RetrogeneDB ID: retro_nleu_1820

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397312.1:1843233..1845015(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: OSBPL9
• Ensembl ID: ENSNLEG00000016138
• Aliases: None
• Description: Oxysterol-binding protein [Source:UniProtKB/TrEMBL;Acc:G1S285]

Sequence

>retro_nleu_1820
AGACTCAGAGGTTTGGATTCAGCATTTGTTCCTAGTGTCCAAGATTTTGATACAGAAGCTGATGCTTACCTACAAATCTT
GATTGAACAATTAAAGCTTTTTGATGACAAGCTTCAAAACTGCAAAGAAGATGAACAGAGAAAGAAAATTGAAACTCTCA
AAGAGACAACAAATAGCATGGTAGAATCAATTAAACACTGCATTGTGTTGCTGCAGATTGCCAAAAGTACTATTAATCCT
GTAGATGCAATATATCAACCTAGTCCTTTGGAACCTGTGATCAGCACAATGCCTTCCCAGACTGTGTTACCTCCAGAACC
TGTTCAGTTGCGTAAGTCAGAGCAGCGTCCATCTTCCCTACCAGTTGGACCTGTGTTGGCTACCTTGGGACATCATCAGA
CTCCTACACCAAATAGTACGGGCAGTGGCCATTCACCACCAAGTAGTAGTCTCACTTCTCCAAGCCATGTGAACTTGTCT
CCAAATACAGTCCCAGAGTTCTCTTACTCCAGCAGTGAAGAAGAATTTTATGATGCTGATGAATTCCATCAAAGTGGCTC
ATCCCCAAAGCGCTTAATAGATTCTTCTGGATCTGCCTTGGTCCTGACACACAGCAGCTTGGTAAATAGTCTGAAATGCC
CAGATATCACAGATATCACTTAATTCTTCCATGTCCAATGAAACAAGTGATGCTGACCTTCTCGATTCACATGATGACAG
AGATGATGATGTGCAGCCAGGGTCTGTGGAGGAGCACAAGAGCGTTACCATGCATCTCTTGTCACAGGTTAGACTTGGAA
TGGATCTTACTAAGGTAGTTCTTCCAACGTTTATCTTGAAAGATCTCTTTTAGAAATGTATGCAGACTTTTTTGCACATC
TGGACCTGTTTGTGAGCATTAGTGACCAGAAGGATCCCAAGGATCGAATGGTTCAGGTTGTGAAATGGTACCTCTTAGCC
TTTCATGCGGGAAGGAAAGGATCAGTTGCCAAAAAGCCATACAATCCCATTTTGGGAAAGATTTTTCAGTGTCATTGGAC
GTTACCAAATGATACTGAAGAGAACACAGAACTAGTTTCAGAAGGACCAGTTCCCTGGGTTTCCAAAAACAGTGTAACAT
TCGTGGCTAAGCAGGTTTCCCATCATCCACCCATTTCAGCCTTTTATGCTGAGTGTTTTAACAAGAAGATACAATTCAAT
GCTCATATCTGGACCAAATCAAAATTCCTTGGGATGTCAACTGGGGTGCACAACATAGGGCAGGGCTGTGTCTCATGTCT
GGACTATGATGAACATTACATTCTCACATTCCCCAATGGCTATGGAAGGTCTATCCTCACAGTGCCCTGGGTGGAATTAG
GAGGAGAATGCAATATTAATTGTTCCAAAACAGGCTATAGTGCAAATATCATCTTCCAAACTAAACCTTTCTATGGGGGC
AAGAAGCACAGAATTACTGCTGAGGTTTTTTCTCCAAATGATAGGAAGTCTTTTTGCTCAATTGAAGGGGAATGGAATGG
TGTGATGTATGCAAAATATGCAACAGGGGAAAATACAGTCTTTGTAGATACCAAGAAGTTGCCTATAAACAAGGAAAAAG
TGAAAAAGTTGGAAGATCAGAATGAGTATGAATCCCGCAGCCTTTGGAAGGATATCACTTTCAACTTAAAAAACAGAGAC
ATTGATGCAGCAGCTGAAGCAAAGCACAGGCTTGAAGAAGGACAAAGAGCACAAGCCCGAGAAAGGAAGGAGAAGGAAAT
TCAGTGGGAGAGAAGGTTATTT

Alignment

ORF - retro_nleu_1820 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93. %
• Parental protein coverage: 80.16 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KIIGLDSGFVPSVQDFDKKLTEADAYLQILIEQLKLFDDKLQNCKEDEQRKKIETLKETTNSMVESIKHC
          ...GLDS.FVPSVQDFD...TEADAYLQILIEQLKLFDDKLQNCKEDEQRKKIETLKETTNSMVESIKHC
Retrocopy RLRGLDSAFVPSVQDFD---TEADAYLQILIEQLKLFDDKLQNCKEDEQRKKIETLKETTNSMVESIKHC

