RetrogeneDB ID: | retro_mmul_2277 | ||
Retrocopy location | Organism: | Rhesus macaque (Macaca mulatta) | |
| Coordinates: | 7:169152494..169154120(-) | ||
| Located in intron of: | ENSMMUG00000015202 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | TLK1 | ||
| Ensembl ID: | ENSMMUG00000011189 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_mmul_2277
GGTGCAGTGGATGAGCTTCATAGTCTGGAACCAAGAAGGCAAGAGTTATCGAAAGCTAGATTTTCTGGAGTTGCAAGTGG
GAGCACTGCGAGTGCAGGCAGTTGCAGTGTTGGAGCTAAAGCTTCAACAAATAACGAAAGCTCTAATCACAGTTTTGGAA
GCTTGGGATCTTTAAGTGACAAAGAATCAGAGACACCGGAGAAGAAACAATCAGAATCATCCAGGGGAAGAAAGAGAAAA
GCAGAAAACCGGAATGAAAGTAATCAGGGAAAAAGTATTGGGGGATGTGGCCACAAAATTAGCGACTATTTTGAATACCA
GGGTGGAAATGGCTCAAGTCCAGTAAGAGGCATACCTCCTGCAATCCGTTCTCCTCAAAATTCACATTCACGTTCCACTC
CTTCCTCATCTGTTTGACCCAATAGCCATTCTCCTACTGCATTAGCATTTGGGGACCACCCTATTGTACAACCAAAGCAG
TTATCCTTTAAAATTATTCAGACAGATCTCACAATGCTGAAATTAGCAGCATTAGAAAGTAATAAAATCCAGGACCTGGA
AGAGAAGGAGGGACGTATAGATGATTTTCTCAGGGCTAACTGTGATCTCAGACGGCAAATAGATGAACAACAAAAATTAC
TTGAAAAATACAAAGAACGATTAAGTAAGTGCATATCAATGAGCAAGAAACTTCTTATTGAAAAGAGTACACAAGAAAAA
TTGTCAAGCAGAGAGAAGAGTATGCAAGATCGATTACCCCTTGGGCACTTTACAACAGTTAGACATGGCGCTTCATTTAC
TGAACAATAGACAGATGGTTTTGCATTTCAGAATCTTGTGAAGCAACAAGAATGGGTGAATCAGCAAAGGGAAGATATTG
AAAGGCAAAGGAAACTTTTAGCCAAACCCTAACCTCCCACAGCTAATAATTCTCAGGCACCCTCTACCAATTCTGAGCCA
AAATAAAGGAAAAACAAAGCAGTCAATGGAGCAGAGAATGATCCCTTTGTTAGACCAAATTTACCCCAACTGTTGACTTT
GGCAGAATATCATGAACAGGAAGAAATTTTCAAACTTAGACTAGGACATCTCAAAAAGGAAGAGGCAGAAATCCAGGCAG
AACTTGAACGTTTGGAAAGAGTCAGAAATCTTCACACACATGAGCTGAAAAGAAACAATGAAGATAATTCACAGTTCAAA
GATCACCCAACATTAAATGAAAGATATTTATTACTTCATCTACTTGGTAGAGGTGGCTTTAGTGAAGTATATAAGGCTTT
TGACCTTTATGAACAAAGATGTGCTGCTGTGAAGATACATCAGCTTAATAAAAGCTGGAGAGATGAGAAGAAAGAAAACT
ACCACAAACATGCCTGCAGAGAGTATAGAATACACAAAGAACTGGATCACCCCTGAATAGTTAAACTCTATGATTATTTC
TCCTTGGATACAGATACGTTTTGTATAGTGTTAGAATACTGTGAAGGCAATGACTTGGATTTCTATCTGAAGCAACACAA
GTTAATGTCAGAGAAAGAAGCTAGGTCTATTGTAATGCAGATTGCAAATGCGCCAAGATATCTCAATGAGATCAAACCCC
CTATTATACATTATGATCTTAAGCCA
ORF - retro_mmul_2277 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 94.48 % |
| Parental protein coverage: | 75.42 % |
| Number of stop codons detected: | 5 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | GAMDELHSLDPRRQELLEARFTGVASGSTGSTGSCSVGAKASTNNESSNHSFGSLGSLSDKESETPEKKQ |
| GA.DELHSL.PRRQEL..ARF.GVASGST.S.GSCSVGAKASTNNESSNHSFGSLGSLSDKESETPEKKQ | |
| Retrocopy | GAVDELHSLEPRRQELSKARFSGVASGSTASAGSCSVGAKASTNNESSNHSFGSLGSLSDKESETPEKKQ |
