RetrogeneDB ID: | retro_ptro_2620 | ||
Retrocopy location | Organism: | Chimpanzee (Pan troglodytes) | |
| Coordinates: | 7:44618001..44619156(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | TTC4 | ||
| Ensembl ID: | ENSPTRG00000041368 | ||
| Aliases: | None | ||
| Description: | tetratricopeptide repeat domain 4 [Source:HGNC Symbol;Acc:12394] |
Retrocopy-Parental alignment summary:
>retro_ptro_2620
ATGGAGTAACCTGAGCAGGACCCCACCTCAGACGATGCCATGGACTCGTTCCTGGAAAAGTTCCAGAGCCAGCCTTACCG
TGGTGGCTTTCATGAGAATCAGTGGGAAGAGGAATTTGAAAAGGTCCCCCTGTTTATGAAGAAAGTGCCATCAGAAATTG
ATCCCAGGGAGAATCCTGACTTGGCTTTTCTCCAGTCAATTATTTTTGATGAGGAGCATTCTCCAGAACAGGCCAAGACC
TATAAAGATGAGGGCAATGATTATTTTAAAGAAAAAGACTACAAGAAAGCTGTAATTTCCTACACTGAAGGATTAAAGAA
GAAATGTGCAAATCCTGATTTGAATGCTGTCCATTATACCAACCGGGCAGCAGCACAATACTATCTGGGCAATTTTCATT
CTGCTCTCAGTGATGTGACAGCTGCCAAAAAGTTAAAACCGTGCTACCTCAAAGCAATAATAAGAGGTGCCTTATGCCAT
CTGGAACTGAAACACTTTGCCAAGGCTGTGAACTGATGTGATGAGGGACTGCAGATAGATGCCAAAGAGAAGAAGCTTCT
GGAAATGAGGGCTAAAGTAGACAAGCTGAAGCTAATTGAACAGAGGGATGTGAGGAAAGCCAACTTGAAAGAAAAGGAGA
GGAATCAGAATGAAGTTTTACTCCAGGATATCAAGGCTAGGAATATCAGGCTCTCTGAAGCTGCCTGTGAGGATGAAGTT
TCAGCCTCAGAAGGTCTAGGTGAGCTTTTCCTGGATGGACTCAGCTCTGAGAACCCCCATGGAGCCAGACTGAGTCTAGA
TGACCAGGGCAGACTGAGCTGGCCTGTGCTCTTTCTGTACCCAGCGTATGCCCAATCGGACTTCATCTCTGCTTTTCATG
AGGACTCCAGGTTTATTGATCATCTAATGGTGATGTTTGGTGAAACACCCTCTTGGGACCTAGAGCAAAAATATTGCCCT
GATAATTTGGAGGTCTACACTGAGGATGAGGACAGGGCAGAACTGTACTGGGTGCCTGCCAAGAGCCCCTTGCTGCAGGA
TCTACAGCACCACAGGCACTTTGTAAAAGCCCTGACACCAGCATTTTTGGTCTGTGTAGGATCCAAACTTTTTTGAAAGA
ATTATCTCTGGGGGAGAAAGGTGCACCAGATAAGA
ORF - retro_ptro_2620 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 89.41 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MEQPGQDPTSDDVMDSFLEKFQSHPYRGGFHEDHWEKEFEKVPLFMTRAPSEIDPRENPDLACLQSIIFD |
| ME.P.QDPTSDD.MDSFLEKFQS.PYRGGFHE..WE.EFEKVPLFM...PSEIDPRENPDLA.LQSIIFD | |
| Retrocopy | ME*PEQDPTSDDAMDSFLEKFQSQPYRGGFHENQWEEEFEKVPLFMKKVPSEIDPRENPDLAFLQSIIFD |
| Parental | EERSPEEQAKTYKDEGNDYFKEKDYKKAVISYTEGLKKKCADPDLNAVLYTNRAAAQYYLGNFCSALNDV |
| EE.SPE.QAKTYKDEGNDYFKEKDYKKAVISYTEGLKKKCA.PDLNAV.YTNRAAAQYYLGNF.SAL.DV | |
| Retrocopy | EEHSPE-QAKTYKDEGNDYFKEKDYKKAVISYTEGLKKKCANPDLNAVHYTNRAAAQYYLGNFHSALSDV |
| Parental | TAARKLKPCHLKAIIRGALCHLELKHFAEAVNWCDEGLQIDAKEKKLLEMRAKADKLKRIEQRDVRKANL |
| TAA.KLKPC.LKAIIRGALCHLELKHFA.AVN.CDEGLQIDAKEKKLLEMRAK.DKLK.IEQRDVRKANL | |
| Retrocopy | TAAKKLKPCYLKAIIRGALCHLELKHFAKAVN*CDEGLQIDAKEKKLLEMRAKVDKLKLIEQRDVRKANL |
| Parental | KEKKERNQNEALLQAIKARNIRLSETACEDEDSASEGLGELFLDGLSTENPHGARLSLDDQGRLSWPVLF |
| KEK.ERNQNE.LLQ.IKARNIRLSE.ACEDE.SASEGLGELFLDGLS.ENPHGARLSLDDQGRLSWPVLF | |
| Retrocopy | KEK-ERNQNEVLLQDIKARNIRLSEAACEDEVSASEGLGELFLDGLSSENPHGARLSLDDQGRLSWPVLF |
| Parental | LYPEYAQSDFISAFHEDSRFIDHLMVMFGETPSWDLEQKYCPDNLEVYFEDEDRAELYRVPAKSTLLQVL |
| LYP.YAQSDFISAFHEDSRFIDHLMVMFGETPSWDLEQKYCPDNLEVY.EDEDRAELY.VPAKS.LLQ.L | |
| Retrocopy | LYPAYAQSDFISAFHEDSRFIDHLMVMFGETPSWDLEQKYCPDNLEVYTEDEDRAELYWVPAKSPLLQDL |
| Parental | QHQRYFVKALTPAFLVCVGSSPFCKNYLRGRKVYQIR |
| QH.R.FVKALTPAFLVCVGS..F.KNYL.GRKV.QIR | |
| Retrocopy | QHHRHFVKALTPAFLVCVGSKLF*KNYLWGRKVHQIR |
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 .00 RPM | 17 .45 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 13 .01 RPM |
| SRP007412_heart | 0 .00 RPM | 8 .66 RPM |
| SRP007412_kidney | 0 .00 RPM | 13 .21 RPM |
| SRP007412_liver | 0 .00 RPM | 13 .13 RPM |
| SRP007412_testis | 0 .00 RPM | 18 .44 RPM |
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_2620 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_2620 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ptro_2620 has 3 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_3843 |
| Gorilla gorilla | retro_ggor_2588 |
| Macaca mulatta | retro_mmul_1616 |
Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Homo sapiens | ENSG00000243725 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000001312 | 1 retrocopy | |
| Pan troglodytes | ENSPTRG00000041368 | 1 retrocopy |
retro_ptro_2620 ,
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