RetrogeneDB ID: retro_nleu_279

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397262.1:23921542..23922706(-)
• 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_279
AAAACTTTAATTGTTCAATCAAGATTTGTAGGTAATCACATCAGCAGCAGCTCAGGAAATAGTCTAAAACGTCCAGATAC
CAGAGAATCACTTAATTCTTCCATGTCCAATGGAACAAGTGATGCTGACCTTTTCGATTCGTATGATAGTAGAGATGATG
ATGCTAGGCAGGGTCCACAGAGGAGCACATGGGCGTCATCATGCTTCTCTTGTCACAGGTTAGGCTTGGGATGGATCTTA
CTGAGGTAGTTCTTCCAAGGTTTATTCTTGAAAGAAGATCTCGTTTAGAAATGTATGCAGACTTTTTGCACACTGGAACC
TGTTTGTGCCCATTAGTGACTAGAAGGATCACAAGGATCGAATGGTTCTGGTTGTGAAATGGTACCTCTCAGCCTTTCAT
GCAAGAAGGAAAGGATCAGTTGCCAAAAAGCCATACAATCCCATTTTGGGCAAGATTTTTCAGTGTCACTGGACACTACC
AAATGATACTGAAGAGAACACAAAACTAGTTTCAGAAAGACCAGTTCCCTGGGTTTCCAAAAATATGTAACATTCATGGC
TGAGCAGCTTTCCCATCCACCCATTTCAGCTTTTTATGTTGAGTGTTTTAACAAGAAGATACAATTCAATACTCACGTCT
GGACCAAATCAAAATTCCCTGGGATGTCAATTGGTGTGCACAACATAGGGCAGGGCTGTGTCTCATGTCTACACTACGAT
GAACATTACATTCTCACATTCCTCAGTGGCTATAGAAAGTCTATCCTCACATTGTCCTGGGTGGAATTAGGTGGAGAATG
TTGTATTAATTTTTCCAAACAGGCTAGAGTGCAAATTTCATCTTCCATACTAAACCCTTCTATGCGGGCAAGAAGCACAA
AATTACTGCTGAGAATTTTTTTCTCCAAATGACAAGAAGTCTTTTTGCTCAACTGAAGGGGAATGGAATGGTGTGATATG
TGCAAAATATGCAATAGGGGAAAATACATCCTTTGTAGATACCAAGAAGTTGCCTGTAATCAAGAAGAAAGTGAGGAAGC
TAGAAGATCAGAGCAAGTATGAATCCCGCAGCCTTTGGAAGGATGTCACTTTCAACTTAAAAATCAGCAACTGAAGCAAA
GCACAGGCTTGAATAAAAGAGCAGAACCCCAAGAAGGGAAAGAG

Alignment

ORF - retro_nleu_279 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.82 %
• Parental protein coverage: 52.28 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  KRLIDSSGSASVLTHSSSGNSLKRPDTTESLNSSMSNGTSDADLFDSHDDRDDDAE-AGSVEEHKSVIMH
          K.LI..S........SSSGNSLKRPDT.ESLNSSMSNGTSDADLFDS.D.RDDDA..AGS.EEH..VIM.
Retrocopy KTLIVQSRFVGNHISSSSGNSLKRPDTRESLNSSMSNGTSDADLFDSYDSRDDDAR<AGSTEEHMGVIML

Parental  LLSQVRLGMDLTKVVLPTFILERRSLLEMYADF-FAHPDLFVSISDQKDPKDRMVQVVKWYLSAFHAGRK
          LLSQVRLGMDLT.VVLP.FILERRS.LEMYADF.FAH..LFV.ISD.KD.KDRMV.VVKWYLSAFHA.RK
Retrocopy LLSQVRLGMDLTEVVLPRFILERRSRLEMYADF<FAHWNLFVPISD*KDHKDRMVLVVKWYLSAFHARRK

Parental  GSVAKKPYNPILGEIFQCHWTLPNDTEENTELVSEGPVPWVSKNS-VTFVAEQVSHHPPISAFYAECFNK
          GSVAKKPYNPILG.IFQCHWTLPNDTEENT.LVSE.PVPWVSKN..VTF.AEQ.SH.PPISAFY.ECFNK
Retrocopy GSVAKKPYNPILGKIFQCHWTLPNDTEENTKLVSERPVPWVSKNM<VTFMAEQLSH-PPISAFYVECFNK

Parental  KIQFNAHIWTKSKFLGMSIGVHNIGQGCVSCLDYDEHYILTFPNGYGRSILTVPWVELGGECNINCSK-T
          KIQFN.H.WTKSKF.GMSIGVHNIGQGCVSCL.YDEHYILTF..GY..SILT..WVELGGEC.IN.SK.T
Retrocopy KIQFNTHVWTKSKFPGMSIGVHNIGQGCVSCLHYDEHYILTFLSGYRKSILTLSWVELGGECCINFSK<T

Parental  GYSAIIIFHTKPFYGGKKHRITAE-IFSPNDKKSFCSIEG-EWNGVMYAKYATGENTVFVDTKKLPIIKK
          G.SA..IFHTKPFY.GKKH.ITAE..F.......F....G.EWNGV..AKYA.GENT.FVDTKKLP.IKK
Retrocopy G*SANFIFHTKPFYAGKKHKITAENFFLQMTRSLFAQLKG<EWNGVICAKYAIGENTSFVDTKKLPVIKK

Parental  KVRKLEDQNEYESRSLWKDVTFNLKI-RDIDAATEAKHRLEERQRAE
          KVRKLEDQ..YESRSLWKDVTFNLKI.......T....R.E.....E
Retrocopy KVRKLEDQSKYESRSLWKDVTFNLKI<QQLKQSTGLNKRAEPQEGKE

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_279 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,