RetrogeneDB ID: | retro_ptro_2281 | ||
Retrocopy location | Organism: | Chimpanzee (Pan troglodytes) | |
| Coordinates: | 5:89405032..89406431(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSPTRG00000021972 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | RDX | ||
| Ensembl ID: | ENSPTRG00000004259 | ||
| Aliases: | None | ||
| Description: | Radixin [Source:UniProtKB/TrEMBL;Acc:K7DB88] |
Retrocopy-Parental alignment summary:
>retro_ptro_2281
ATGCCCAAAACGATCAGTGTGCGTGTGACCACCATGGATGCAGAGCTGGAGTTTACCATCCAGCCCAACACCACCGGGAA
GCAGCTATTTGACCAGGTGGTGAAAACTGTTGGCTTGAGGGAAGTTTGTTTCTTTGGTCTGCAGTACCAGGACACCAAAG
GTTTCTCCACCTGGCTGAAACTCAATTAAGAAGGTGACTGCCCAGGAAGTGCGGAAGGAAAGCCCCCTGCTCTTTAAGTT
CAGTGCCAAGTTCTACCCTGAGGATGTGTCCGAGGAATTGATTCAGGACACCATTCAGCGTCTGTTCTTTCTGCAAGTGA
AAGAGGGCATTCTCAATGATGATATTTACTGCTGGCCTGAGACTGCTGTGCTGCTGGCCTCCCATGCTGTCCAGTCTAAG
TATGGGAACTTCAGTAAGGAGGTGCATAAGTCTGGCTACCTGGCCGGAGACGAGTTGCTCCCACAGAGAGTCCTGGAAAA
GCACAAACTCAGCAAGGACCAGTGGGAGGAGCGGATCCAGGTGTGGCATGAGGAACACCGTGGCATGCTCAGGGAGGATG
CTGTCCTGGAATATCTGAAGATTGCTCAAGATCTGGAGATGTATGGTGTAAACTACTTCAGCATCAAGAAAAAGAAAGGC
TCAGAGCTGTGGCTGGGGGTGGATGCACTGGGTCTCAACATCTATGAGCAGCATGACAGACTAACTCCCAAGATAGGCTT
TCCTTGGAGTGAAATCAGGAGCATTTCTTTCAATGATAAGAAATTTGTCATCAAGCCCATTGACAAAAAAGCCCCGGACT
TTGTCTTCTATGCTCCCTGGCTGCGGATTAACAAGCGGATCTTGGCCTTGTGCATGGGGAACCATGAACTATACATGCGC
AGTCGCAAGCCTGACACCATTGAGGTGCAGCAGATGAAGGCACAGGCCCGGGAGGAGAAGCACCAGAAGCAGATGGAGCG
TGCTATGCTGGAAAATGAGAAGAAGCGTGAAATGGCAGAAAAGGAGAAAGAGAAGATTGAACGGGAGAAGGAGCTGATGG
AGAGGCTGAAGCAGATCGAGGAACAGACTAAGAAGGCTCAGCAAGAACTGGAAGAACAGACCCGTAGGGCTCTGGAACTT
GGGAAGGAACGGAAGCATGCCCAGAGTGAGGCTGAAAAGCTGGCCAAGGAGCTTCAAGAAGCTGAAGAGGCCAAGGAAGT
CTTGCTGCAGGCCTCCCGGGACCAGAAAAAGACTCAGGAATAGCTGGCCTTGGAAATGGCAGAGCTGACAGCTCAAATCT
CTCAGCTGGAACTGGCCTGACAGAAGAAAGAGAGTGAGGCTATGGAGTCGCAGCAGAAGGCCCAGATGGTACAGGAAGAC
TTGGAGAAGACCCGTGCTGAGCTGAAGACTGCCATGAGT
ORF - retro_ptro_2281 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 79.74 % |
| Parental protein coverage: | 77.48 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MPKPINVRVTTMDAELEFAIQPNTTGKQLFDQVVKTVGLREVWFFGLQYVDSKGYSTWLKLN-KKVTQQD |
| MPK.I.VRVTTMDAELEF.IQPNTTGKQLFDQVVKTVGLREV.FFGLQY.D.KG.STWLKLN.KKVT.Q. | |
| Retrocopy | MPKTISVRVTTMDAELEFTIQPNTTGKQLFDQVVKTVGLREVCFFGLQYQDTKGFSTWLKLN>KKVTAQE |
| Parental | VKKENPLQFKFRAKFFPEDVSEELIQEITQRLFFLQVKEAILNDEIYCPPETAVLLASYAVQAKYGDYNK |
