RetrogeneDB ID: | retro_pabe_2495 | ||
Retrocopy location | Organism: | Orangutan (Pongo abelii) | |
| Coordinates: | 4:182637163..182638550(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | TSEN2 | ||
| Ensembl ID: | ENSPPYG00000013647 | ||
| Aliases: | None | ||
| Description: | tRNA splicing endonuclease 2 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:28422] |
Retrocopy-Parental alignment summary:
>retro_pabe_2495
ATGGCAGAAGCAGTTTTCCATGCCCCAAACAGGAAAGGAAGAATGTATGAGACTTATGAGTCTCCATTGCCAATCCTTTC
TGGTCAGGACCGTGGTCCTCAGAAAGCAAGATATTCTATGCTGAAATGATTAACAACAATGTGATTGTGAGGAATGCAGA
GGACATTGAGCAGCTCTATGGGGAAGGTTCTTTTGGAAAAGGTATTCTTTCAAGAAACTGTCCAGCGATCACAGTTTCAG
ATCCTAAATTGGTTGCGAAATGGAAAGATATGAAGACAAACATGCTTATCATCACATCAAAGAAGTATCAACGTAGTGTT
GAGTGGGTGGCAGAGCTGATGCGTAGACAGGGACAGAATGAGAATACAGTGCGCAGAATCCTCAAGGATTACATGAATCC
GCTTGAGCATCGCCCTGTGAAAAGGAATGAACAGGCTCAAATGCATGATGAGCTTAACTCTGGAATGGTTTCCAACGTGG
AAGGCACAGCGGTAGGAGAGAGATCTTCTGTGATAAACGGGGACTCTGGAAAGTCAGGTGTTATGGGTGATCCCAGTGAG
CCATTAGGCTGCCTGCAGGAGGGCTCTGGGAGCGACCCACCAACAGAAGGCTTTGAGGAAAGGGTGGGAGAGGACGCTTC
ACCTCCGCCCCAAGCATGTTGCTGCAAACACGATGCTCTTGTCCTCCCGTCTGGCCCTCACCGGGAGGACAGCAGCCAGC
ATTTTGGTCTCCTGCATGCTGGGGACAGAGGGCCTGACCAGTACGTGCTGGTGCAGGAAGCCGAGTGTGCAGTGAGCGAG
AGGAAGGATGCCTCAAATGAGGAATTGGTGCAAAGAAAGAGACTAATCTGCAGAAGAAATCCATATAGGATCTCTGAGTA
TTTGCAGCTCAGCCTAGAAGAGGCCTTTTTCCTGGTCTGTGCTCTGGAATGTTTAAGTATTTGCTACGAGAAGGAGCCTT
TAACGATAGTGAAGCTCTGGAAAGCTTTCACTGTAGTTCAGCCCACGTTTAGGACCACCTACATGGCCTACCATTACTTC
CCAAGCAAGGGCTAGTGCCCAGAGTGGGGCTCAAGTACGGGACAGATTTGCTGCTATGTTGGAAAGGCCCTCCGTTTTAC
CATGCAAGCTATTCTGTCGTTATTGAGCTAGTTGATGAGCAGTTTGAAGGCTGTCTCTGCAGGCCTTTCAGTTGGATGTC
CCTGGCTGCCTTGAGCAGAGTTTCCGTTAATGTCTCCAAGGAACTCATGCTGTGCTGTTTCATTAAACCCTCTACTATGA
CTGACAAGGAAATGGAGTCACCAGAATGTATGAAAAAAATTAGAGTTCAGGAGGTGATTCTGAGTTGATGGGTGTCTTCA
CGAGAGAGGAGTGACCAAGACGAACTT
ORF - retro_pabe_2495 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 81.62 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | MAEAVFHAPKRKRRVYETYESPLPI-PFGQDHGP-QKEFKIFRAEMINNNVIVRNAEDIEQLYGKGYFGK |
| MAEAVFHAP.RK.R.YETYESPLPI.PF....GP...E.KIF.AEMINNNVIVRNAEDIEQLYG.G.FGK | |
| Retrocopy | MAEAVFHAPNRKGRMYETYESPLPI<PFWS--GPWSSESKIFYAEMINNNVIVRNAEDIEQLYGEGSFGK |
| Parental | GILSRSRPSFTISDPKLVAKWKDMKTNMPIITSKRYQRSVERAAELMCRQGQDESTVRRILKDYTKPLEH |
| GILSR..P..T.SDPKLVAKWKDMKTNM.IITSK.YQRSVE..AELM.RQGQ.E.TVRRILKDY..PLEH | |
