RetrogeneDB ID: | retro_ptro_265 | ||
Retrocopy location | Organism: | Chimpanzee (Pan troglodytes) | |
| Coordinates: | 1:219288966..219290420(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | HMGCS1 | ||
| Ensembl ID: | ENSPTRG00000016845 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_ptro_265
TCAAAGTTGGAAAAGTATGTTGATATAGATGCTGGAAAGTATACCATTGGCTTGGGCCAGGCCAAGATGGGCTCCTGCAC
ACATGGAGAAGAGATCAACTCTCTTTGCATGCCTGTGGTTCAGAATCTTATGGAGAGAAAAAATCTTTCCTACGATTGCA
CTGGGCGACTGGAAGTTGGAACAGAGACAATCAAGGACAAATCAAAGTCAGTGAAGACTAATTTGATGCAGCTGTTTGAG
GAGTCTGGGAATATAGATATAGAAGGAACCGACACAACTCATGCATGCTGTGGAGGCCCAGCTGCTGTCTTCAGTGCTGT
TAATTGGATTGAGTCCAGCTCCTGGGATGGACAGTTTGCCCTGGAGCTTGTAGGAGATATTGCTGTATATTCCATAGGAA
AAGTTAGACTGACAGGTGGAGTCGGAGCAGTAGCTCTGCTAATTGAGCCAAATGCAACCTTAATTTTTGAACGAGGGCTT
CGTGGGACACATATGCAACACGCCTATGACTTTTATGAGCCTGATATGCCCTCTGAATGTCCTATAGTAGATGGAAAACC
CTCCACACAGTGCTGCTTCAGTGCATTAGATCACTGCTATTCTGTCGACTGCAAAACGATCCATGCCCAGTGGCAGAAAG
ACGGAAATGATAAAGATTTTACCTTGAATAATTTTGGCTTCTTGATACTTCACTCACCATATTGTAAACTGGTGAGTTTA
TCTCTAGCTCGGATGTTGCGGAATGACTTCCTTAATGATCAGAACAGAGATAAAAATAGTGTTTAGAATGTCCTGGAAGC
CTTTGGGAATGTTAAATTAGAAGACATCTATTTTGATACAGATGTGGAGATGGCATTTATGAAGGATAGTTCCGAACTCT
CCCATCAGAAAACAAAGGCATCTTTGCTGTATCCAGTGAAAATGGAAATACGTACACATCGTCAGTATATGGTTCCCCAC
AACTGTCCCAGCACAGTACTCACCTCAGCAATGATCAGGGAAGAGACTGGAGTGTTCTCATACGGTTCTGGTTCAGCCGG
CACCCTGTACTCTCTTAAAGTTACACAAGATGCCACACCAGGGTCTGCTGTTGATAAAATAACAGCAAGCTATGGGATCT
TAAATCAAAGTGTAGCTCAAGAACTTGTGTGGTACCAGATGTCTTTGTTGAAAACATGAAGCTCAGAGAGGACACCCATC
ACTTGGTCAACTCTGTTCCCCGGGGCCCAAGAGATTCACTCTTTGAAGAAACATGGTACTTAGCTAGGGTGGGTGAAAAG
CACAGAAGTTACACTCCGTGTCCTTCTCCAAATGATGACACTTGGGATGAAGGAGTCAGACTTGTGCATTCAAACACAGT
AACTGATCATATTCCAAGCCCTGCTAAGACAGTGCCAAGACTCCCTGCCACAGCAGCAGAAACGGGAGCAGCTGTCATTA
GTAATGGGGAACAT
ORF - retro_ptro_265 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 78.41 % |
| Parental protein coverage: | 93.65 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 4 |
Retrocopy - Parental Gene Alignment:
| Parental | AELEKYDGVDAGKYTIGLGQAKMGFCTDREDINSLCMTVVQNLMERNNLSYDCIGRLEVGTETIIDKSKS |
| ..LEKY...DAGKYTIGLGQAKMG.CT..E.INSLCM.VVQNLMER.NLSYDC.GRLEVGTETI.DKSKS | |
| Retrocopy | SKLEKYVDIDAGKYTIGLGQAKMGSCTHGEEINSLCMPVVQNLMERKNLSYDCTGRLEVGTETIKDKSKS |
| Parental | VKTNLMQLFEESGNTDIEGIDTTNACYGGTAAVFNAVNWIESSSWDGRYALVVAGDIAVYATGNARPTGG |
| VKTNLMQLFEESGN.DIEG.DTT.AC.GG.AAVF.AVNWIESSSWDG..AL...GDIAVY..G..R.TGG | |
