RetrogeneDB ID: | retro_pabe_88 | ||
Retrocopy location | Organism: | Orangutan (Pongo abelii) | |
| Coordinates: | 17:38573147..38575172(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSPPYG00000008261 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | KIF2C | ||
| Ensembl ID: | ENSPPYG00000001427 | ||
| Aliases: | None | ||
| Description: | kinesin family member 2C [Source:HGNC Symbol;Acc:6393] |
Retrocopy-Parental alignment summary:
>retro_pabe_88
ATGGCCAGCCAGTTCTGCCTTCCTGAATCCCCATGCCTCTCGCCCCTGAAACCCTTGAAGCCACATTTCGGAGACATCCA
AGTGGGCATCTACGTGGCGATCCAGCGCAGTGACAAGCGGATCCACCTCGCTGTGGTAACGGAGATCAACAGAGAAAACT
ATTGGGTCACGGTAGAGTGGGTGGAGAAAGCAGTCAAAAAAGGCAAGAAGATTGACCTGGAGACCATACTCCTGCTGAAT
CCAGCTCTGGACTCTGCTGAACACCCCATGCCGCCCCCGCCCTTATCCCCCTTGGCTCCGGCGCCCTCTTCGGCCATCAG
GGACCAGCGTACCGCCACGAAATGGGTTGTGATGATCCCCCAGAAAAACAAAACAGCCTCTGGGGACAGCCTGGACGTGA
GGATCCCCAGCAAACCTTGTCTGATGAAGCAGAAAAAGTCTCCTTGCCTCTGGGAAATCCAGAAACTGCAGAAGCAGCGG
GAAAAGCGCAGGCGGCTGCAGCAGGAGATCCGAGCTAGACGTGCCCTCGATGTCAACATCAGAAACCCCAACTACGAAAT
CATGCACATGATCGAAGAGTATCGCAGGCACCTGGACAGCAGCAAGATTTCAGTCCTGGAGCCCCCGCAAGAACATCGCA
TCTGCGTCTGCGTGAGGAAGCGGCCTCTCAACCAGCGAGAGACAACCTTGAAGGACCTGGATATCATCACCGTCCCCTCG
GACAATGTGGTTATGGTGCATGAGTCCAAGCAAAAGGTGGACCTCACTCGCTACCTGCAGAACCAGACCTTCTGCTTCGA
CCATGCCTTCGACGACAAAGCCTCCAACGAGTTGGTGTACCAGTTCACCGCCCAGCCACTGGTGGAGTCCATCTTCCGCA
AGGGCATGGCCACCTGCTTTGCCTATGGGCAGACGGGAAGTGGGAAGACGTACACCATGGGTGGAGACTTTTCAGGAAGG
GCCCAAGATTGTTCTAAGGGCATTTATGCTCTGGTGGCACAGGATGTCTTTCTCCTGCTCAGAAACTCCACATATGAGAA
GCTGGACCTCAAAGTCTATGGGACATTTTTTGAGATTTATGGGGGCAAGGTGTATGATTTGTTGAACTGGAAGAAGAAAC
TGCAAGTCCTTGAGGATGGCAATCAGCAAATCCAAGTGGTCGGGCTGCAGGAGAAAGAGGTGTGTTGTGTGGAGGAAGTG
CTGAACCTGGTGGAAATAGGGAATAGCTGTCGGACTTCCAGGCAAACATCTGTCAACGCTCACTCATCCAGGAGCCATGC
AGTGTTCCAGATCATCTTGAAGTCAGGAGGGATATTGCATGGCAAGTTTTCCCTCGTTGATTTAGCTGGGAATGAAAGGG
GAGCAGATACGACCAAGGCCAGCCGGAAAAGGCAGCTGGAAGGGGCAGAGATTAACAAGAGTCTTCTAGCCCTCAAAGAA
TGTATTCTAGCTTTGGGTCAGAACAAGCCTCACACCCCATTCAGAGCCAGCAAACTCACACAGGTGCTCCGGGACTCCTT
TATAGGCCAGAACTCCTCCACTTGCATGATCGCTACTATCTCTCCAGGAATGACCTCTTGTGAAAACACTCTCAACACTT
TAAGATATGCAAACAGAGTAAAAAAATTAAATGTAGATGTAAGGCCATACCATCGTGGCCTCTATCCGATTGGACATGAG
ACACCAAGGATGTTAAAAAGTCACATCGGAAATTCAGAAATGTCCCTTCAGAGGGATGAATTTATTAAAATACCTTATGT
ACAGTGTGAGGGGCAGCACAAAGAGATTGAAGAGGTTGAAACATTACCCATTCCGTTAGGGAAGGATACCACAACTTCAG
GGAAGGGATCTAGCCAATGGTTGGAAAATATCCAGGAGAGAGCTGGTGGAGTAAACCATGATATTGATTTTTGCGTTGCC
CGGTCTTTGTCCATTTTGGAGCAGAAAATTGATGTTCTGACCGAGATCCAAAAGAAACTGAAATTATTACGAGCTGACCT
CCACATGAAGAGCAAGGTAGAGTGA
ORF - retro_pabe_88 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 61.76 % |
