RetrogeneDB ID: retro_pabe_689

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 11:48134289..48136176(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: OSBPL9
• Ensembl ID: ENSPPYG00000001358
• Aliases: OSBPL9, ORP-9
• Description: oxysterol-binding protein-related protein 9 [Source:RefSeq peptide;Acc:NP_001125850]

Sequence

>retro_pabe_689
TTGGATTCAGGATTTGTTCCTAGTGTCCAAGATTTTGGTAAGAAGCTTAGAGAAGCTGATGCTTACCTACAAATCTTGAT
TGAACAATTAAAGCTTTTTGATGACAAGCTTCAAAACTGCAAAGAAGATGAACAAAGAAAGAAAATTGAGACTGTCTAAG
AGACAACAAATAGCATAGTAGAATCAACTAAACACTGCATTGTGTTGCTGCAGATTACCAAAGACCAGAGTAATGCGGAG
AAGCACGCAGATGGAATGATAAGTACTATTAATCCCGTAGATGCAATATATCAACCTAGTCCTTTGGAACCTGTGATCAG
CACAATGCCTTCCCAGACTGTGTTACCTCCAGAACCTGTTCAGTTGTGTAAGTCAGAGCAGCGTCCATCTTCCCTACCAG
TTGGACCTGTGTTGGCTACCTTGGGACATTATCAGACTCCTAAACCGAATAGTACAGGCAGTGGCCATTCACTACCGAGT
AGCAGTCTCACTTCTCCAAGCCATGTGAACTTGTCTCCAAATACAGTCCCAGAGTTCTCTTACTCCAGCAGTGTAGATGA
ATTTTATGATGCTGATGAATTCCATCAAAGTGGCTCATCCCCAAAGCGCTTAATAGATTCTTCTGGATCTGCCTCAGTCC
TGACACACAGCAGCTCAGGAAATAGTCTAAAAGGACCAGATACCACAGAATCACTTAATTCTTCCATGTCCAATGGAACA
AGTGATGCTGACCTTTTCGATTCACATGATGACAGAGATGATGATGCAGAGGCAGGGTCTGTGGAGGAGCACAAGAGCGT
TATCATGCATCTCTTGTTACAGGTTAGACTTGGAATGGATCTTACCAAGGTAGTTCTTCCAACGTTTATTCTTGAAAGAA
GATCTCTTTTAGAAATGTATGCAGACTTTTTTGCACATCCGGACCTGTTTGTGAGCATTAGTGACCAGAAGGATCCCAAG
GATCGAATGGTTCAGGTTGTGAAATGGTACCTCTCAGCCTTTCATGCGGGAAGGAAAGGATCAGTTGCCAAAAAGCCATA
CAATCCCATTTTGGGTGAGATTTTTCAGTGTCATTGGACGTTACCAAATGATACTGAAGAGAACACAGAATTAGTTTCAG
AAGGACCAGTTCCCTGGGTTTCCAAAAATAGTGTAACATTTGTGGCTGAGCAGGTTTCCCATCATCTACCCATTTCAGCC
TTTTATGCTGAGTGTTTTAACAAGAAGATACAATTCAATGCTCATATCTGGACCAAATCACAATTCCTTGGGATGTCAAT
TGGGGTGCACAACATAGGGCACGGGTGTATCTCATGTCTAGACTATGATGAACATTACATTCTCACATTCCCCAATGGCT
ATGGAAGGTCTATCCTCACAGTGCCCTGGGTGGAATTAGGAGGAGAATGCAATATTAATTGTTCCAAAACAGGCTATAGT
GCAAATATCATCTTCCACACTAAACCCTTCTATGGGGGCAAGAAGCACAGAATTACTGCTGAGATTTTTTCTCCAAATGA
CAAGAAGTCTTTTTGCTCAATTGAAGGGGAATGGAATGGTGTGATGTATGCAAAATATGCAACAGGGGAAAATACAGTCT
TTGTAGATACCAAGAAGTTGCCTATAATCAAGAAGAAAGTGAGGAAGTTGGAAGATCAGAACGAGTATGAATCCCGCAGC
CTTTGGAACGATGTCACTTTCAACTTAAAAATCAGAGACATTGATGCAGCAACTGAAGCAAAGCACAGGCTTGAAGAAAG
ACAAAGAGCAGAAGCCCAAGAAAGGAAGGAGAAGGAAATTCAGTGGGAGACAAGGTTATTTCATGAAGATGGAGAATGCT
GGGTTTATGATGAACCATTACTGAAACGTCTTGGTGCTGCCAAGCAT

Alignment

ORF - retro_pabe_689 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.82 %
• Parental protein coverage: 85.46 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LDSGFVPSVQDFDKKLTEADAYLQILIEQLKLFDDKLQNCKEDEQRKKIETLKETTNSMVESIKHCIVLL
          LDSGFVPSVQDF.KKL.EADAYLQILIEQLKLFDDKLQNCKEDEQRKKIET..ETTNS.VES.KHCIVLL
Retrocopy LDSGFVPSVQDFGKKLREADAYLQILIEQLKLFDDKLQNCKEDEQRKKIETV*ETTNSIVESTKHCIVLL

