RetrogeneDB ID: | retro_pabe_870 | ||
Retrocopy location | Organism: | Orangutan (Pongo abelii) | |
| Coordinates: | 12:90375422..90376991(+) | ||
| Located in intron of: | ENSPPYG00000004819 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | CENPC | ||
| Ensembl ID: | ENSPPYG00000014736 | ||
| Aliases: | None | ||
| Description: | centromere protein C [Source:HGNC Symbol;Acc:1854] |
Retrocopy-Parental alignment summary:
>retro_pabe_870
ACACGTATTCAGTCACCAAGCAAAGAGTGCCAGAAATCACATCCAAAGTCAGTTCCACTTTCTTCAAGGAAGAAAGAAGC
CTCTCTGCAGTTTGTTGTAGAACCAAGTGAAGCCACCAACAGATCAGTTCAGGCCCATGAAGTTCGTCAGAAAATTCTGG
CAACTGATGTTAGTTCCAAAAATACACCTGACTCGAAAAAAATGTCAAGTAGAAACATAAATGATCATCACAGTGAAGCT
GATGAAGAATTTTACTTATCTGTTGGCTCACCTTCTGTTCTTTTGGATGCAAAAACATCTGTATTGCAAAATGTTATTCC
ATCTAGTGCCCAAAAGAAAGAGACTTACACTTTTGAAAATTCAGTAAATATGCTGCCTTCAAGTACAGAGGTTTCACTTA
AAACCAAACAAAGGTTAAACTTTGAAGATAAAGTTATTTTAAAGAAAATAGAAATAGATAATAAAGTATCAGATGAAGAG
GATACAACATCAGAAGGACAAGAAAGAAAACCATCAGGATCATCTCAGAATAGAATACGAAATTCAGAATATGAAATTCA
ATGACAAGCTAAAAAAAGTTTTTCAACATTGTTTTTAGAAACAGCAAAACGAAAAAGTGAATCCAGTCCCATTGTTAGGC
ATGGAGAAATTGCTCCACCTCATTCGTGTCCTCCCGATGATATGAAGTTGACAGAGGATGAATTTATAATTGATGAGTCA
GATCAAAGTTTTGCCAGTAGATCTTGGATTACTATACCAAGAAAGGCAGGGCCTCTGAAACAACGCACCATATCCCCGGC
TGAGAGCACTGCACTCCTTCAAGATAGAAAGTCAAGAGAAAAGCATTATAATATATTAGCTATGACTTTGGCAAATGACA
AACATTCCCATAAACCTCACCTAGTAGAGACATCTCAGCCCTCTGATAAAACAGTACTGGATACAAGTTATGCTTTGACA
GGTGAAACACAAAATGACTGTAGATCTACAAAATATGAAATGTATTCCAAGAATGCAGAAAAATCATCTAGAAGCAAAAG
GACTAAAAAACAAAAACAGAGAAGAAAATTTATGGCTAAACCAGCTGAAGAACAGCTCGATGTGGGACAGTCTAAAGATG
AAAACATACATACGTCACATATTACCCAAGACAAATTTCAAAGAAATTCAGACAGAAATATGGAAGAGTGTGAAGAGATG
GGAAATGATTGTGCTTCCAAAAAACAGATGCCACCTGTGGGAAGCAAGAAAAGTAGCACTAGAAAAGATAAGGAAGAATC
TAAAAAGAAGCGCTTTTCCAGTGAGTCCAAGAACAAACTTGTACCTGAAGAAGTGACTTCAACTGTCACGAGAAGTCGAA
GAATTTCCAGACATCCATCTAATTGGTGGGTGGTAAAATCAGAGGAGAGTCCTGTTGATAGCAATTCTTCAATAAGAAAT
GAATTACCAGTGCATCACAACAGTAGGCAAAAATCTGCTAAGAAAACAAATCAGTCATCTAAGAATATTGGGAAAAAAAC
TATTCCACTTAAAAGGCAGAAGACAGCAACTAAAGACAGCCAAAGAGTA
ORF - retro_pabe_870 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 85.85 % |
| Parental protein coverage: | 55.89 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | TRIQSPSKECQKSHSKSVPVSSRNKEASLQSVVESSEATNRSVQAHEVRQKILATDVSSKNTPDSKKKSS |
| TRIQSPSKECQKSH.KSVP.SSR.KEASLQ.VVE.SEATNRSVQAHEVRQKILATDVSSKNTPDSKK.SS | |
| Retrocopy | TRIQSPSKECQKSHPKSVPLSSRKKEASLQFVVEPSEATNRSVQAHEVRQKILATDVSSKNTPDSKKMSS |
| Parental | RNINDHHSEADEEFYLSVGSPSVLLDAKTSVSQNVIPSSAQKRETYTFENSVNMLPSSTEVSVKTKKRLN |
