RetrogeneDB ID: retro_ggor_737

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 11:88390378..88391557(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: OSBPL9
• Ensembl ID: ENSGGOG00000004787
• Aliases: None
• Description: Oxysterol-binding protein [Source:UniProtKB/TrEMBL;Acc:G3QQ34]

Sequence

>retro_ggor_737
GGTTGTCATCAAAAAACTTTAACTGTTCAATCAAGATTTGTAGGTAATTACATAAGCAGCAGCTTAGGAAATAGTCTAAA
ACATCCAGATACCAGAGAATCACTTAATTCTTCCATGTCCAATGGAACAAGTGATGCTGACCTTTTTGATTCATATGACA
GTAGAGATGATGATGAGTAGGCAGGGTCCGCAGGGAGCACAAGAGCGTTATCATGCATCTCTTGTCACAGGTTAGGCTTG
GGATGGATCTTACTAAGGTAGTTCTTCCAAGGTTTATTCTTGAAAGAAGATCTCTTTTAGAAATGTATGCAGACTTTTTG
CACACTGGGACCTGTTTGTGTCCATTAGTGACTAGATGGATCACAAGGATAGAATGGTTCTGGTTGTGAAATGGTACCTC
TCAGCCTTTCATGCAAGAAGAAAAGGGTCAGTTGCCAAAAAGCCATACAATCCCATTTTGGGCAAGATTTTTCAGTGTCA
CTGGACACTACCAAATGATACTGAAGAGAACACAAAACTAGTTTCAGAAAGACCAGTTCCCTGGGTTTCCAAAAATACTG
TAACATTCATGGCTGAGCAGGTTTCCCATCATCCACCCATTTCAGCCTTTTATGTTGAGTATTTTAACAAGAAGATACAA
TTCACTGCTCATGTCTGGACCAAGTCAAAATTCCTTGGGATGTCAATTGGTGTTCACAACATAGGGCAGGGCTGTGTCTC
ATGTCTAGACTATGATGAACATTACATTCTCACATTCCCCAATGGCTATGGAAGGTCTATCCTCACATGGTCCTGGGTGA
AATTAGGTGGAGAATGTTGTATTAATTGTTCCAAACAGGCTAGAGTGCAAATATCATCTTCCATACTAAACCCTTCTATG
TGGGCAAGAAGCACAAAATTACTGCTGAGATTTTTTTCTCCAAATGACAAGAAGTCTTTTTGCTCAACTGAAGGGGAATG
GAATGGTGTGTTGTATGCAAAATATGCAACATGGGAAAATACATCCTTTGCAGATACCAAGAAGTTGCCTGTAATCAAGA
AGAAAGTGATGAAGCTAGAAGATCAGAACAAGTAAGAATCCCGCAGCCTTTGGAAGGATGTCACTTTCAACTTAAAAATC
AGCAACTGAAGCAAAGCACAGGCTTGAACAAAAGAGCAGAACCCCAAGAAAGGAAAGAG

Alignment

ORF - retro_ggor_737 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.7 %
• Parental protein coverage: 51.71 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  GSSPKRLIDSSGSASVLTHSSSGNSLKRPDTTESLNSSLSNGTSDADLFDSHDDRDDDAEAGSV-EEHKS
          G...K.L...S........SS.GNSLK.PDT.ESLNSS.SNGTSDADLFDS.D.RDDD..AGS...EHKS
Retrocopy GCHQKTLTVQSRFVGNYISSSLGNSLKHPDTRESLNSSMSNGTSDADLFDSYDSRDDDE*AGSA<REHKS

Parental  VIMHLLSQVRLGMDLTKVVLPTFILERRSLLEMYADF-FAHPDLFVSISDQKDPKDRMVQVVKWYLSAFH
          VIMHLLSQVRLGMDLTKVVLP.FILERRSLLEMYADF.FAH.DLFVSISD..D.KDRMV.VVKWYLSAFH
Retrocopy VIMHLLSQVRLGMDLTKVVLPRFILERRSLLEMYADF<FAHWDLFVSISD*MDHKDRMVLVVKWYLSAFH

Parental  AGRKGSVAKKPYNPILGEIFQCHWTLPNDTEENTELVSEGPVPWVSKNSVTFVAEQVSHHPPISAFYAEC
          A.RKGSVAKKPYNPILG.IFQCHWTLPNDTEENT.LVSE.PVPWVSKN.VTF.AEQVSHHPPISAFY.E.
Retrocopy ARRKGSVAKKPYNPILGKIFQCHWTLPNDTEENTKLVSERPVPWVSKNTVTFMAEQVSHHPPISAFYVEY

Parental  FNKKIQFNAHIWTKSKFLGMSIGVHNIGQGCVSCLDYDEHYILTFPNGYGRSILTVPWVELGGECNINCS
          FNKKIQF.AH.WTKSKFLGMSIGVHNIGQGCVSCLDYDEHYILTFPNGYGRSILT..WV.LGGEC.INCS
Retrocopy FNKKIQFTAHVWTKSKFLGMSIGVHNIGQGCVSCLDYDEHYILTFPNGYGRSILTWSWVKLGGECCINCS

Parental  K-TGYSANIIFHTKPFYGGKKHRITAEI-FSPNDKKSFCSIEGEWNGVMYAKYATGENTVFVDTKKLPII
          K.TG.SANIIFHTKPFY.GKKH.ITAEI.FSPNDKKSFCS.EGEWNGV.YAKYAT.ENT.F.DTKKLP.I
Retrocopy K<TG*SANIIFHTKPFYVGKKHKITAEI>FSPNDKKSFCSTEGEWNGVLYAKYATWENTSFADTKKLPVI

Parental  KKKVRKLEDQNEYESRSLWKDVTFNLKI-RDIDAATEAKHRLEERQRAE
          KKKV.KLEDQN..ESRSLWKDVTFNLKI.......T....R.E...R.E
Retrocopy KKKVMKLEDQNK*ESRSLWKDVTFNLKI<QQLKQSTGLNKRAEPQERKE

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	29.49 RPM
SRP007412_cerebellum	0.00 RPM	34.08 RPM
SRP007412_heart	0.03 RPM	20.20 RPM
SRP007412_kidney	0.00 RPM	67.96 RPM
SRP007412_liver	0.05 RPM	55.95 RPM
SRP007412_testis	0.10 RPM	141.41 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_737 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_737 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_787

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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,