RetrogeneDB ID: | retro_pabe_361 | ||
Retrocopy location | Organism: | Orangutan (Pongo abelii) | |
| Coordinates: | 1:9361063..9362518(-) | ||
| 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: | ENSPPYG00000015439 | ||
| Aliases: | None | ||
| Description: | Hydroxymethylglutaryl-CoA synthase, cytoplasmic [Source:UniProtKB/Swiss-Prot;Acc:Q5R7Z9] |
Retrocopy-Parental alignment summary:
>retro_pabe_361
AAGTTGGAAAAGTATGTTGATATAGATGCTGGAAAGTATACCACTGGCTTGGGCTAGGCCAAGATAGGCTCCTGCACACA
TAGAGAAAAGATCAACTCTCTTTGCATGCCTGTGGTTCAGAATCCTATGGAGAGAAAAAACCTTTCCTATGATTGCACTG
GGTGACTAGAAGTTGGAACAGAGACAATCACTGACAAATCAAAGTCAGTAAAGACTAATTTGATGCAGCTGTTTGAGGAG
TCTGGGGATATAGATATAGAAGGAACTGACACAACTCATGCACGCCATGGAGCCCCAGCTGCTGTCTTCAGTGCCGTTAA
ATGGATTGAGTCCAGCTCCTGGGATGGACAGTTTGCCCTGGAGCTTGTAGGAGATATTGCTGTATATCTCACAGGAAATA
TTAGACTGACAGGTGGAGTCGGAGCAGTAGCTCTGCTAATTGAGCCAAAGGCAACTTTAATTTTTGAATGAGGGCTTCAT
GGGACACATATGCAACATGCCTATGACTTTTATGAGCCTGATATGCTCTCTGAATGTCCTATAGTAGATGGAAAACCCTC
CACACAGTGCTGCTTCAGTGCGTTACACCACTGCTATTCTGTTGACTGCAAAAAGATCCGTGCCCAGTGGCAGAAAGAGG
GAAATGATAAAGATTTTACCTTGAATAATTTTGGCGTCTTGATCCTTCACTCACCATATTGTAAACTGGTGAGTTTATCT
CTAGCTCGGATGTTGCGGAATAACTTCCTTAATGATCAGAACAGAGATAAAAATAGTGTTTAGAATGTCCTGGAAGCCTT
TGGGAATGTTAAATTAGAAGACATCTATTTTGATACAGATGTGGAGATGGCATTTATGAAGGATAGTTCTGAACTCTTCC
ATCAGAAAACAAAGGCATCTTTGCTGTATCCATTGAAAATGGAAATACATGCACATTGTCAGTATATGGCTCCCTGCAAC
TGTCCCAGCACAGTACTCACCTCAGCAACGATCAGGGAAGAGACTGGAGTGTTCTCGTATGGTTCTGGTTCAGCCGCCAC
CCTGTACTCTCTTAAAGTTACACAAGATGCCACAACAGTTTCTGCTATTGATAAAGTAACAGCAAGCTTATGGGATCTTA
AATCAAGGTGTAGCTCAAGAACTTGTGTGGTACCAGATGTCTTTGTTGAAAACACGAAGCTCAGAGAGGACACCCATCAC
TTGGTCAACTCTGTTCCCCAGGGCCCAAGAGATTCACTCTTTGAAGAAACATGGTACTTAGCTAGGGTGCGTGAAAAGCA
CAGAAGAACTTACGCTCCGTGTCCTTCTCCAAATGATGACACTTGGGATGAAGGAGTCAGACTTGTGCATTCAAACACAG
TAACTGATCATATTCGAAGCCCTGCTAAGACAGTGCCAAGACTCCCTGCCACAGCAGCAGAAACAGGAGCAGCTGTCATT
AGTAACGGGGAACAT
ORF - retro_pabe_361 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 77.3 % |
| Parental protein coverage: | 93.46 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | ELEKYDGVAAGKYTIGLGQAKMGFCTDREDINSLCMTVVQNLMERNNLSYDCIGRLEVGTETIIDKSKSV |
| .LEKY....AGKYT.GLG.AK.G.CT.RE.INSLCM.VVQN.MER.NLSYDC.G.LEVGTETI.DKSKSV | |
