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 symbol: HMGCS1
• Ensembl ID: ENSPPYG00000015439
• Aliases: None
• Description: Hydroxymethylglutaryl-CoA synthase, cytoplasmic [Source:UniProtKB/Swiss-Prot;Acc:Q5R7Z9]

Sequence

>retro_pabe_361
AAGTTGGAAAAGTATGTTGATATAGATGCTGGAAAGTATACCACTGGCTTGGGCTAGGCCAAGATAGGCTCCTGCACACA
TAGAGAAAAGATCAACTCTCTTTGCATGCCTGTGGTTCAGAATCCTATGGAGAGAAAAAACCTTTCCTATGATTGCACTG
GGTGACTAGAAGTTGGAACAGAGACAATCACTGACAAATCAAAGTCAGTAAAGACTAATTTGATGCAGCTGTTTGAGGAG
TCTGGGGATATAGATATAGAAGGAACTGACACAACTCATGCACGCCATGGAGCCCCAGCTGCTGTCTTCAGTGCCGTTAA
ATGGATTGAGTCCAGCTCCTGGGATGGACAGTTTGCCCTGGAGCTTGTAGGAGATATTGCTGTATATCTCACAGGAAATA
TTAGACTGACAGGTGGAGTCGGAGCAGTAGCTCTGCTAATTGAGCCAAAGGCAACTTTAATTTTTGAATGAGGGCTTCAT
GGGACACATATGCAACATGCCTATGACTTTTATGAGCCTGATATGCTCTCTGAATGTCCTATAGTAGATGGAAAACCCTC
CACACAGTGCTGCTTCAGTGCGTTACACCACTGCTATTCTGTTGACTGCAAAAAGATCCGTGCCCAGTGGCAGAAAGAGG
GAAATGATAAAGATTTTACCTTGAATAATTTTGGCGTCTTGATCCTTCACTCACCATATTGTAAACTGGTGAGTTTATCT
CTAGCTCGGATGTTGCGGAATAACTTCCTTAATGATCAGAACAGAGATAAAAATAGTGTTTAGAATGTCCTGGAAGCCTT
TGGGAATGTTAAATTAGAAGACATCTATTTTGATACAGATGTGGAGATGGCATTTATGAAGGATAGTTCTGAACTCTTCC
ATCAGAAAACAAAGGCATCTTTGCTGTATCCATTGAAAATGGAAATACATGCACATTGTCAGTATATGGCTCCCTGCAAC
TGTCCCAGCACAGTACTCACCTCAGCAACGATCAGGGAAGAGACTGGAGTGTTCTCGTATGGTTCTGGTTCAGCCGCCAC
CCTGTACTCTCTTAAAGTTACACAAGATGCCACAACAGTTTCTGCTATTGATAAAGTAACAGCAAGCTTATGGGATCTTA
AATCAAGGTGTAGCTCAAGAACTTGTGTGGTACCAGATGTCTTTGTTGAAAACACGAAGCTCAGAGAGGACACCCATCAC
TTGGTCAACTCTGTTCCCCAGGGCCCAAGAGATTCACTCTTTGAAGAAACATGGTACTTAGCTAGGGTGCGTGAAAAGCA
CAGAAGAACTTACGCTCCGTGTCCTTCTCCAAATGATGACACTTGGGATGAAGGAGTCAGACTTGTGCATTCAAACACAG
TAACTGATCATATTCGAAGCCCTGCTAAGACAGTGCCAAGACTCCCTGCCACAGCAGCAGAAACAGGAGCAGCTGTCATT
AGTAACGGGGAACAT

Alignment

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

Expression

RNA-Seq

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

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_361 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_361 was not experimentally validated.

Homology

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	retro_cjac_1754,
Echinops telfairi	ENSETEG00000003583	1 retrocopy	retro_etel_526,
Homo sapiens	ENSG00000112972	1 retrocopy	retro_hsap_328,
Pongo abelii	ENSPPYG00000015439	1 retrocopy	retro_pabe_361 ,
Pan troglodytes	ENSPTRG00000016845	1 retrocopy	retro_ptro_265,