Parental  QIAKDQSNAEKHADGMISTINPVDAIYQPSPLEPVISTMPSQTVLPPEPVQLCKSEQRPSSLPVGPVLAT
          QI.KDQSNAEKHADGMISTINPVDAIYQPSPLEPVISTMPSQTVLPPEPVQLCKSEQRPSSLPVGPVLAT
Retrocopy QITKDQSNAEKHADGMISTINPVDAIYQPSPLEPVISTMPSQTVLPPEPVQLCKSEQRPSSLPVGPVLAT

Parental  LGHHQTPTPNSTGSGHSPPTSSLTSPSHVNLSPNTVPEFSYSSSEDEFYDADEFHQSGSSPKRLIDSSGS
          LGH.QTP.PNSTGSGHS.P.SSLTSPSHVNLSPNTVPEFSYSSS.DEFYDADEFHQSGSSPKRLIDSSGS
Retrocopy LGHYQTPKPNSTGSGHSLPSSSLTSPSHVNLSPNTVPEFSYSSSVDEFYDADEFHQSGSSPKRLIDSSGS

Parental  ASVLTHSSSGNSLKRPDTTESLNSSMSNGTSDADLFDSHDDRDDDAEAGSVEEHKSVIMHLLSQVRLGMD
          ASVLTHSSSGNSLK.PDTTESLNSSMSNGTSDADLFDSHDDRDDDAEAGSVEEHKSVIMHLL.QVRLGMD
Retrocopy ASVLTHSSSGNSLKGPDTTESLNSSMSNGTSDADLFDSHDDRDDDAEAGSVEEHKSVIMHLLLQVRLGMD

Parental  LTKVVLPTFILERRSLLEMYADFFAHPDLFVSISDQKDPKDRMVQVVKWYLSAFHAGRKGSVAKKPYNPI
          LTKVVLPTFILERRSLLEMYADFFAHPDLFVSISDQKDPKDRMVQVVKWYLSAFHAGRKGSVAKKPYNPI
Retrocopy LTKVVLPTFILERRSLLEMYADFFAHPDLFVSISDQKDPKDRMVQVVKWYLSAFHAGRKGSVAKKPYNPI

Parental  LGEIFQCHWTLPNDTEENTELVSEGPVPWVSKNSVTFVAEQVSHHPPISAFYAECFNKKIQFNAHIWTKS
          LGEIFQCHWTLPNDTEENTELVSEGPVPWVSKNSVTFVAEQVSHH.PISAFYAECFNKKIQFNAHIWTKS
Retrocopy LGEIFQCHWTLPNDTEENTELVSEGPVPWVSKNSVTFVAEQVSHHLPISAFYAECFNKKIQFNAHIWTKS

Parental  KFLGMSIGVHNIGQGCVSCLDYDEHYILTFPNGYGRSILTVPWVELGGECNINCSKTGYSANIIFHTKPF
          .FLGMSIGVHNIG.GC.SCLDYDEHYILTFPNGYGRSILTVPWVELGGECNINCSKTGYSANIIFHTKPF
Retrocopy QFLGMSIGVHNIGHGCISCLDYDEHYILTFPNGYGRSILTVPWVELGGECNINCSKTGYSANIIFHTKPF

Parental  YGGKKHRITAEIFSPNDKKSFCSIEGEWNGVMYAKYATGENTVFVDTKKLPIIKKKVRKLEDQNEYESRS
          YGGKKHRITAEIFSPNDKKSFCSIEGEWNGVMYAKYATGENTVFVDTKKLPIIKKKVRKLEDQNEYESRS
Retrocopy YGGKKHRITAEIFSPNDKKSFCSIEGEWNGVMYAKYATGENTVFVDTKKLPIIKKKVRKLEDQNEYESRS

Parental  LWKDVTFNLKIRDIDAATEAKHRLEERQRAEARERKEKEIQWETRLFHEDGECWVYDEPLLKRLGAAKH
          LW.DVTFNLKIRDIDAATEAKHRLEERQRAEA.ERKEKEIQWETRLFHEDGECWVYDEPLLKRLGAAKH
Retrocopy LWNDVTFNLKIRDIDAATEAKHRLEERQRAEAQERKEKEIQWETRLFHEDGECWVYDEPLLKRLGAAKH

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	0.17 RPM	15.65 RPM
SRP007412_cerebellum	1.46 RPM	36.24 RPM
SRP007412_heart	0.81 RPM	40.88 RPM
SRP007412_kidney	0.63 RPM	39.18 RPM
SRP007412_liver	0.98 RPM	34.40 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_689 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_689 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_689 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000021574	1 retrocopy	retro_cjac_1235,
Felis catus	ENSFCAG00000010298	1 retrocopy	retro_fcat_1134,
Gorilla gorilla	ENSGGOG00000004787	1 retrocopy	retro_ggor_737,
Microcebus murinus	ENSMICG00000002731	1 retrocopy	retro_mmur_1035,
Myotis lucifugus	ENSMLUG00000009199	1 retrocopy	retro_mluc_2149,
Nomascus leucogenys	ENSNLEG00000016138	2 retrocopies	retro_nleu_1820, retro_nleu_279,
Oryctolagus cuniculus	ENSOCUG00000004303	1 retrocopy	retro_ocun_281,
Pongo abelii	ENSPPYG00000001358	2 retrocopies	retro_pabe_689 , retro_pabe_787,
Pan troglodytes	ENSPTRG00000000730	1 retrocopy	retro_ptro_632,
Ictidomys tridecemlineatus	ENSSTOG00000000692	1 retrocopy	retro_itri_1537,