| Retrocopy | GILSRNCPAITVSDPKLVAKWKDMKTNMLIITSKKYQRSVEWVAELMRRQGQNENTVRRILKDYMNPLEH |
| Parental | PPVKRNEEAQVHDELNSGMVSNMEGTAGGVRPSVVNGDSGKSGGMGDPSEPFGCLQEGSGCDPTTDGFEK |
| .PVKRNE.AQ.HDELNSGMVSN.EGTA.G.R.SV.NGDSGKSG.MGDPSEP.GCLQEGSG.DP.T.GFE. | |
| Retrocopy | RPVKRNEQAQMHDELNSGMVSNVEGTAVGERSSVINGDSGKSGVMGDPSEPLGCLQEGSGSDPPTEGFEE |
| Parental | SMGEDASLLPQVCCCKQDALILQCGPHHEDSSQHVGLLHAGDRGPDHEYVLVEEAQCAVSEREHVPNEEL |
| ..GEDAS..PQ.CCCK.DAL.L..GPH.EDSSQH.GLLHAGDRGPD..YVLV.EA.CAVSER....NEEL | |
| Retrocopy | RVGEDASPPPQACCCKHDALVLPSGPHREDSSQHFGLLHAGDRGPD-QYVLVQEAECAVSERKDASNEEL |
| Parental | VQRNRLICRRNPYRIFEYLQLSLEEAFFLVYALGCLSIYYEKEPLTIVKLWKAFTVVQPTFRTTYMAYHY |
| VQR.RLICRRNPYRI.EYLQLSLEEAFFLV.AL.CLSI.YEKEPLTIVKLWKAFTVVQPTFRTTYMAYHY | |
| Retrocopy | VQRKRLICRRNPYRISEYLQLSLEEAFFLVCALECLSICYEKEPLTIVKLWKAFTVVQPTFRTTYMAYHY |
| Parental | FRSK-GWVPKVGLKYGTDLLLYRKGPPFYHASYSVIIELVDDHFEGSLRRPFSWKSLAALSRVSINVSKE |
| F.SK.G.VP.VGLKYGTDLLL..KGPPFYHASYSV.IELVD..FEG.L.RPFSW.SLAALSRVS.NVSKE | |
| Retrocopy | FPSK<GLVPRVGLKYGTDLLLCWKGPPFYHASYSVVIELVDEQFEGCLCRPFSWMSLAALSRVSVNVSKE |
| Parental | LMLCYLIKPSTMTDKEMESPECMKRIKVQEVILSRWVSSRERSDQDDL |
| LMLC..IKPSTMTDKEMESPECMK.I.VQEVILS.WVSSRERSDQD.L | |
| Retrocopy | LMLCCFIKPSTMTDKEMESPECMKKIRVQEVILS*WVSSRERSDQDEL |
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 | 8 .40 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 13 .13 RPM |
| SRP007412_heart | 0 .00 RPM | 4 .82 RPM |
| SRP007412_kidney | 0 .00 RPM | 6 .23 RPM |
| SRP007412_liver | 0 .00 RPM | 3 .98 RPM |
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_2495 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_2495 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_pabe_2495 has 4 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_3011 |
| Pan troglodytes | retro_ptro_2035 |
| Gorilla gorilla | retro_ggor_2085 |
| Macaca mulatta | retro_mmul_1925 |
Parental genes homology:
Parental genes homology involve 6 parental genes, and 7 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Homo sapiens | ENSG00000154743 | 1 retrocopy | |
| Gorilla gorilla | ENSGGOG00000012488 | 2 retrocopies | |
| Microcebus murinus | ENSMICG00000016672 | 1 retrocopy | |
| Macaca mulatta | ENSMMUG00000007195 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000013647 | 1 retrocopy |
retro_pabe_2495 ,
|
| Pan troglodytes | ENSPTRG00000014633 | 1 retrocopy |