RetrogeneDB ID: | retro_pabe_1245 | ||
Retrocopy location | Organism: | Orangutan (Pongo abelii) | |
| Coordinates: | 15:46340882..46342411(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | RLIM | ||
| Ensembl ID: | ENSPPYG00000020481 | ||
| Aliases: | None | ||
| Description: | ring finger protein, LIM domain interacting [Source:HGNC Symbol;Acc:13429] |
Retrocopy-Parental alignment summary:
>retro_pabe_1245
ATGGAAAACTCAGATTCTAACGACAAAGGAAGTGGTGATCAGTCTGCAGCACAGCGCAGAAGTCAGATGGACCGATTGGA
TCGGGAAGAAGCTTTCTATCCATTTGTAAATAACCTGAGTGAAGAAGATTATAGGCTTATGAGAGATAATAATTTGCTAG
GCACCCCAGGTGAAAGTACTGAGGAAGAGTTGCTGAGAAGACTACAGCAAATTAAAGAAGGCCCACCACCGCAAAACTCA
GGTGAAAATAGAGGAGGAGACTCTTCAGATGATGTGTCTAATGGTGACTCTATAATAGACTGGCTTAACTCTGTCAGACA
AACTGGAAATACAACAAGTGGGCAAAGAGGTAACCAATCTTGGAGAGCAGTGAGCCGGACTAATCCAAACAGTGGTGATT
TCGGATTCAGTTTAGAGATAAATGTTAACAGTAATAATGGGAGCCAAAATTCAGAGAATGAAAATGAGCCATCTGCAAGA
CGTTCTAGTGGAGAAAATGTGGAAAACAACAGCCAAAGGCAAGTGGAAAACCCATGATCTGAATCAACATCTTCAAGGCC
ATCTAGATCAGAACGAAATTCAACTGAAGCATTAACAGAAGTCCCACCTACCAGAGGTCAGAGGAGGGCAAGAAGCAGGA
GCCCAGACCGTGGGAGAACCAGAGCAAGAGCTGAGAGAAGTAGTTCACCTCTGCATCCAATGAGTGAAATTCCACGAAGA
TCTCATCATAGTATCTCATCTCAGACTTTTGAACATCCTTTGGTAAATGAGATGGAGGGAAGTTCTAGAACCCGGCCCTG
TGTGACATTGAGACAGCAAATATCTGGGCCTGAGTTGCTAAGTAGAGGTCTTTTTGCAGCTTCTGGAACAAGAAATGCCT
CTCAAGGAGCAGGTTCTTCAGACACAGCTGCCAATGGTAAATCTACAGGATCAGCACAGAGACCTCCAACCATAGTCCTT
GATCTTCAAGTAAAAAGAGTTCGTCCTGCAGAATATCGGCAGAGAGATAGCACAGCCAGCAGAACTCGGTCTAGGTCTCA
GAGGCCAAACAACACTGTCACCTATGAAAGTGAACGAGGAGGTTTTAGGCGTACGTTTTCACGTTCTGAGTGGGCAGGTG
TGAGAACGTATGTCAGTACCATCAGAATTCCCATTCGTAGAATCTTAAATACTGGTTTATGTGAGACTACATCTGTTGCA
ACTCAGACCATGTTAAGGCGGATAATGACAGGTTTTGGTGAGTTAAGCTATTTTATGTACAGTGATAGCAACTCAGAGCC
TACTGGCTCAGTCCCAAATCAAAATATGGAAAGGGCAGAGTCACGGAGTGGAAGGGGGGTTCTGGTGGTGGTAGTAGTTC
TGGTTCCAGTTCCAGTTCCAGTCCTAGTTCCAGTTCCGGTGGTGAAAGTTCAGAAACTAGCTCAGATTTATTTGAAGGCA
GTAATGAAGGAAGCTCATCATCAGGCTCATCAGGTGTCAGGCGAGAGGGTCGACATAGGGCCCCAGTCATATTTGATGAA
AGTGGCTCT
ORF - retro_pabe_1245 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 85.74 % |
| Parental protein coverage: | 81.41 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MENSDSNDKGSGDQSAAQRRSQMDRLDREEAFYQFVNNLSEEDYRLMRDNNLLGTPGESTEEELLRRLQQ |
| MENSDSNDKGSGDQSAAQRRSQMDRLDREEAFY.FVNNLSEEDYRLMRDNNLLGTPGESTEEELLRRLQQ | |
| Retrocopy | MENSDSNDKGSGDQSAAQRRSQMDRLDREEAFYPFVNNLSEEDYRLMRDNNLLGTPGESTEEELLRRLQQ |
| Parental | IKEGPPPQNSDENRGGDSSDDVSNGDSIIDWLNSVRQTGNTTRSGQRGNQSWRAVSRTNPNSGDFRFSLE |
