RetrogeneDB ID: retro_nleu_1504

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397296.1:8111574..8112180(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NIF3L1
• Ensembl ID: ENSNLEG00000006935
• Aliases: None
• Description: None

Sequence

>retro_nleu_1504
ACCGAAGACCTGGACAAAGTCATGTCTGCAGTGAAAAAAAGTTGTGAATGTTTCTGTCACTTCTTTGTCTGCTGGGATTG
ATGACGAAAAACAAACATGGCTCAGTGTCAATTATAGTCAGAAGACTTTGATGCAGGTAGTGGCTTTTCTCTCCCAGAAC
ATAAAATCACATCAGAAGACTGAAATTATGTACTGGAGAAGCCTTTGCTTCTACATACTGGAATGGGATGGTAATGCATA
CTAGATGAATCTATCTCCCTGACAACCATGACTGAGCAAATCACAAGCCGCTTAAAACTATCACATATGTGCTTAGTTCT
TAGAGTAGGGAGGACCGTAGAGTTCTAAAGTCAAAGTCGTGGCCCTGTGTGCTGGTTCTGGGAGCAGCGTTCTGCAGAGT
ATAGAAGTTGACCTTTACCTCCCAGGTGGGATGTCTCATCATAATATTCTGAATGCTGCTTCCTAAGGAATAAATGTCAT
CCTTTATGAACTCAGCAACACTGAATATGACTTTCTTTCTGACATTTGAGATATACTGGGTGCTTATTTGAAGAGTACGA
TTAATATTATCCTTCAGAGACAAGCAAGGACCCTCTTTATGTAGTA

Alignment

ORF - retro_nleu_1504 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.48 %
• Parental protein coverage: 53.58 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  TQDLDKVMSAVKG-IDNVSVTSFSARIGNEEQTRISLNCTQKALIQVVDFLSQNKQLYQKTEILS-LEKP
          T.DLDKVMSAVK....NVSVTS.SA.I..E.QT..S.N..QK.L.QVV.FLSQN....QKTEI...LEKP
Retrocopy TEDLDKVMSAVKK>VVNVSVTSLSAGIDDEKQTWLSVNYSQKTLMQVVAFLSQNIKSHQKTEIMY<LEKP

Parental  LLLHTGMGRLCTLDESVSLETMIDRIKRHLKLSHIRLALGVGRTLE-SQVKVVALCAGSGSSVLQGVEAD
          LLLHTGMG..C.LDES.SL.TM...I...LKLSH..L.L.VGRT.E.S.VKVVALCAGSGSSVLQ..E.D
Retrocopy LLLHTGMGW*CILDESISLTTMTEQITSRLKLSHMCLVLRVGRTVE>SKVKVVALCAGSGSSVLQSIEVD

Parental  LYLTGEMSHHDILDAASQGINVILCEHSNTERGFLSDLRDMLGSHLENKINIIL-SETDRDPLQVV
          LYL.G.MSHH.IL.AAS.GINVIL.E.SNTE..FLSD..D.LG..L...INIIL.SET..DPL.VV
Retrocopy LYLPGGMSHHNILNAAS*GINVILYELSNTEYDFLSDI*DILGAYLKSTINIIL<SETSKDPLYVV

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_1504 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 6 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000023186	1 retrocopy	retro_fcat_589,
Macaca mulatta	ENSMMUG00000006639	1 retrocopy	retro_mmul_444,
Nomascus leucogenys	ENSNLEG00000006935	1 retrocopy	retro_nleu_1504 ,
Oryctolagus cuniculus	ENSOCUG00000010667	16 retrocopies	retro_ocun_1105, retro_ocun_1534, retro_ocun_1539, retro_ocun_1691, retro_ocun_1692, retro_ocun_1710, retro_ocun_1729, retro_ocun_1749, retro_ocun_1789, retro_ocun_1828, retro_ocun_1837, retro_ocun_1841, retro_ocun_1846, retro_ocun_1847, retro_ocun_1854, retro_ocun_929,
Pongo abelii	ENSPPYG00000013063	1 retrocopy	retro_pabe_244,
Tupaia belangeri	ENSTBEG00000000704	1 retrocopy	retro_tbel_3512,