RetrogeneDB ID: | retro_pabe_2678 | ||
Retrocopy location | Organism: | Orangutan (Pongo abelii) | |
| Coordinates: | 5:116561567..116562957(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | CCT5 | ||
| Ensembl ID: | ENSPPYG00000015342 | ||
| Aliases: | None | ||
| Description: | chaperonin containing TCP1, subunit 5 (epsilon) [Source:HGNC Symbol;Acc:1618] |
Retrocopy-Parental alignment summary:
>retro_pabe_2678
ATCTTAAGCATGATGGATGTCGATCATCAAATTGCTAAGCTGATGGCGGAACTGTCCAAGTCTCAGGATGATGAAATTGG
ACTTGGAACCACAGGAGTGGTAGTCCTGGCTGCTGCCTTGTTACAAGAAGCCAAGCAGTTGCTAGACTGAGGCATTCACC
CAATCAGAATAGCTGATGGTTATGAGCAGGCTGTCAGCGTTGCTGTTGAACACCTGGACAAGATCAGTCATAGTGTCCTT
GTCGACATAAAGGACACTGAACCCCTGATTCCAACTGCAAAAACCATGCTGGGCTCCAAAGTGGTCAAAGTTGGCACCAA
CAAATGGCTGAGATTGCTGTGAATGCTGTCCTCACTGTAGCAGATATGGAGCGGAGAGATACTGACTTTGAGCTCGTCAA
CGTAGAAGGCAAAGTGGGCGGGAGGCTGGAGGACAGAAAACTGATTAAGGGCGTGATTGTGGACAAGGATTTCCAGTCAC
CTATAGGTGCTGAAAAAAGTGGAAGATGCCAAGATTGCAATTCTCACATGTCCATTTGAACCACCGAAGCCAAAAAACAA
AGCATAAGCTGGATGTGACCTCCATAGATCATAAAGCTCTTCAGAAATATGAAAAGGAGAAATTTGAAGAGATGATTCAA
AAAATTAAACAGACTGGTGCTAACCTAGCAATTTGTCAGTGGGGCTTTGATGATGAAGCAAATCACTTATTTCTTCAGAA
CAACTTGCCTGTGGTTCGCTGGGTAGGGGGACTTGAAATTGAACTTATTGCCATCTCAACAAAAGGGCGGATTGTCCCAG
GTTCTCAGAGCTCATGGGCGAGACGCTGGGCTTTACCGGTCTTGTACAGGAGATCTCATTTGGGACAACTAAGGATAAAA
TGCTGGTCATCGAGCAGTGTAAGAACTCCAGAGCTGTAACCATTTTTATTAGAGGAGGAAATAAGATGATCATTGAGGAG
GTGAAACGATCCCTTCACGATGCTTTGTGTGTCATCAGCAACCTCATCCGCAATAATTGTGTGGCATACGGAGGAGGGTT
TGCTGAGATATCCTGTGCTCTGGCAGTTAGCCAAGAGGTGGATAAGCGCCCCACCTTAGACCAGTACACCACAAGAGCGT
TTGCCAACGCTCTGGAGTTGCCCCATGGGCCTTTTTGAAAACAGTGGCATGAATCCCATCCAGACTATGACAAAAGTCCG
AGCCAGACAAGTGAAAGATATGAACCCTGCTCTCGGTACTGACTGTTTCCACAAGGGGACAAATGATATGAAGCAACAGC
ATGTCATAGAAATCTTAATTGGCAAAAAGCAACAGACATCTTTCACAACACAAATGGTTAGAATGATTGTGAAGATTGAT
GACATTCATAAGCCTGGAGAATCTGAAGAA
ORF - retro_pabe_2678 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 83.83 % |
| Parental protein coverage: | 85.95 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 5 |
Retrocopy - Parental Gene Alignment:
| Parental | ILSMMDVDHQIAKLMVELSKSQDDEIGDGTTGVVVLAGALLEEAEQLLDRGIHPIRIADGYEQAARVAIE |
| ILSMMDVDHQIAKLM.ELSKSQDDEIG.GTTGVVVLA.ALL.EA.QLLD.GIHPIRIADGYEQA..VA.E | |
| Retrocopy | ILSMMDVDHQIAKLMAELSKSQDDEIGLGTTGVVVLAAALLQEAKQLLD*GIHPIRIADGYEQAVSVAVE |
| Parental | HLDKISDSVLVDIKDTEPLIQTAKTTLGSKVVN-SCHRQMAEIAVNAVLTVADMERRDVDFELIKVEGKV |
