RetrogeneDB ID: | retro_ptro_2034 | ||
Retrocopy location | Organism: | Chimpanzee (Pan troglodytes) | |
| Coordinates: | 4:172161453..172163100(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSPTRG00000040747 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | MTMR9 | ||
| Ensembl ID: | ENSPTRG00000019986 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_ptro_2034
ATGGAGTTTGCGGAGCTGATTAAGACCCCGCGGGTGGACAATGTGGTGCTGCACCGGCCTTTCTACCCGGCTGTCGAGGG
CACCCTGTGCCTGACGGGCCACCACTTGATCCTGTCCTCCCGGCAGGACAACACGGAGGAGCTGTGGCTCCTCCATTCAA
ACATCGACGCCATCGACAAGCGATTTGTGGGATCACTGGGTACCATCATCATAAAATGTAAAGATTTTCGAATTATTCAG
TTGGATATTCCTGGAATGGAGGAATGCTTGAATATAGCCAGTTCCATTGAGGCATTGTCTACTCTGGACTCCATCACTCT
GATGTACCCTTTCTTTTACCGTCCTATGTTTGAAGTGATAGAAGATGGCTGGCATTCCTTCCTTCCTGAGCAAGAATTTG
AACTCTATTCCTCAGCTACCAGTGAATGGAGGCTAAGCTCTGTCAATAAGGAATTTGCTGTCTGTCCCTCTTACCCACCA
ATTGTCACGGTGCCCAAATCCATCGATGATGAAGCTCTTTGGAAGGTAGCTACATTTCGACATGGAGGGCGCTTCCCAGT
ACTAAGCTATTATCACAAAAAAAATGGGATGGTAATTATGCGAAGTGGTCAGCCACTCACTGGTACAAACGGGAGGAGGT
GCAAGGAAGACGAGAAGCTGATAAATGCTACCCTCAGGGCTGGAAAGCGTGGCTACATCATTGACACCCGATCCCTGAAC
GTGGCTCAGCAAACTAGAGCCAAAGGAGGTGGCTTTGAACAAGAAGCTCATTATCCCCAGTGGAGGCGAATTCGTAAGTC
CATTGAGAGGTATCACATTCTTCAGGAGAGCTTAATCAAACTTGTGGAAGCTTGTAATGACCAAACCCATAACATGGACC
GATGGCTCAGTAAATTGGAGGCCTCTAACTGGCTGACTCACATCAAAGAGATTCTGACAACTGCCTGCCTAGCGGCTCAG
TGCATCGACAGGGAAGGAGCATCAATATTGATTCACGGAACAGAAGGAACTGATTCCACACTTCGGGTGACCTCCCTGGC
CCAGATCATCTTAGAGCCAAGAAGCAGGACCATTCGTGGTTTTGAGGCCCTGATTGAAAGAGAGTGGCTGCAGGCTGGTC
ACCCGTTCCAGCAGCGCTGTGCACAGTCAGCCTACTGTAACACCAAGCAGAAGTGGGAGGCTCCTGTATTTCTTCTCTTC
TTGGACTGCGTGTGGCAGATCCTTCATCAGTTTCCCTGTTCTTTTGAATTTAATGAGAATTTCCTCATCATGCTCTTTGA
GCATGCTTATGCCTCACAGTTTGGAACATTTCTGGGCAACAATGAAAGTGAAAGATGTAAGTTGAAGCTACAGCAGAAGA
CGACGTCTTTGTGGTCCTGGGTTAATCAGCCCAGTGAGCTGAGTAAATTCACCAATCCCCTCTTTGAAGCCAACAACCTT
GTCATCTGGCCTTCAGTTGCTCCGCAGAGTCTTCTGCTGTGGGAAGGTATTTTCCTACGTTGGAATAGATCCTCTAAGTA
TTTGGATGAAGCATATGAAGAAATGGTTAACATCATTGAATATAATAAAGAATTACAAGCAAAAGTCAATATCCTTAGAA
GGCAGTTGGCAGAACTGGAAACAGAGGACAGGATGCAGGAGAGTCCC
ORF - retro_ptro_2034 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 98.0 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MEFAELIKTPRVDNVVLHRPFYPAVEGTLCLTGHHLILSSRQDNTEELWLLHSNIDAIDKRFVGSLGTII |
| MEFAELIKTPRVDNVVLHRPFYPAVEGTLCLTGHHLILSSRQDNTEELWLLHSNIDAIDKRFVGSLGTII | |
| Retrocopy | MEFAELIKTPRVDNVVLHRPFYPAVEGTLCLTGHHLILSSRQDNTEELWLLHSNIDAIDKRFVGSLGTII |
