RetrogeneDB ID: retro_nleu_3063

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397722.1:7467..8499(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNX6
• Ensembl ID: ENSNLEG00000003310
• Aliases: None
• Description: None

Sequence

>retro_nleu_3063
CTTAAAGCAATAAATGTGGATCTTCAAAGTGATCCTGCTCTACAGGTGGACATTTCTGATGCTCTTAGTGAGTGGGATAA
AGTAAAATTCACTGTTCACACACAGAGTTTATTGCCAAATTTTAAACAAAATGAGTTTTCTGTTGTTCAGCAACACAAGC
AATTTATCTGGCTTCATGATTCCTTTGTTAAAAATGAAGACTATGCAGGTTACATCATTCCACCAGCACCACCAAGACCT
GATTTTGATACTTCAAGGGAAAAAGTACAGAAGCTTGGAGAAGGAGAAGGGTCAATGACAAAGGAAGAATTCACAAAGAT
GAAACAGGAAATGGAAGCTGAATATTTCGGAATATTCAAGAAGACAGTTGCGATGCATGAAGTATTCCTATGTCATGTGA
CAGCACATCCTATTTTGAGAAAATATTTAAATTTCCATGTCTTCTTGGAATATAATCAAGATTTGAGTGTGCAAGGAAAA
ATAAGAAGAGAAACTTGAAGATTTCTTTGAAAACATGGTTAAATCGCAGATGGAGTAATTGTTTCAGGAGTAACGGATGT
AGATAATTTCTTTCAGCATGAACAAACATTTCTTTTAGAATATCATAACCGAGTTAAGGATGCATCTGCTAACTCTGATA
GAATGACAAGATCCCACAAAAGTGCTGCAGATGATTACAATAGAATTGGTTCTTCATTATATGCTTTAGGAACTCAGGAT
TCAGGTATATGCAAGTTTTTTCTCAAAGTTTCAGAAGTGTTTGATAAAACAAGAAAAATAGAAGCATGAGTGTCTGCTGA
TGAGGACCTCAAACTTTCTGACCCTTAAAAATATTACTTAAGAGAAACTCAAGCTGCTAAGGATCTCCTGTATTGAACTT
CTAGGTCACTAGTGGATTATGAAAATGCTAATGAAGCACTGGATAAAGCAAGAGCAAAAAATAAAGATGTTCTGCTGGCT
AAAACTTCCCAACAATTATGTAGTCAGAAATTTGAAAAAAAAAAAAAATCTCAGTCTGCAAAACAGTTCTTG

Alignment

ORF - retro_nleu_3063 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.82 %
• Parental protein coverage: 83.9 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LKAINVDLQSDAALQVDISDALSERDKVKFTVHTKSSLPNFKQNEFSVVRQHEEFIWLHDSFVENEDYAG
          LKAINVDLQSD.ALQVDISDALSE.DKVKFTVHT.S.LPNFKQNEFSVV.QH..FIWLHDSFV.NEDYAG
Retrocopy LKAINVDLQSDPALQVDISDALSEWDKVKFTVHTQSLLPNFKQNEFSVVQQHKQFIWLHDSFVKNEDYAG

Parental  YIIPPAPPRPDFDASREKLQKLGEGEGSMTKEEFTKMKQELEAEYLAIFKKTVAMHEVFLCRVAAHPILR
          YIIPPAPPRPDFD.SREK.QKLGEGEGSMTKEEFTKMKQE.EAEY..IFKKTVAMHEVFLC.V.AHPILR
Retrocopy YIIPPAPPRPDFDTSREKVQKLGEGEGSMTKEEFTKMKQEMEAEYFGIFKKTVAMHEVFLCHVTAHPILR

Parental  KDLNFHVFLEYNQDLSVRG-KNKK-EKLEDFFKNMVKS-ADGVIVSGVKDVDDFFEHERTFLLEYHNRVK
          K.LNFHVFLEYNQDLSV.G.KNKK.EKLEDFF.NMVKS.ADGVIVSGV.DVD.FF.HE.TFLLEYHNRVK
Retrocopy KYLNFHVFLEYNQDLSVQG<KNKK<EKLEDFFENMVKS<ADGVIVSGVTDVDNFFQHEQTFLLEYHNRVK

Parental  DASAKSDRMTRSHKSAADDYNRIGSSLYALGTQDSTDICKFFLKVSELFDKTRKIEARVSADEDLKLSDL
          DASA.SDRMTRSHKSAADDYNRIGSSLYALGTQDS..ICKFFLKVSE.FDKTRKIEA.VSADEDLKLSD.
Retrocopy DASANSDRMTRSHKSAADDYNRIGSSLYALGTQDS-GICKFFLKVSEVFDKTRKIEA*VSADEDLKLSDP

Parental  LKYYLRESQAAKDLLYRRSRSLVDYENANKALDKARAKNKDVLQAETSQQLCCQKF--EKISESAKQEL
          .KYYLRE.QAAKDLLY..SRSLVDYENAN.ALDKARAKNKDVL.A.TSQQLC.QKF.....S.SAKQ.L
Retrocopy *KYYLRETQAAKDLLY*TSRSLVDYENANEALDKARAKNKDVLLAKTSQQLCSQKFXXXXXSQSAKQFL

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_3063 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 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012873	1 retrocopy	retro_btau_870,
Cavia porcellus	ENSCPOG00000006862	1 retrocopy	retro_cpor_1145,
Nomascus leucogenys	ENSNLEG00000003310	1 retrocopy	retro_nleu_3063 ,
Nomascus leucogenys	ENSNLEG00000009714	1 retrocopy	retro_nleu_2071,
Pongo abelii	ENSPPYG00000005736	2 retrocopies	retro_pabe_1668, retro_pabe_1698,
Pan troglodytes	ENSPTRG00000006253	1 retrocopy	retro_ptro_1362,