| Retrocopy | KLEKYVDIDAGKYTTGLG*AKIGSCTHREKINSLCMPVVQNPMERKNLSYDCTG*LEVGTETITDKSKSV |
| Parental | KTNLMQLFEESGNTDIEGIDTTNACYGGTAAVFNAVNWIESSSWDGRYALVVAGDIAVYATGNARPTGGV |
| KTNLMQLFEESG..DIEG.DTT.A..G..AAVF.AV.WIESSSWDG..AL...GDIAVY.TGN.R.TGGV | |
| Retrocopy | KTNLMQLFEESGDIDIEGTDTTHARHGAPAAVFSAVKWIESSSWDGQFALELVGDIAVYLTGNIRLTGGV |
| Parental | GAVALLIGPNAPLIFERGLRGTHMQHAYDFYKPDMLSEYPIVDGKLSIQCYLSALDRCYSVYCKKIRAQW |
| GAVALLI.P.A.LIFE.GL.GTHMQHAYDFY.PDMLSE.PIVDGK.S.QC..SAL..CYSV.CKKIRAQW | |
| Retrocopy | GAVALLIEPKATLIFE*GLHGTHMQHAYDFYEPDMLSECPIVDGKPSTQCCFSALHHCYSVDCKKIRAQW |
| Parental | QKEGNDKDFTLNDFGFMIFHSPYCKLVQKSLARMLLNDFLNDQNRDKNSIYSGLEAFGDVKLEDTYFDRD |
| QKEGNDKDFTLN.FG..I.HSPYCKLV..SLARML.N.FLNDQNRDKNS....LEAFG.VKLED.YFD.D | |
| Retrocopy | QKEGNDKDFTLNNFGVLILHSPYCKLVSLSLARMLRNNFLNDQNRDKNSV*NVLEAFGNVKLEDIYFDTD |
| Parental | VEKAFMKASSELFSQKTKASLL-VSNQNGNMYTSSVYGSL-ASVLAQYSPQQLAGKRI-GVFSYGSGLAA |
| VE.AFMK.SSELF.QKTKASLL.VS..NGN..T.SVYGSL.A.V.AQYSPQQ..GKR..GVFSYGSG.AA | |
| Retrocopy | VEMAFMKDSSELFHQKTKASLL<VSIENGNTCTLSVYGSL<ATVPAQYSPQQRSGKRL<GVFSYGSGSAA |
| Parental | TLYSLKVTQDATPGSALDKITASLCDLKSRLDSRTGVAPDVFAENMKLREDTHHLVNYIPQGSIDSLFEG |
| TLYSLKVTQDAT..SA.DK.TASL.DLKSR..SRT.V.PDVF.EN.KLREDTHHLVN..PQG..DSLFE. | |
| Retrocopy | TLYSLKVTQDATTVSAIDKVTASLWDLKSRCSSRTCVVPDVFVENTKLREDTHHLVNSVPQGPRDSLFEE |
| Parental | TWYLVRVDEKHRRTYARRPTPNDDTLDEGVGLVHSNIATEHIPSPAKKVPRLPATAAEPEAAVISNGEH |
| TWYL.RV.EKHRRTYA..P.PNDDT.DEGV.LVHSN..T.HI.SPAK.VPRLPATAAE..AAVISNGEH | |
| Retrocopy | TWYLARVREKHRRTYAPCPSPNDDTWDEGVRLVHSNTVTDHIRSPAKTVPRLPATAAETGAAVISNGEH |
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 | 81 .33 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 34 .41 RPM |
| SRP007412_heart | 0 .00 RPM | 12 .94 RPM |
| SRP007412_kidney | 0 .00 RPM | 30 .50 RPM |
| SRP007412_liver | 0 .00 RPM | 46 .55 RPM |
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_361 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_361 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_pabe_361 has 2 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_328 |
| Pan troglodytes | retro_ptro_265 |
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 |
retro_pabe_361 ,
|
| Pan troglodytes | ENSPTRG00000016845 | 1 retrocopy |