RetrogeneDB ID: retro_nleu_2030

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397323.1:8870357..8870892(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GPN3
• Ensembl ID: ENSNLEG00000002831
• Aliases: None
• Description: None

Sequence

>retro_nleu_2030
TTTGATTGTCCAGCCTGGACTGAGTTGTACATTCACCTGACTGTGATGAAGCAGCTGGTCCTGCAGCTCAAGCAGTGGGG
TTTCTGAGTCTATGGAGTTTTTCTTGTTGAGTCTCAGTTCATGGTGGAGTCATTCAAGTGTATTTCTGGCATCTTGGCAG
TCCTGAGTGCCATGCTCTCTCTAGAAATTCCATAAGTTAACATCGTGATCAAAATGTAGCTGCAGAGTAAAAAAGCTAAA
AAGGAAACTGAAAGTTTCTAGATCCAGACATGGATTCCTTATTTGATGATTCTACAAGTGGCTTAAGAAGCAAAAAATTC
AAAAAAGTAACTAGAGCTGTATGTGGACTGACGACTGTGGCATAGTTCTCTTCTTACATCATGATCAGTCAGATGAAGAA
AGTATGAACATTGTATTATAGCATATTGATTTTGCCATTCAATGTGGAGAAGATTCAAAATTTAAATAACCAAAGGAACA
TGAAAATGAGCCTTCTTCTATGTTTGATGAATATTTTCAAGAACACCAGGATGAA

Alignment

ORF - retro_nleu_2030 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.33 %
• Parental protein coverage: 63.38 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FDCPGQIELYTHLPVMKQLVQQLEQWEFRVCGVFLVDSQFMVESFKFISGILAALSAMISLEIPQVNIMT
          FDCP...ELY.HL.VMKQLV.QL.QW.F.V.GVFLV.SQFMVESFK.ISGILA.LSAM.SLEIP.VNI..
Retrocopy FDCPAWTELYIHLTVMKQLVLQLKQWGF*VYGVFLVESQFMVESFKCISGILAVLSAMLSLEIP*VNIVI

Parental  KMDLLSKKAKKEIE-KFLDPDMYSLLEDSTSDL-RSKKFKKLTKAICGLIDDYSMVRFLPYDQSDEESMN
          KM.L.SKKAKKE.E.KFLDPDM.SL..DSTS.L....K..K.....C...DD...V.FL..DQSDEESMN
Retrocopy KM*LQSKKAKKETE<KFLDPDMDSLFDDSTSGL<KKQKIQKSN*S-CMWTDDCGIVLFLHHDQSDEESMN

Parental  IVLQHIDFAIQYGEDLEFKEPKEREDESSSMFDEYFQECQDE
          IVL.HIDFAIQ.GED..FK.PKE.E.E.SSMFDEYFQE.QDE
Retrocopy IVL*HIDFAIQCGEDSKFK*PKEHENEPSSMFDEYFQEHQDE

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_2030 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009339	1 retrocopy	retro_cjac_2969,
Dasypus novemcinctus	ENSDNOG00000016646	1 retrocopy	retro_dnov_2095,
Homo sapiens	ENSG00000111231	1 retrocopy	retro_hsap_652,
Gorilla gorilla	ENSGGOG00000001697	1 retrocopy	retro_ggor_570,
Myotis lucifugus	ENSMLUG00000015510	1 retrocopy	retro_mluc_408,
Macaca mulatta	ENSMMUG00000006494	1 retrocopy	retro_mmul_2435,
Nomascus leucogenys	ENSNLEG00000002831	1 retrocopy	retro_nleu_2030 ,