RetrogeneDB ID: | retro_ggor_2588 | ||
Retrocopy location | Organism: | Gorilla (Gorilla gorilla) | |
| Coordinates: | 7:47064336..47065395(-) | ||
| 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: | ENSGGOG00000005420 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_ggor_2588
GACCAGTGGGAAGAGGAATTTGAAAAGGTCCCCCTGTTTATGAAGAAAGTGCCATCAGAAATTGATCCCAGGGAGAATCC
TGACTTGGCTTGTCTCCAGTCAATTATTTTTGATGAGGAGCATTCTCCAGAACAGGCCAAGACCTATAAAGATGAGGGCA
ATGATTATTTTAAAGAAAAAGACTACAAGAAAGCTGTAATTTCCTACACTGAAGGATTAAAGAAGAAATGTGCAAATCCT
GATTTGAATGCTGTCCTTTATACCAACCGGGCAGCAGCACAATACTATCTGGGCAATTTTCATTCTGCTCTCAGTGATGT
GACAGCTGCCAAAAAGTTAAAACCGTGCTACCTCAAAGCAATAATAAGAGGTGCCTTATGCCATCTGGAACTGAAACACT
TTGCCAAGGCTGTGAACTGATGTGATGAGGGACTGCAGATAGATGCCAAAGAGAAGAAGCTTCTGGAAATGAGGGCTAAA
GTAGACAAGCTGAAGCTAATTGAACAGAGGGATGTGAGGAAAGCCAACTTGAAAGAAAAGGAGAGGAATCAGAATGAAGT
TTTACTCCAGGATATCAAGGCTAGGAATATCAGGCTCTCTGAAGCTGCCTGTGAGGATGAAGTTTCAGCCTCAGAAGGTC
TAGGTGAGCTTTTCCTGGATGGACTCAGCTCTGAGAACCCCCATGGAGCCAGACTGAGTCTAGATGACCAGGGCAGGCTG
AGCTGGCCTGTGCTCTTTCTGTACCCAGAGTGTGCCCAATCGGACTTCATCTCTGCTTTTCATGAGGACTCCAGGTTTAT
TGATCATCTAATGGTGATGTTTGGTGAAACACCCTCTTGGGACCTAGAGCAAAAATATTGCCCTGATAATTTGGAGGTCT
ACACTGAGGATGAGGACAGGGCAGAACTGTACTGGGTGCCTGCCAAGAGCACCTTGCTGCAGGATCTACAGCACCACAGG
CACTTTGTAAAAGCCCTGACACCAGCATTTTTGGTCTGTGTAGGATCCAAACTTTTTTGAACGAATTATCTCTGGGGGAG
AAAGGTGCACCAGATAAGA
ORF - retro_ggor_2588 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 90.14 % |
| Parental protein coverage: | 89.2 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | DRWFLEFEKVPLFMTRAPSEIDPRENPDLACLQSIIFDEERSPEEQAKTYKDEGNDYFKEKDYKKAVISY |
| D.W..EFEKVPLFM...PSEIDPRENPDLACLQSIIFDEE.SPE.QAKTYKDEGNDYFKEKDYKKAVISY | |
| Retrocopy | DQWEEEFEKVPLFMKKVPSEIDPRENPDLACLQSIIFDEEHSPE-QAKTYKDEGNDYFKEKDYKKAVISY |
| Parental | TEGLKKKCADPDLNAVLYTNRAAAQYYLGNFRSALNDVTAARKLKPCHLKAIIRGALCHLELKHFAEAVN |
| TEGLKKKCA.PDLNAVLYTNRAAAQYYLGNF.SAL.DVTAA.KLKPC.LKAIIRGALCHLELKHFA.AVN | |
| Retrocopy | TEGLKKKCANPDLNAVLYTNRAAAQYYLGNFHSALSDVTAAKKLKPCYLKAIIRGALCHLELKHFAKAVN |
| Parental | WCDEGLQIDAKEKKLLEMRAKADKLKRIEQRDVRKANLKEKKERNQNEALLQAIKARNIRLSEAACEDED |
| .CDEGLQIDAKEKKLLEMRAK.DKLK.IEQRDVRKANLKEK.ERNQNE.LLQ.IKARNIRLSEAACEDE. | |
| Retrocopy | *CDEGLQIDAKEKKLLEMRAKVDKLKLIEQRDVRKANLKEK-ERNQNEVLLQDIKARNIRLSEAACEDEV |
| Parental | SASEGLGELFLDGLSTENPHGARLSLDDQGRLSWPVLFLYPEYAQSDFISAFHEDSRFIDHLMLMFGETP |
| SASEGLGELFLDGLS.ENPHGARLSLDDQGRLSWPVLFLYPE.AQSDFISAFHEDSRFIDHLM.MFGETP | |
| Retrocopy | SASEGLGELFLDGLSSENPHGARLSLDDQGRLSWPVLFLYPECAQSDFISAFHEDSRFIDHLMVMFGETP |
| Parental | SWDLEQKYCPDNLEVYFEDEDRAELYRVPAKSTLLQVLQHQRYFVKALTPAFLVCVGSSPFCKNYLQGRK |
| SWDLEQKYCPDNLEVY.EDEDRAELY.VPAKSTLLQ.LQH.R.FVKALTPAFLVCVGS..F..NYL.GRK | |
| Retrocopy | SWDLEQKYCPDNLEVYTEDEDRAELYWVPAKSTLLQDLQHHRHFVKALTPAFLVCVGSKLF*TNYLWGRK |
| Parental | VYQIR |
| V.QIR | |
| Retrocopy | VHQIR |
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 | 6 .28 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 6 .46 RPM |
| SRP007412_heart | 0 .00 RPM | 2 .35 RPM |
| SRP007412_kidney | 0 .04 RPM | 8 .46 RPM |
| SRP007412_liver | 0 .03 RPM | 4 .64 RPM |
| SRP007412_testis | 0 .10 RPM | 17 .61 RPM |
Gorilla gorilla was not studied using ChIP-Seq data.
Gorilla gorilla was not studied using EST data.
Gorilla gorilla was not studied using FANTOM5 data.
retro_ggor_2588 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ggor_2588 has 3 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_3843 |
| Pan troglodytes | retro_ptro_2620 |
| Macaca mulatta | retro_mmul_1616 |
Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Gorilla gorilla | ENSGGOG00000005420 | 1 retrocopy |
retro_ggor_2588 ,
|
| Macaca mulatta | ENSMMUG00000006754 | 1 retrocopy | |
| Nomascus leucogenys | ENSNLEG00000003044 | 1 retrocopy |