RetrogeneDB ID: retro_pabe_787

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 11:86947841..86948978(-)
• 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_787
TCAGGAAATAGTGTAAACGTCCAGATACCAGGGATCACTAATCTTCCATGTCCAATGAACAAGTGATGCTGACCTTTTCG
ATTCATATGATAGTAGAGATGATGATGCGTAGGCAGGTCCGCAGAGGCGCATAAGAGCGTTATCATGCATCTCTGTCACA
GGTTAGGCTTGGGATGGATCTTACTAAGGTAGTTCTTCCAAGGTTTATTCTTGAAAGAAGATCTCTTTTAGGAATGTATG
CAGACTTTTTGCACACCGGGACCTGTTTGTGTCCATTAGTGACTGGAAGGATCACAAGGATCGAATGGTACTGGTTGTGA
AATGGTACCTCTCAGCCTTTCATGCAAGAAGGAAAGGATCAGTTGCCAAAAAGCCATACAATCCCATTTTGGGCAAGATT
TTTCAGTGTCACTGGACACTACCAAATGATACTGAAGAGAACACAAAACTACTTTCGGAAAGACCAGTTCCCTGGGTTTC
CAAAAATACTGTAACATTCGTGGCTGAGCAGGTTTCCCATCATCCACCCATTTCAGCCTTTTATGTTGAATATTTTAACA
AGAAGATACAATTCAATGCTCATGTATGGACCAAATGAAAATTCCTTGGGATGTCAATTGGTGTGCACAACATAGGGCAG
GGCTGTGTCTCATGTCTACATTATGATGAACATTACATTCTCACATTCCCCAGTGGCTATGGAAGGTCTATCCTCACATG
GTCCTGGGTGGAATTAGGTGGAGAATGTTGTATTAATTGTTCCAAACAGGCTAGAGTGCAAATATCATCTTCTATACTAA
ACCCTTCTATGCAGGCAAGAAGCACAAAATTACTGCTGAGATTTTTTTCTCCAAATAACAAGAAGTCTTTTTGCTCAACT
AAAGGGGAATAGAATGGTGTGCTGTATGCAAAATATGCAACAAGGGAAAATACATCCTTTGTAGATACCAAGAAGTTACC
TGTAATCAAGAAGAAAGTGAGGAAGCTAGAAGATCAGAACGAGTATGAATCCCGCGGCCTTTGGAAGGATGTCACTTTCA
ACTTAAAAATCAGCAACTGAAGCAAAGCACAGGCTTGAATAAAAGAGCAGAACCCCAAGAAAGGAAAGAGAAGGAAATTC
GGTGGGAGACAAGGTTA

Alignment

ORF - retro_pabe_787 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.51 %
• Parental protein coverage: 51.9 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 8

Retrocopy - Parental Gene Alignment:

Parental  SGNSL-KRPDTTESLNSSMSNG-TSDADLFDSHDDRDDDAEAG-SVEEHKSVIMHL-LSQVRLGMDLTKV
          SGNS..KRPDT.....SSMSN..TSDADLFDS.D.RDDDA.AG.S.E.HKSVIMHL.LSQVRLGMDLTKV
Retrocopy SGNSV<KRPDTRDH*-SSMSNE<TSDADLFDSYDSRDDDA*AG<SAEAHKSVIMHL<LSQVRLGMDLTKV

Parental  VLPTFILERRSLLEMYADF-FAHPDLFVSISDQKDPKDRMVQVVKWYLSAFHAGRKGSVAKKPYNPILGE
          VLP.FILERRSLL.MYADF.FAH.DLFVSISD.KD.KDRMV.VVKWYLSAFHA.RKGSVAKKPYNPILG.
Retrocopy VLPRFILERRSLLGMYADF<FAHRDLFVSISDWKDHKDRMVLVVKWYLSAFHARRKGSVAKKPYNPILGK

Parental  IFQCHWTLPNDTEENTELVSEGPVPWVSKNSVTFVAEQVSHHPPISAFYAECFNKKIQFNAHIWTKSKFL
          IFQCHWTLPNDTEENT.L.SE.PVPWVSKN.VTFVAEQVSHHPPISAFY.E.FNKKIQFNAH.WTK.KFL
Retrocopy IFQCHWTLPNDTEENTKLLSERPVPWVSKNTVTFVAEQVSHHPPISAFYVEYFNKKIQFNAHVWTK*KFL

Parental  GMSIGVHNIGQGCVSCLDYDEHYILTFPNGYGRSILTVPWVELGGECNINCSK-TGYSANIIFHTKPFYG
          GMSIGVHNIGQGCVSCL.YDEHYILTFP.GYGRSILT..WVELGGEC.INCSK.TG.SANIIF.TKPFY.
Retrocopy GMSIGVHNIGQGCVSCLHYDEHYILTFPSGYGRSILTWSWVELGGECCINCSK<TG*SANIIFYTKPFYA

Parental  GKKHRITAEI-FSPNDKKSFCSIEGEWNGVMYAKYATGENTVFVDTKKLPIIKKKVRKLEDQNEYESRSL
          GKKH.ITAEI.FSPN.KKSFCS..GE.NGV.YAKYAT.ENT.FVDTKKLP.IKKKVRKLEDQNEYESR.L
Retrocopy GKKHKITAEI>FSPNNKKSFCSTKGE*NGVLYAKYATRENTSFVDTKKLPVIKKKVRKLEDQNEYESRGL

Parental  WKDVTFNLKI-RDIDAATEAKHRLEERQRAEARERKEKEI
          WKDVTFNLKI.......T....R.E...R.E...R.E...
Retrocopy WKDVTFNLKI<QQLKQSTGLNKRAEPQERKEKEIRWETRL

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	15.65 RPM
SRP007412_cerebellum	0.00 RPM	36.24 RPM
SRP007412_heart	0.00 RPM	40.88 RPM
SRP007412_kidney	0.00 RPM	39.18 RPM
SRP007412_liver	0.00 RPM	34.40 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_787 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_787 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_787 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_737

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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,