| IKEGPPPQNS.ENRGGDSSDDVSNGDSIIDWLNSVRQTGNTT.SGQRGNQSWRAVSRTNPNSGDF.FSLE | |
| Retrocopy | IKEGPPPQNSGENRGGDSSDDVSNGDSIIDWLNSVRQTGNTT-SGQRGNQSWRAVSRTNPNSGDFGFSLE |
| Parental | INVNRNNGSQNSENENEPSARRSSGENVENNSQRQVENPRSESTSARPSRSERNSTEALTEVPPTRGQRR |
| INVN.NNGSQNSENENEPSARRSSGENVENNSQRQVENP.SESTS.RPSRSERNSTEALTEVPPTRGQRR | |
| Retrocopy | INVNSNNGSQNSENENEPSARRSSGENVENNSQRQVENP*SESTSSRPSRSERNSTEALTEVPPTRGQRR |
| Parental | ARSRSPDHRRTRARAERSRSPLHPMSEIPRRSHHSISSQTFEHPLVNETEGSSRTRHHVTLRQQISGPEL |
| ARSRSPD..RTRARAERS.SPLHPMSEIPRRSHHSISSQTFEHPLVNE.EGSSRTR..VTLRQQISGPEL | |
| Retrocopy | ARSRSPDRGRTRARAERSSSPLHPMSEIPRRSHHSISSQTFEHPLVNEMEGSSRTRPCVTLRQQISGPEL |
| Parental | LSRGLFAASGTRNASQGTGSSDTAANGESTGSGQRPPTIVLDLQVRRVRPGEYRQRDSIASRTRSRSQTP |
| LSRGLFAASGTRNASQG.GSSDTAANG.STGS.QRPPTIVLDLQV.RVRP.EYRQRDS.ASRTRSRSQ.P | |
| Retrocopy | LSRGLFAASGTRNASQGAGSSDTAANGKSTGSAQRPPTIVLDLQVKRVRPAEYRQRDSTASRTRSRSQRP |
| Parental | NNTVTYESERGGFRRTFSRSERAGVRTYVSTIRIPIRRILNTGLSETTSVAIQTMLRQIMTGFGELSYFM |
| NNTVTYESERGGFRRTFSRSE.AGVRTYVSTIRIPIRRILNTGL.ETTSVA.QTMLR.IMTGFGELSYFM | |
| Retrocopy | NNTVTYESERGGFRRTFSRSEWAGVRTYVSTIRIPIRRILNTGLCETTSVATQTMLRRIMTGFGELSYFM |
| Parental | YSDSDSEPTGSVSNRNMERAESRSGR-GGSGGGSSSGSSSSSSSSSSSSSSSSSSSS---PSSSSGGESS |
| YSDS.SEPTGSV.N.NMERAESRSGR.GGSGGGS.................SS..SS.....S..G..SS | |
| Retrocopy | YSDSNSEPTGSVPNQNMERAESRSGR<GGSGGGSXXXXXXXXXXXXXXXGESSETSSDLFEGSNEGSSSS |
| Parental | ETSSDLFEGSNEGSSSSGSSGA |
| ..S....EG..........SG. | |
| Retrocopy | GSSGVRREGRHRAPVIFDESGS |
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 | 10 .78 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 10 .09 RPM |
| SRP007412_heart | 0 .00 RPM | 4 .61 RPM |
| SRP007412_kidney | 0 .00 RPM | 5 .80 RPM |
| SRP007412_liver | 0 .00 RPM | 4 .04 RPM |
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_1245 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_1245 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_pabe_1245 has 3 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_1495 |
| Pan troglodytes | retro_ptro_1014 |
| Macaca mulatta | retro_mmul_2139 |
Parental genes homology:
Parental genes homology involve 4 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Homo sapiens | ENSG00000131263 | 1 retrocopy | |
| Macaca mulatta | ENSMMUG00000009249 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000020481 | 1 retrocopy |
retro_pabe_1245 ,
|
| Pan troglodytes | ENSPTRG00000022037 | 1 retrocopy |