| Parental | IKCKDFRIIQLDIPGMEECLNIASSIEALSTLDSITLMYPFFYRPMFEVIEDGWHSFLPEQEFELYSSAT |
| IKCKDFRIIQLDIPGMEECLNIASSIEALSTLDSITLMYPFFYRPMFEVIEDGWHSFLPEQEFELYSSAT | |
| Retrocopy | IKCKDFRIIQLDIPGMEECLNIASSIEALSTLDSITLMYPFFYRPMFEVIEDGWHSFLPEQEFELYSSAT |
| Parental | SEWRLSYVNKEFAVCPSYPPIVTVPKSIDDEALRKVATFRHGGRFPVLSYYHKKNGMVIMRSGQPLTGTN |
| SEWRLS.VNKEFAVCPSYPPIVTVPKSIDDEAL.KVATFRHGGRFPVLSYYH...GMVIMRSGQPLTGTN | |
| Retrocopy | SEWRLSSVNKEFAVCPSYPPIVTVPKSIDDEALWKVATFRHGGRFPVLSYYHXXXGMVIMRSGQPLTGTN |
| Parental | GRRCKEDEKLINATLRAGKRGYIIDTRSLNVAQQTRAKGGGFEQEAHYPQWRRIHKSIERYHILQESLIK |
| GRRCKEDEKLINATLRAGKRGYIIDTRSLNVAQQTRAKGGGFEQEAHYPQWRRI.KSIERYHILQESLIK | |
| Retrocopy | GRRCKEDEKLINATLRAGKRGYIIDTRSLNVAQQTRAKGGGFEQEAHYPQWRRIRKSIERYHILQESLIK |
| Parental | LVEACNDQTHNMDRWLSKLEASNWLTHIKEILTTACLAAQCIDREGASILIHGTEGTDSTLQVTSLAQII |
| LVEACNDQTHNMDRWLSKLEASNWLTHIKEILTTACLAAQCIDREGASILIHGTEGTDSTL.VTSLAQII | |
| Retrocopy | LVEACNDQTHNMDRWLSKLEASNWLTHIKEILTTACLAAQCIDREGASILIHGTEGTDSTLRVTSLAQII |
| Parental | LEPRSRTIRGFEALIEREWLQAGHPFQQRCAQSAYCNTKQKWEAPVFLLFLDCVWQILRQFPCSFEFNEN |
| LEPRSRTIRGFEALIEREWLQAGHPFQQRCAQSAYCNTKQKWEAPVFLLFLDCVWQIL.QFPCSFEFNEN | |
| Retrocopy | LEPRSRTIRGFEALIEREWLQAGHPFQQRCAQSAYCNTKQKWEAPVFLLFLDCVWQILHQFPCSFEFNEN |
| Parental | FLIMLFEHAYASQFGTFLGNNESERCKLKLQQKTMSLWSWVNQPSELSKFTNPLFEANNLVIWPSVAPQS |
| FLIMLFEHAYASQFGTFLGNNESERCKLKLQQKT.SLWSWVNQPSELSKFTNPLFEANNLVIWPSVAPQS | |
| Retrocopy | FLIMLFEHAYASQFGTFLGNNESERCKLKLQQKTTSLWSWVNQPSELSKFTNPLFEANNLVIWPSVAPQS |
| Parental | LPLWEGIFLRWNRSSKYLDEAYEEMVNIIEYNKELQAKVNILRRQLAELETEDGMQESP |
| L.LWEGIFLRWNRSSKYLDEAYEEMVNIIEYNKELQAKVNILRRQLAELETED.MQESP | |
| Retrocopy | LLLWEGIFLRWNRSSKYLDEAYEEMVNIIEYNKELQAKVNILRRQLAELETEDRMQESP |
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 | 0 .63 RPM | 34 .62 RPM |
| SRP007412_cerebellum | 1 .25 RPM | 22 .48 RPM |
| SRP007412_heart | 0 .50 RPM | 12 .39 RPM |
| SRP007412_kidney | 0 .39 RPM | 8 .76 RPM |
| SRP007412_liver | 0 .13 RPM | 3 .47 RPM |
| SRP007412_testis | 14 .23 RPM | 30 .98 RPM |
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_2034 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_2034 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ptro_2034 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Pan troglodytes | ENSPTRG00000019986 | 1 retrocopy |
retro_ptro_2034 ,
|
| Ictidomys tridecemlineatus | ENSSTOG00000020537 | 1 retrocopy |