| Parental protein coverage: | 57.79 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | ANPVNSVRRKSCLVKEVEKMKNKREEKKAQNSEMRMKRAQEYDSSFPNWEFARMIKEFRATLECHPLTMT |
| ..P......KS....E..K....RE.......E.R..RA.......PN.E...MI.E.R..L........ | |
| Retrocopy | SKPCLMKQKKSPCLWEIQKLQKQREKRRRLQQEIRARRALDVNIRNPNYEIMHMIEEYRRHLDSSKISVL |
| Parental | DPIEEHRICVCVRKRPLNKQELAKKEIDVISIPSKCLLLVHEPKLKVDLTKYLENQAFCFDFAFDETASN |
| .P..EHRICVCVRKRPLN..E...K..D.I..PS.....VHE.K.KVDLT.YL.NQ.FCFD.AFD..ASN | |
| Retrocopy | EPPQEHRICVCVRKRPLNQRETTLKDLDIITVPSDNVVMVHESKQKVDLTRYLQNQTFCFDHAFDDKASN |
| Parental | EVVYRFTARPLVQAIFEGGKATCFAYGQTGSGKTHTMGGDLSGKAQNASKGIYAMASRDVFLLKNQPCYR |
| E.VY.FTA.PLV..IF..G.ATCFAYGQTGSGKT.TMGGD.SG.AQ..SKGIYA....DVFLL.....Y. | |
| Retrocopy | ELVYQFTAQPLVESIFRKGMATCFAYGQTGSGKTYTMGGDFSGRAQDCSKGIYALVAQDVFLLLRNSTYE |
| Parental | KLGLEVYVTFFEIYNGKLFDLLNKKAKLRVLEDGKQQVQVVGLQEHLVNSADDVIKMIDMGSACRTSGQT |
| KL.L.VY.TFFEIY.GK..DLLN.K.KL.VLEDG.QQ.QVVGLQE..V.....V......G..CRTS.QT | |
| Retrocopy | KLDLKVYGTFFEIYGGKVYDLLNWKKKLQVLEDGNQQIQVVGLQEKEVCCVEEVLNLVEIGNSCRTSRQT |
| Parental | FANSNSSRSHACFQILLRAKGRMHGKFSLVDLAGNERGADTSSADRQTRMEGAEINKSLLALKECIRALG |
| ..N..SSRSHA.FQI.L...G..HGKFSLVDLAGNERGADT..A.R....EGAEINKSLLALKECI.ALG | |
| Retrocopy | SVNAHSSRSHAVFQIILKSGGILHGKFSLVDLAGNERGADTTKASRKRQLEGAEINKSLLALKECILALG |
| Parental | QNKSHTPFRESKLTQVLRDSFIGENSRTCMIATISPGISSCEYTLNTLRYADRVKELS |
| QNK.HTPFR.SKLTQVLRDSFIG.NS.TCMIATISPG..SCE.TLNTLRYA.RVK.L. | |
| Retrocopy | QNKPHTPFRASKLTQVLRDSFIGQNSSTCMIATISPGMTSCENTLNTLRYANRVKKLN |
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 | 0 .61 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 1 .70 RPM |
| SRP007412_heart | 0 .00 RPM | 0 .24 RPM |
| SRP007412_kidney | 0 .00 RPM | 0 .80 RPM |
| SRP007412_liver | 0 .00 RPM | 1 .25 RPM |
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_88 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_88 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_pabe_88 has 2 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_69 |
| Equus caballus | retro_ecab_32 |
Parental genes homology:
Parental genes homology involve 7 parental genes, and 8 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Mus musculus | ENSMUSG00000028678 | 1 retrocopy | |
| Otolemur garnettii | ENSOGAG00000006916 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000001427 | 1 retrocopy |
retro_pabe_88 ,
|
| Pteropus vampyrus | ENSPVAG00000009856 | 1 retrocopy | |
| Sus scrofa | ENSSSCG00000003931 | 1 retrocopy | |
| Tursiops truncatus | ENSTTRG00000000748 | 1 retrocopy | |
| Drosophila melanogaster | FBgn0030268 | 2 retrocopies |