RetrogeneDB ID: retro_nleu_1430

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397292.1:23920031..23921141(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PANK3
• Ensembl ID: ENSNLEG00000004896
• Aliases: None
• Description: None

Sequence

>retro_nleu_1430
ATGACGATCAAAGATGCCAAGAAACCCCCTTTCCCACGGTTTGGCACGGACACTGGGGGAACTCTAGCAAAGCTCTCGTA
CTTTGAACCTATTGATATCACAGCAGAGGAAGAACAAGAAGAAGTTGAGAGTTTAAAAAGTCTTCGGAAATACTTGACTT
CTGACGTGGCATGTGGATCCACCGGCTTTCGGGATGAACACCTTGAACTGAAAGATTTCACACTTTTTGGCCGAAGAGGG
AGCTTGCACTTTATCAGGTTTCCAACCCAGGACCTGCCTACTTTTATCCAGATGGGAAGAGATAAAAACTTCTCAACATT
GCAAACGGTGCTGTGTGCTACAGGAGGTGGTGCTTACAAGTTTGAAAAACATTTTCGCACAATCGGAAACCTCCACCTGC
ACAAACTGGATGAATTGACCCCCTTGTAAAGGGCTTGCTGTGTATAGACTCTGTCAGTTTCAGTGGACCAGCCGAGTGCT
ATTATTTTGCTAACGCCTCAGAACCTGAGCGATGCCAAAAGACGCCTTTTAACCTGGGTGACCCCTCCCCACTGCTCGTA
GTGAACATTGGCTCAGGAGTCAGGATTTTAGCAGGTCCATTCCAAAGACAGCTATAAACGAGCGCCTGGGACAAGCCTTG
GAGGGGGTACCTTTCTGGGTTTATGCAGTTTATCGACTGGCTGTGAAAGCTTTGAAGAGGCTCTTGAAATGGCATCCAAA
GGTGACAGCACACAAGCTGACAAGCTGATCCGTGATATTGATGGAGGAGATCATGAAAGATTTGGTCTGCCAGGTTAGGC
TGTAGCATCTAGTTTTGGGAATATGATTTATAAGGAGAAGCAAGAATCTGTTAGTAAAGAAGATCTGGCAGGAGCTACTT
TAGTTACTATCACCAGTAACATTGGTTCTGTGGCACGAATGTGTGCTGTTAATGAGAAAATAAACAGAGTTGTCTTTGTT
GGAAGCTTTTTACATGTCAATACCCTCTCAATGAAACTTTTGGCATATGCACTGGATTACTGGTCAAAAGGTCAACTAAA
AGCCTTGTTTCTGGAACATGAGGGATACTTTGGAGCAGTTGGTGCACTTCTTGGGCTGCCAAATGTCAGC

Alignment

ORF - retro_nleu_1430 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.78 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MKIKDAKKPSFPWFGMDIGGTLVKLSYFEPIDITAEEEQEEVESLKSIRKYLTSNVAYGSTGIRDVHLEL
          M.IKDAKKP.FP.FG.D.GGTL.KLSYFEPIDITAEEEQEEVESLKS.RKYLTS.VA.GSTG.RD.HLEL
Retrocopy MTIKDAKKPPFPRFGTDTGGTLAKLSYFEPIDITAEEEQEEVESLKSLRKYLTSDVACGSTGFRDEHLEL

Parental  KDLTLFGRRGNLHFIRFPTQDLPTFIQMGRDKNFSTLQTVLCATGGGAYKFEKDFRTIGNLHLHKLDEL-
          KD.TLFGRRG.LHFIRFPTQDLPTFIQMGRDKNFSTLQTVLCATGGGAYKFEK.FRTIGNLHLHKLDEL.
Retrocopy KDFTLFGRRGSLHFIRFPTQDLPTFIQMGRDKNFSTLQTVLCATGGGAYKFEKHFRTIGNLHLHKLDEL<

Parental  DCLVKGLLYIDSVSFNGQAECYYFANASEPERCQKMPFNLDDPYPLLVVNIGSGVSILA-VHSKDNYKRV
          D.LVKGLL.IDSVSF.G.AECYYFANASEPERCQK.PFNL.DP.PLLVVNIGSGV.ILA.VHSKD.YKR.
Retrocopy DPLVKGLLCIDSVSFSGPAECYYFANASEPERCQKTPFNLGDPSPLLVVNIGSGVRILA>VHSKDSYKRA

Parental  TGTSLGGGTFLGLCSLLTGCESFEEALEMASKGDSTQADKLVRDIYGGDYERFGLPGWAVASSFGNMIYK
          .GTSLGGGTFLGLCSL.TGCESFEEALEMASKGDSTQADKL.RDI.GGD.ERFGLPG.AVASSFGNMIYK
Retrocopy PGTSLGGGTFLGLCSLSTGCESFEEALEMASKGDSTQADKLIRDIDGGDHERFGLPG*AVASSFGNMIYK

Parental  EKRESVSKEDLARATLVTITNNIGSVARMCAVNEKINRVVFVGNFLRVNTLSMKLLAYALDYWSKGQLKA
          EK.ESVSKEDLA.ATLVTIT.NIGSVARMCAVNEKINRVVFVG.FL.VNTLSMKLLAYALDYWSKGQLKA
Retrocopy EKQESVSKEDLAGATLVTITSNIGSVARMCAVNEKINRVVFVGSFLHVNTLSMKLLAYALDYWSKGQLKA

Parental  LFLEHEGYFGAVGALLGLPNFS
          LFLEHEGYFGAVGALLGLPN.S
Retrocopy LFLEHEGYFGAVGALLGLPNVS

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_1430 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 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011633	4 retrocopies	retro_chof_1188, retro_chof_1391, retro_chof_1837, retro_chof_830,
Callithrix jacchus	ENSCJAG00000015550	1 retrocopy	retro_cjac_2037,
Homo sapiens	ENSG00000120137	1 retrocopy	retro_hsap_779,
Gorilla gorilla	ENSGGOG00000004947	1 retrocopy	retro_ggor_646,
Nomascus leucogenys	ENSNLEG00000004896	5 retrocopies	retro_nleu_1430 , retro_nleu_144, retro_nleu_2975, retro_nleu_3058, retro_nleu_3099,
Pongo abelii	ENSPPYG00000016024	1 retrocopy	retro_pabe_2848,
Pan troglodytes	ENSPTRG00000017509	1 retrocopy	retro_ptro_608,
Tursiops truncatus	ENSTTRG00000016157	3 retrocopies	retro_ttru_1947, retro_ttru_29, retro_ttru_994,