| V.KE.PL.FKF.AKF.PEDVSEELIQ...QRLFFLQVKE.ILND.IYC.PETAVLLAS.AVQ.KYG...K | |
| Retrocopy | VRKESPLLFKFSAKFYPEDVSEELIQDTIQRLFFLQVKEGILNDDIYCWPETAVLLASHAVQSKYGNFSK |
| Parental | EIHKPGYLANDRLLPQRVLEQHKLTKEQWEERIQNWHEEHRGMLREDSMMEYLKIAQDLEMYGVNYFEIK |
| E.HK.GYLA.D.LLPQRVLE.HKL.K.QWEERIQ.WHEEHRGMLRED...EYLKIAQDLEMYGVNYF.IK | |
| Retrocopy | EVHKSGYLAGDELLPQRVLEKHKLSKDQWEERIQVWHEEHRGMLREDAVLEYLKIAQDLEMYGVNYFSIK |
| Parental | NKKGTELWLGVDALGLNIYEHDDKLTPKIGFPWSEIRNISFNDKKFVIKPIDKKAPDFVFYAPRLRINKR |
| .KKG.ELWLGVDALGLNIYE..D.LTPKIGFPWSEIR.ISFNDKKFVIKPIDKKAPDFVFYAP.LRINKR | |
| Retrocopy | KKKGSELWLGVDALGLNIYEQHDRLTPKIGFPWSEIRSISFNDKKFVIKPIDKKAPDFVFYAPWLRINKR |
| Parental | ILALCMGNHELYMRRRKPDTIEVQQMKAQAREEKHQKQLERAQLENEKKKREIAEKEKERIEREKEELME |
| ILALCMGNHELYMR.RKPDTIEVQQMKAQAREEKHQKQ.ERA.LENE.KKRE.AEKEKE.IEREK.ELME | |
| Retrocopy | ILALCMGNHELYMRSRKPDTIEVQQMKAQAREEKHQKQMERAMLENE-KKREMAEKEKEKIEREK-ELME |
| Parental | RLKQIEEQTIKAQKELEEQTRKALELDQERKRAKEEAERLEKERRAAEEAKSAIAKQAADQMKNQEQLAA |
| RLKQIEEQT.KAQ.ELEEQTR.ALEL..ERK.A..EAE.L.KE...AEEAK........DQ.K.QE.LA. | |
| Retrocopy | RLKQIEEQTKKAQQELEEQTRRALELGKERKHAQSEAEKLAKELQEAEEAKEVLLQASRDQKKTQE*LAL |
| Parental | ELAEFTAKIALLEEAKKKKEEEATEWQHKAFAAQEDLEKTKEELKTVMS |
| E.AE.TA.I..LE.A..KKE.EA.E.Q.KA...QEDLEKT..ELKT.MS | |
| Retrocopy | EMAELTAQISQLELA*QKKESEAMESQQKAQMVQEDLEKTRAELKTAMS |
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 |
|---|---|---|
| SRP007412_brain_prefrontal_cortex | 4 .90 RPM | 19 .39 RPM |
| SRP007412_cerebellum | 10 .54 RPM | 22 .98 RPM |
| SRP007412_heart | 24 .60 RPM | 31 .83 RPM |
| SRP007412_kidney | 35 .49 RPM | 37 .79 RPM |
| SRP007412_liver | 24 .68 RPM | 24 .88 RPM |
| SRP007412_testis | 1 .69 RPM | 34 .46 RPM |
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_2281 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_2281 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ptro_2281 has 3 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_3153 |
| Gorilla gorilla | retro_ggor_1359 |
| Pongo abelii | retro_pabe_2623 |
Parental genes homology:
Parental genes homology involve 4 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Dasypus novemcinctus | ENSDNOG00000019413 | 1 retrocopy | |
| Homo sapiens | ENSG00000137710 | 1 retrocopy | |
| Gorilla gorilla | ENSGGOG00000027218 | 1 retrocopy | |
| Pan troglodytes | ENSPTRG00000004259 | 1 retrocopy |
retro_ptro_2281 ,
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