RetrogeneDB ID: retro_nleu_1460

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397294.1:15259422..15260413(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP6V1B2
• Ensembl ID: ENSNLEG00000000794
• Aliases: None
• Description: None

Sequence

>retro_nleu_1460
CTAGATGGCACAAAGAGACATGGGCAAGTTCTAGAAGTTGGTGGCTCCAAGGCAGTGGTTCAGGTATTCCAAGGGACTGG
GGATATTTTCCAAACATCAGTGTCTGAGGATATGCTTGGTTGGGTATTCACTGAATCGGGAAAACCCACTGACAAAGGTC
CTCTTGTACTGGCTGAAGATTTCTTTGATATCATGGGATGGCCAACCAATCCTCAATGTCAAATCTACCCAGAGGAGATG
ATTCGGACCAGCATTTCAGCCATAGTTGCTATGAACAGTATTGCCGGGGCAGAAAATTTTTATCTTCTCTGCTGCTGGGT
TACTACACAAAGATTGCAGCTCAAATCTGCCACCAGACTGGTTTGCTAAATAAATCCAAAGATGTAGACTACACTGAGGA
AAATTTTTCAATTGTATTTGCTGCTAGGGATGTAAACAAGGAAGCTGCCTGGTTCTTCAAATCTGGTGTTGAAGAAAATG
GCTCAATGGACAACATCTGCCTGTTTTCGAACTTGGCTAATGACCCAACTATTGGGTGGATTATCATCCCTCACCCGGTT
CTAACCACAGCCGAATTTCTGGCATACCAATGTGAGAAACATGTATTGGTTATCTTAACAGACATGAGTTCATCTACTGA
AGCACTTCAAGAGGTTTCTACAGCCAGAGAAGAGGTTCCTGGTTGATGAGGCTTCCCAGGTTACACTTATACAGACTTAG
CCACTATATATGAACATACAGGTCGAGGAGAAGGTAGAAATGGCTCAATTACTCAGATTCTTACTCTTACCATGCCTACC
AACGATATCATTCACCCATCTCTGACCTGACTGGGACAGATCTATGTGGACAGACAGAGAGACACAAGAGAGAGATTTAT
CCACCTATCAATGTGCTGCCTGAACTATCACTGTTCATGAAGTCTGCTATTGGAGAAGGGATGGCCAGGAAGAATCATGC
AGATATATGTAACTAGCTGTATGCAAGCTAT

Alignment

ORF - retro_nleu_1460 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.35 %
• Parental protein coverage: 66.14 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VSGSKAVVQVFEGTSGIDAKKTSCEFTGDILRTPVSEDMLGRVFNGSGKPIDRGPVVLAEDFLDIMGQPI
          ..G.K...QV.E...G..A.......TGDI..T.VSEDMLG.VF..SGKP.D.GP.VLAEDF.DIMG.P.
Retrocopy LDGTKRHGQVLE-VGGSKAVVQVFQGTGDIFQTSVSEDMLGWVFTESGKPTDKGPLVLAEDFFDIMGWPT

Parental  NPQCRIYPEEMIQTGISAIDGMNSIA-RGQKIPIFSAAGLPHNEIAAQICRQAGLVKKSKDVVDYSEENF
          NPQC.IYPEEMI.T.ISAI..MNSIA.RG.K.......G.....IAAQIC.Q.GL..KSKDV.DY.EENF
Retrocopy NPQCQIYPEEMIRTSISAIVAMNSIA<RGRKFLSSLLLGY-YTKIAAQICHQTGLLNKSKDV-DYTEENF

Parental  AIVFAAMGVNMETARFFKSDFEENGSMDNVCLFLNLANDPTIERIITPRLALTTAEFLAYQCEKHVLVIL
          .IVFAA..VN.E.A.FFKS..EENGSMDN.CLF.NLANDPTI..II.P...LTTAEFLAYQCEKHVLVIL
Retrocopy SIVFAARDVNKEAAWFFKSGVEENGSMDNICLFSNLANDPTIGWIIIPHPVLTTAEFLAYQCEKHVLVIL

Parental  TDMSSYAEALREVSAAREEVPGRRGFPGYMYTDLATIYERAGRVEGRNGSITQIPILTMPNDDITH-PIP
          TDMSS..EAL.EVS.AREEVPG..GFPGY.YTDLATIYE..GR.EGRNGSITQI..LTMP..DI.H.PI.
Retrocopy TDMSSSTEALQEVSTAREEVPG**GFPGYTYTDLATIYEHTGRGEGRNGSITQILTLTMPTNDIIH<PIS

Parental  DLTGYITEGQIYVDRQLHNRQIYPPINVLPSLSRLMKSAIGEGMTRKDHADVSNQLYACY
          DLTG....GQ.......H.R.IYPPINVLP.LS..MKSAIGEGM.RK.HAD..N.LYA.Y
Retrocopy DLTGTDLCGQ----TERHKREIYPPINVLPELSLFMKSAIGEGMARKNHADICN*LYASY

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_1460 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003668	1 retrocopy	retro_chof_2287,
Homo sapiens	ENSG00000147416	1 retrocopy	retro_hsap_4308,
Gorilla gorilla	ENSGGOG00000003888	1 retrocopy	retro_ggor_2879,
Microcebus murinus	ENSMICG00000001791	1 retrocopy	retro_mmur_854,
Nomascus leucogenys	ENSNLEG00000000794	1 retrocopy	retro_nleu_1460 ,
Pan troglodytes	ENSPTRG00000020040	1 retrocopy	retro_ptro_2917,
Tarsius syrichta	ENSTSYG00000010477	1 retrocopy	retro_tsyr_2096,
Tursiops truncatus	ENSTTRG00000013650	1 retrocopy	retro_ttru_1845,