| RNINDHHSEADEEFYLSVGSPSVLLDAKTSV.QNVIPSSAQK.ETYTFENSVNMLPSSTEVS.KTK.RLN | |
| Retrocopy | RNINDHHSEADEEFYLSVGSPSVLLDAKTSVLQNVIPSSAQKKETYTFENSVNMLPSSTEVSLKTKQRLN |
| Parental | FDDKVMLKKIEIDNKVSDEEDKTSEGQERKPSGSSQNRIRDSEYEIQRQAKKSFSTLFLETVKRKSESSP |
| F.DKV.LKKIEIDNKVSDEED.TSEGQERKPSGSSQN...........QAKKSFSTLFLET.KRKSESSP | |
| Retrocopy | FEDKVILKKIEIDNKVSDEEDTTSEGQERKPSGSSQNXXXXXXXXXX*QAKKSFSTLFLETAKRKSESSP |
| Parental | IVRHVATAPPHSCPPDDTKLIEDEFIIDESDQSFASRSWITIPRKAGPLKQRTVSPAESTALLQGRKSRE |
| IVRH...APPHSCPPDD.KL.EDEFIIDESDQSFASRSWITIPRKAGPLKQRT.SPAESTALLQ.RKSRE | |
| Retrocopy | IVRHGEIAPPHSCPPDDMKLTEDEFIIDESDQSFASRSWITIPRKAGPLKQRTISPAESTALLQDRKSRE |
| Parental | KHHNILPKTLANDKHSHKPHPVETSQPSDKTVLDTSHALIGETENNYRSTKYEMYSKNAEKPSRSKRTIK |
| KH.NIL..TLANDKHSHKPH.VETSQPSDKTVLDTS.AL.GET.N..RSTKYEMYSKNA........... | |
| Retrocopy | KHYNILAMTLANDKHSHKPHLVETSQPSDKTVLDTSYALTGETQNDCRSTKYEMYSKNAXXXXXXXXXXX |
| Parental | QKQRRKFMAKPAEEQLDVGQSKDENIHTSHITQDEFQRNSDRNMEEREEMGNDCVSKKQMPPVGSKKSST |
| ......FMAKPAEEQLDVGQSKDENIHTSHITQD.FQRNSDRNMEE.EEMGNDC.SKKQMPPVGSKKSST | |
| Retrocopy | XXXXXXFMAKPAEEQLDVGQSKDENIHTSHITQDKFQRNSDRNMEECEEMGNDCASKKQMPPVGSKKSST |
| Parental | RKDKEESKKKRFSSESKNKLVPEEVTSTVTRSRRISRRPSDWWVVKSEESPVYSNSSIRNE-PVPHNSRQ |
| RKDKEESKKKRFSSESKNKLVPEEVTSTVTRSRRISR.PS.WWVVKSEESPV.SNSSIRNE.PV.HNSRQ | |
| Retrocopy | RKDKEESKKKRFSSESKNKLVPEEVTSTVTRSRRISRHPSNWWVVKSEESPVDSNSSIRNELPVHHNSRQ |
| Parental | KSAKKTKESSKNIRKKTIPLKRQKTANKQRQKL |
| KSAKKT..SSKNI.KKTIPLKRQKTA.K..Q.. | |
| Retrocopy | KSAKKTNQSSKNIGKKTIPLKRQKTATKDSQRV |
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 .11 RPM | 6 .41 RPM |
| SRP007412_cerebellum | 0 .24 RPM | 16 .78 RPM |
| SRP007412_heart | 0 .09 RPM | 5 .06 RPM |
| SRP007412_kidney | 0 .23 RPM | 6 .63 RPM |
| SRP007412_liver | 0 .18 RPM | 3 .92 RPM |
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_870 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_870 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_pabe_870 has 2 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_1038 |
| Pan troglodytes | retro_ptro_708 |
Parental genes homology:
Parental genes homology involve 5 parental genes, and 5 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Homo sapiens | ENSG00000145241 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000029253 | 1 retrocopy | |
| Nomascus leucogenys | ENSNLEG00000009058 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000014736 | 1 retrocopy |
retro_pabe_870 ,
|
| Pan troglodytes | ENSPTRG00000016096 | 1 retrocopy |