| Parental | SESSRGRKRKAENQNESSQGKSIGGRGHKISDYFEYQGGNGSSPVRGIPPAIRSPQNSHSHSTPSSSVRP |
| SESSRGRKRKAEN.NES.QGKSIGG.GHKISDYFEYQGGNGSSPVRGIPPAIRSPQNSHS.STPSSSV.P | |
| Retrocopy | SESSRGRKRKAENRNESNQGKSIGGCGHKISDYFEYQGGNGSSPVRGIPPAIRSPQNSHSRSTPSSSV*P |
| Parental | NSPSPTALAFGDHPIIQPKQLSFKIIQTDLTMLKLAALESNKIQDLEKKEGRIDDLLRANCDLRRQIDEQ |
| NS.SPTALAFGDHPI.QPKQLSFKIIQTDLTMLKLAALESNKIQDLE.KEGRIDD.LRANCDLRRQIDEQ | |
| Retrocopy | NSHSPTALAFGDHPIVQPKQLSFKIIQTDLTMLKLAALESNKIQDLEEKEGRIDDFLRANCDLRRQIDEQ |
| Parental | QKLLEKYKERLNKCISMSKKLLIEKSTQEKLSSREKSMQDRLRLGHFTTVRHGASFTEQWTDGFAFQNLV |
| QKLLEKYKERL.KCISMSKKLLIEKSTQEKLSSREKSMQDRL.LGHFTTVRHGASFTEQ.TDGFAFQNLV | |
| Retrocopy | QKLLEKYKERLSKCISMSKKLLIEKSTQEKLSSREKSMQDRLPLGHFTTVRHGASFTEQ*TDGFAFQNLV |
| Parental | KQQEWVNQQREDIERQRKLLAKRKPPTANNSQAPSTNSEPKQRKNKAVNGAENDPFVRPNLPQLLTLAEY |
| KQQEWVNQQREDIERQRKLLAK..PPTANNSQAPSTNSEPK.RKNKAVNGAENDPFVRPNLPQLLTLAEY | |
| Retrocopy | KQQEWVNQQREDIERQRKLLAKP*PPTANNSQAPSTNSEPK*RKNKAVNGAENDPFVRPNLPQLLTLAEY |
| Parental | HEQEEIFKLRLGHLKKEEAEIQAELERLERVRNLHIRELKRINNEDNSQFKDHPTLNERYLLLHLLGRGG |
| HEQEEIFKLRLGHLKKEEAEIQAELERLERVRNLH..ELKR.NNEDNSQFKDHPTLNERYLLLHLLGRGG | |
| Retrocopy | HEQEEIFKLRLGHLKKEEAEIQAELERLERVRNLHTHELKR-NNEDNSQFKDHPTLNERYLLLHLLGRGG |
| Parental | FSEVYKAFDLYEQRYAAVKIHQLNKSWRDEKKENYHKHACREYRIHKELDHPRIVKLYDYFSLDTDTFCT |
| FSEVYKAFDLYEQR.AAVKIHQLNKSWRDEKKENYHKHACREYRIHKELDHP.IVKLYDYFSLDTDTFC. | |
| Retrocopy | FSEVYKAFDLYEQRCAAVKIHQLNKSWRDEKKENYHKHACREYRIHKELDHP*IVKLYDYFSLDTDTFCI |
| Parental | VLEYCEGNDLDFYLKQHKLMSEKEARSIVMQIVNALRYLNEIKPPIIHYDLKP |
| VLEYCEGNDLDFYLKQHKLMSEKEARSIVMQI.NA.RYLNEIKPPIIHYDLKP | |
| Retrocopy | VLEYCEGNDLDFYLKQHKLMSEKEARSIVMQIANAPRYLNEIKPPIIHYDLKP |
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 | 0 .34 RPM | 40 .67 RPM |
| SRP007412_brain_prefrontal_cortex | 0 .79 RPM | 25 .62 RPM |
| SRP007412_cerebellum | 0 .26 RPM | 33 .00 RPM |
| SRP007412_heart | 0 .06 RPM | 7 .71 RPM |
| SRP007412_kidney | 0 .35 RPM | 27 .23 RPM |
| SRP007412_liver | 0 .12 RPM | 12 .07 RPM |
| SRP007412_testis | 1 .06 RPM | 21 .52 RPM |
Macaca mulatta was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_mmul_2277 retrocopy.
Macaca mulatta was not studied using FANTOM5 data.
retro_mmul_2277 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmul_2277 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 | |
|---|---|---|---|
| Macaca mulatta | ENSMMUG00000011189 | 1 retrocopy |
retro_mmul_2277 ,
|
| Pongo abelii | ENSPPYG00000012926 | 1 retrocopy |