Parental  IVLLQIAKSTINPVDAIYQPSPLEPVISTMPSQTVLPPEPVQLCKSEQRPSSLPVGPVLATLGHHQTPTP
          IVLLQIAKSTINPVDAIYQPSPLEPVISTMPSQTVLPPEPVQL.KSEQRPSSLPVGPVLATLGHHQTPTP
Retrocopy IVLLQIAKSTINPVDAIYQPSPLEPVISTMPSQTVLPPEPVQLRKSEQRPSSLPVGPVLATLGHHQTPTP

Parental  NSTGSGHSPPSSSLTSPSHVNLSPNTVPEFSYSSSEDEFYDADEFHQSGSSPKRLIDSSGSASVLTHSSS
          NSTGSGHSPPSSSLTSPSHVNLSPNTVPEFSYSSSE.EFYDADEFHQSGSSPKRLIDSSGSA.VLTHSS.
Retrocopy NSTGSGHSPPSSSLTSPSHVNLSPNTVPEFSYSSSEEEFYDADEFHQSGSSPKRLIDSSGSALVLTHSSL

Parental  GNSLKRPDTTE-SLNSSMSNGTSDADLFDSHDDRDDDAEAGSVEEHKSVIMHLLSQVRLGMDLTKVVLPT
          .NSLK.PD.T..SLNSSMSN.TSDADL.DSHDDRDDD...GSVEEHKSV.MHLLSQVRLGMDLTKVVLPT
Retrocopy VNSLKCPDITD>SLNSSMSNETSDADLLDSHDDRDDDVQPGSVEEHKSVTMHLLSQVRLGMDLTKVVLPT

Parental  FI-LERRSLLEMYADFFAHPDLFVSISDQKDPKDRMVQVVKWYLSAFHAGRKGSVAKKPYNPILGEIFQC
          FI.LER.SLLEMYADFFAH.DLFVSISDQKDPKDRMVQVVKWYL.AFHAGRKGSVAKKPYNPILG.IFQC
Retrocopy FI<LER-SLLEMYADFFAHLDLFVSISDQKDPKDRMVQVVKWYLLAFHAGRKGSVAKKPYNPILGKIFQC

Parental  HWTLPNDTEENTELVSEGPVPWVSKNSVTFVAEQVSHHPPISAFYAECFNKKIQFNAHIWTKSKFLGMSI
          HWTLPNDTEENTELVSEGPVPWVSKNSVTFVA.QVSHHPPISAFYAECFNKKIQFNAHIWTKSKFLGMS.
Retrocopy HWTLPNDTEENTELVSEGPVPWVSKNSVTFVAKQVSHHPPISAFYAECFNKKIQFNAHIWTKSKFLGMST

Parental  GVHNIGQGCVSCLDYDEHYILTFPNGYGRSILTVPWVELGGECNINCSKTGYSAIIIFHTKPFYGGKKHR
          GVHNIGQGCVSCLDYDEHYILTFPNGYGRSILTVPWVELGGECNINCSKTGYSA.IIF.TKPFYGGKKHR
Retrocopy GVHNIGQGCVSCLDYDEHYILTFPNGYGRSILTVPWVELGGECNINCSKTGYSANIIFQTKPFYGGKKHR

Parental  ITAEIFSPNDKKSFCSIEGEWNGVMYAKYATGENTVFVDTKKLPIIKKKVRKLEDQNEYESRSLWKDVTF
          ITAE.FSPND.KSFCSIEGEWNGVMYAKYATGENTVFVDTKKLPI.K.KV.KLEDQNEYESRSLWKD.TF
Retrocopy ITAEVFSPNDRKSFCSIEGEWNGVMYAKYATGENTVFVDTKKLPINKEKVKKLEDQNEYESRSLWKDITF

Parental  NLKIRDIDAATEAKHRLEERQRAEARERKEKEIQWETRLF
          NLK.RDIDAA.EAKHRLEE.QRA.ARERKEKEIQWE.RLF
Retrocopy NLKNRDIDAAAEAKHRLEEGQRAQARERKEKEIQWERRLF

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Nomascus leucogenys was not studied using RNA-Seq expression data.

ChIP-Seq

Nomascus leucogenys was not studied using ChIP-Seq data.

EST

Nomascus leucogenys was not studied using EST data.

TSS

Nomascus leucogenys was not studied using FANTOM5 data.

Lab

retro_nleu_1820 was not experimentally validated.

Homology

Retrocopy orthology:

Nomascus leucogenys does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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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,