGGCAAACCAGCCATGGAGCTGTGTGGAGAAGAGCTGGTCTTTGACACCATGGGGTGGGTGGG
GGACCAGGAGGACGCACTTCTGTGGTACTGCAGGGCGCGCAGGTTCAGGTACAAGAAGACTCCATGACTCAGAAGTGGAA
ATGAAGCAAAAGATAATTTTTCCCCTTGGAAGGAACCAGTTTGGGTGGATGAAGAAGATGAAGATGAGGAAATGGTTGAC
TCGAGAAACAACCGTTTTAGGAAAGCTATGGTGAAAAAGTACCAGGGAAAGTAAACTTTCCAAAGAGAAGCTTCAAGGAG
ACAAAGAAGAATTCTAGCATGCCCTGCGGTGAGTGCCTGCCTAGGCAGAACTTAATTAGCAGAAAATATCTTCAGATGAT
GAAAGTGAAGAGGATGAAGCTAATTTGCTGCAAAGGACTGGGAATTTTTTTCCATATGAGTTTCTCTTGCAAGAGGAATC
TTGACAATAAAGAACTGCTAGCTTGTGGATACAGAGAGCCCTACCACTGCCCAGATCTCATCAGTCCAGTTCCTTCCCTG
TGCCCAGGTTGTGGCAGCTGCTGGCTTAGATAACACCTCTTCACTGTTTCAGGTTGATAGCAAAACAAATCCCTAAATCT
AGAGCATCTATTTGGAGGTTTCCAATCTTTATAGCTTGTTTTAGTGCTAATGGAGTGCAGGTTTTAGCAGGAAACACTCA
CAGCAGGATTCTTTATGTCTATGATATTCAGGCTGGGAAGTTAAGTCCTATGCATCAAGTGAGAGTCTTGAAAGAAAGAA
TATTGAGAACATTTGAAGTCTCCCCAGATGGACCCTTCATGCTCATTCATGGTATTGCTGGCGACTCTTATTTGCTGGCA
ATGAAGACCAAAGAGCTGATTGGAAGTATGAAGGTTACTGAAGGGGTTTCAGCATCTGTGTTTACTTCAGATAGTAAGAA
AATACACACCTATGCTGGGGACCAGAAAGTTTATGTTTGAGATGTGAACTCTAGGAATCGCCTTAACAGATTTGCCGATG
AAGGCAGTTTATGTGGATTAAGCATTGCCATATCGAGGAGTGGGCAGTAGGTCGCTTGTGGTTCTGGTTTTGGAATAGTA
AACATTTACAGTCAAGATTCTTGTGTTCAAGAAACAAACCCAAAGCCAATAAAAGCCATAATGAGCTTGGTAACTGGTGT
TACATCTCTGGCCTTCAATCCTGCTTCAGAAATTTTGGCAGTTGCTTCAGAAAAGATGATGGGAGTGGTCCGATTGGTTC
ATCTTCAATCCTGTACAGTATTTTCTAACTTTCTAGTTGTTAAAAAGGAGAATATTTCTCATGCCCATTTTGTGGATTAT
TCTCCCAGAGGTGGCTGCTTTGCTTTA
ORF - retro_cpor_657 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 70.49 % |
| Parental protein coverage: | 95.26 % |
| Number of stop codons detected: | 8 |
| Number of frameshifts detected: | 6 |
Retrocopy - Parental Gene Alignment:
| Parental | RLTLEEDKPAVERCLEELVF---GDVGGDEDALLRS-LRGARVQVHEDS-DDAEVE-NEAKGNFPPQKRP |
| RL.....KPA.E.C.EELVF...G.VG..EDALL...L.GA.VQV.EDS..D.EVE.NEAK.NF.P.K.P | |
| Retrocopy | RLGISGGKPAMELCGEELVFDTMGWVGDQEDALLWY<LQGAQVQVQEDS<HDSEVE<NEAKDNFSPWKEP |
| Parental | VWVDEEDEDEEMVDMRNNRFRKDMMK-NASESKLSKEKLQKRLKEEFQHAMGGVPAWAETSKRKTSSDDE |
| VWVDEEDEDEEMVD.RNNRFRK.M.K....ESKLSKEKLQ...KEEF.HA...VPA.AE....K.SSDDE | |
| Retrocopy | VWVDEEDEDEEMVDSRNNRFRKAMVK>STRESKLSKEKLQGD-KEEF*HALR*VPA*AELN*QKISSDDE |