| HLDKIS.SVLVDIKDTEPLI.TAKT.LGSKVV..S.H.QMAEIAVNAVLTVADMERRD.DFEL..VEGKV | |
| Retrocopy | HLDKISHSVLVDIKDTEPLIPTAKTMLGSKVVK<SWHQQMAEIAVNAVLTVADMERRDTDFELVNVEGKV |
| Parental | GGRLEDTKLIKGVIVDKDF-SHPQMPKKVEDAKIAILTCPFEPPKPK-TKHKLDVTSVEDYKALQKYEKE |
| GGRLED.KLIKGVIVDKDF.SH....KKVEDAKIAILTCPFEPPKPK.TKHKLDVTS..D.KALQKYEKE | |
| Retrocopy | GGRLEDRKLIKGVIVDKDF>SHL*VLKKVEDAKIAILTCPFEPPKPK>TKHKLDVTSI-DHKALQKYEKE |
| Parental | KFEEMIQQIKETGANLAICQWGFDDEANHLLLQNNLPAVRWVGGPEIELIAIATGGRIVP-RFSELTAEK |
| KFEEMIQ.IK.TGANLAICQWGFDDEANHL.LQNNLP.VRWVGG.EIELIAI.T.GRIVP.RFSEL..E. | |
| Retrocopy | KFEEMIQKIKQTGANLAICQWGFDDEANHLFLQNNLPVVRWVGGLEIELIAISTKGRIVP<RFSELMGET |
| Parental | LGFAGLVQEISFGTTKDKMLVLEQCKNSRASCNHFIRGNKMIIEEAKRSLHDALCVIRNLIRDNRVVYGG |
| LGF.GLVQEISFGTTKDKMLV.EQCKNSRA.......GNKMIIEE.KRSLHDALCVI.NLIR.N.V.YGG | |
| Retrocopy | LGFTGLVQEISFGTTKDKMLVIEQCKNSRAVTIFIRGGNKMIIEEVKRSLHDALCVISNLIRNNCVAYGG |
| Parental | GAAEISCALAVSQEADKCPTLEQYAMRAFADALEVIP-MALSENSGMNPIQTMTEVRARQVKEMNPALGI |
| G.AEISCALAVSQE.DK.PTL.QY..RAFA.ALE..P.M.L.ENSGMNPIQTMT.VRARQVK.MNPALG. | |
| Retrocopy | GFAEISCALAVSQEVDKRPTLDQYTTRAFANALE-LP>MGLFENSGMNPIQTMTKVRARQVKDMNPALGT |
| Parental | DCLHKGTNDMKQQHVIETLIGKKQQISLATQMVRMILKIDDIRKPGESEE |
| DC.HKGTNDMKQQHVIE.LIGKKQQ.S..TQMVRMI.KIDDI.KPGESEE | |
| Retrocopy | DCFHKGTNDMKQQHVIEILIGKKQQTSFTTQMVRMIVKIDDIHKPGESEE |
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 | 6 .14 RPM | 102 .90 RPM |
| SRP007412_cerebellum | 8 .63 RPM | 107 .37 RPM |
| SRP007412_heart | 4 .67 RPM | 63 .13 RPM |
| SRP007412_kidney | 5 .80 RPM | 97 .88 RPM |
| SRP007412_liver | 5 .60 RPM | 87 .89 RPM |
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_2678 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_2678 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_pabe_2678 has 4 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_3230 |
| Pan troglodytes | retro_ptro_2182 |
| Gorilla gorilla | retro_ggor_2197 |
| Macaca mulatta | retro_mmul_2033 |
Parental genes homology:
Parental genes homology involve 3 parental genes, and 5 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Monodelphis domestica | ENSMODG00000002356 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000015342 | 2 retrocopies |
retro_pabe_1012, retro_pabe_2678 ,
|
| Tupaia belangeri | ENSTBEG00000001201 | 2 retrocopies |