| Retrocopy | VKTNLMQLFEESGNIDIEGTDTTHACCGGPAAVFSAVNWIESSSWDGQFALELVGDIAVYSIGKVRLTGG |
| Parental | VGAVALLIGPNAPLIFERGLRGTHMQHAYDFYKPDMLSEYPIVDGKLSIQCYLSALDRCYSVYCKKIRAQ |
| VGAVALLI.PNA.LIFERGLRGTHMQHAYDFY.PDM.SE.PIVDGK.S.QC..SALD.CYSV.CK.I.AQ | |
| Retrocopy | VGAVALLIEPNATLIFERGLRGTHMQHAYDFYEPDMPSECPIVDGKPSTQCCFSALDHCYSVDCKTIHAQ |
| Parental | WQKEGNDKDFTLNDFGFMIFHSPYCKLVQKSLARMLLNDFLNDQNRDKNSIYSGLEAFGDVKLEDTYFDR |
| WQK.GNDKDFTLN.FGF.I.HSPYCKLV..SLARML.NDFLNDQNRDKNS....LEAFG.VKLED.YFD. | |
| Retrocopy | WQKDGNDKDFTLNNFGFLILHSPYCKLVSLSLARMLRNDFLNDQNRDKNSV*NVLEAFGNVKLEDIYFDT |
| Parental | DVEKAFMKASSELFSQKTKASLL-VSNQNGNMYTSSVYGS-LASVLAQYSPQQLAGKRI-GVFSYGSGLA |
| DVE.AFMK.SSEL..QKTKASLL.VS..NGN.YTSSVYGS....V.AQYSPQQ..GKR..GVFSYGSG.A | |
| Retrocopy | DVEMAFMKDSSELSHQKTKASLL<VSSENGNTYTSSVYGS<PTTVPAQYSPQQ*SGKRL<GVFSYGSGSA |
| Parental | ATLYSLKVTQDATPGSALDKITAS-LCDLKSRLDSRTGVAPDVFAENMKLREDTHHLVNYIPQGSIDSLF |
| .TLYSLKVTQDATPGSA.DKITAS.L.DLKS...SRT.V.PDVF.ENMKLREDTHHLVN..P.G..DSLF | |
| Retrocopy | GTLYSLKVTQDATPGSAVDKITAS<LWDLKSKCSSRTCVVPDVFVENMKLREDTHHLVNSVPRGPRDSLF |
| Parental | EGTWYLVRVDEKHRRTYARRPTPNDDTLDEGVGLVHSNIATEHIPSPAKKVPRLPATAAEPEAAVISNGE |
| E.TWYL.RV.EKH.R.Y...P.PNDDT.DEGV.LVHSN..T.HIPSPAK.VPRLPATAAE..AAVISNGE | |
| Retrocopy | EETWYLARVGEKH-RSYTPCPSPNDDTWDEGVRLVHSNTVTDHIPSPAKTVPRLPATAAETGAAVISNGE |
| Parental | H |
| H | |
| Retrocopy | H |
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 | 92 .16 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 53 .24 RPM |
| SRP007412_heart | 0 .00 RPM | 23 .00 RPM |
| SRP007412_kidney | 0 .03 RPM | 46 .81 RPM |
| SRP007412_liver | 0 .00 RPM | 88 .12 RPM |
| SRP007412_testis | 0 .00 RPM | 68 .39 RPM |
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_265 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_265 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ptro_265 has 2 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_328 |
| Pongo abelii | retro_pabe_361 |
Parental genes homology:
Parental genes homology involve 5 parental genes, and 5 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000001303 | 1 retrocopy | |
| Echinops telfairi | ENSETEG00000003583 | 1 retrocopy | |
| Homo sapiens | ENSG00000112972 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000015439 | 1 retrocopy | |
| Pan troglodytes | ENSPTRG00000016845 | 1 retrocopy |
retro_ptro_265 ,
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