| Parental | SEEDEDDLLQRTGNFL-STSVSLPRGILKMKNCQHANAERPTTAQISSVQFHPCAQVVMVAGLDNAFSLF |
| SEEDE..LLQRTGNF..S..VSL.RGIL..KNC.....E.PTTAQISSVQF.PCAQVV..AGLDN..SLF | |
| Retrocopy | SEEDEANLLQRTGNFF<SI*VSLARGILTIKNC*LVDTESPTTAQISSVQFLPCAQVVAAAGLDNTSSLF |
| Parental | QVDGKTN-PKIQSIYLEKFPIFKACFSANGEQVLATSTHSRVLYVYDMLAGKLIPVHQVRGLKERMVKSF |
| QVD.KTN.PK........FPIF.ACFSANG.QVLA..THSR.LYVYD..AGKL.P.HQVR.LKER....F | |
| Retrocopy | QVDSKTN>PKSRAS-IWRFPIFIACFSANGVQVLAGNTHSRILYVYDIQAGKLSPMHQVRVLKERILRTF |
| Parental | EVSPDGSFLLINGIAGYSHLLSMKTKELIGSMKINGRVSASAFTSDSKKIYTYSGEGEVYIWDVNSRKCL |
| EVSPDG.F.LI.GIAG.S.LL.MKTKELIGSMK....VSAS.FTSDSKKI.TY.G...VY..DVNSR..L | |
| Retrocopy | EVSPDGPFMLIHGIAGDSYLLAMKTKELIGSMKVTEGVSASVFTSDSKKIHTYAGDQKVYV*DVNSRNRL |
| Parental | NRFVDEGSLCGLSIATSRNGQYVACGSGCGVVNIYSQDSCLQETNPKPIKAIMNLVTGVTSLAFNPATEI |
| NRF.DEGSLCGLSIA.SR.GQ.VACGSG.G.VNIYSQDSC.QETNPKPIKAIM.LVTGVTSLAFNPA.EI | |
| Retrocopy | NRFADEGSLCGLSIAISRSGQ*VACGSGFGIVNIYSQDSCVQETNPKPIKAIMSLVTGVTSLAFNPASEI |
| Parental | LAIASKKMKEAVKLVHLPSCTVFSNFPIVKRKTISLVHSMDFSPRGGYFAL |
| LA.AS.KM...V.LVHL.SCTVFSNF..VK...IS..H..D.SPRGG.FAL | |
| Retrocopy | LAVASEKMMGVVRLVHLQSCTVFSNFLVVKKENISHAHFVDYSPRGGCFAL |
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 | 46 .99 RPM |
| SRP017611_kidney | 0 .00 RPM | 41 .25 RPM |
| SRP017611_liver | 0 .00 RPM | 19 .72 RPM |
| SRP040447_lung | 0 .00 RPM | 42 .75 RPM |
| SRP040447_skeletal_muscle | 0 .00 RPM | 19 .44 RPM |
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_657 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_657 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 6 parental genes, and 6 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Cavia porcellus | ENSCPOG00000001477 | 1 retrocopy |
retro_cpor_657 ,
|
| Homo sapiens | ENSG00000011260 | 1 retrocopy | |
| Gorilla gorilla | ENSGGOG00000017061 | 1 retrocopy | |
| Myotis lucifugus | ENSMLUG00000016938 | 1 retrocopy | |
| Mustela putorius furo | ENSMPUG00000015582 | 1 retrocopy | |
| Vicugna pacos | ENSVPAG00000010164 | 1 retrocopy |