RetrogeneDB ID: retro_nleu_1279

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397287.1:27382857..27384147(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSNLEG00000010761
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SMYD2
• Ensembl ID: ENSNLEG00000014428
• Aliases: None
• Description: None

Sequence

>retro_nleu_1279
AAGGGCCTCGGTGGCCTGGAGCGCTTCTGCAGCCCCGGCAAGGGCCAGGGACTGTGGGCTCTGCAGCCCTTCCAGGTGGG
GGACTTGCTGTTCTCCTGCCCGCCCTGTGCCTACGTGCTCATGGTCAACGAGCGGGGCAACCACTGCGAGTACTGCTTCG
CCAGGTAAGAAGGATTGTCCAAATGTGGAAGATGCAAGCAGGCATTTTACTGCAATGTGGAGTGTCAGAAAGAAGATTGG
CCCATGCACAAGCTGGAATGTTCTCCCATGGTTGTTTTTGGGGAAAACTGGAATCCCTCAGAGACTGTAAGACTAACAGC
AAGGATTCTGGCCAAACAGAAAATCCACCCAGAGAGAACACCTTCAGAAAAATTGTTAGCTGTGAAGGAGTTTGAATCAC
ATCTGAATAAGTTAGACAACGAGAGGAAGGATTTGATTCAGAGTGACATAGCTGCTCTCCATCACTTTTACTCCAAGCAT
CTCAAATTCCCTGACAATGATAGCCTCGTAGTACTCTTTGCACAGGTTAACTGTAATGGCTTCACAATTGAAGATGAAGA
ACTTTCTCATTTGGGATCAGCGATATTTCCTGATGTCACATTGATGAATCATAGCTGTTGCCCCAATGTCATTGTGACCT
ACAAAGGGACCCTGGCAGAAGTCAGAGCTGTACAGGAAATCAAGCCGGGAGAGGAGGTTTTTACCAGCTATATTGATCTC
CTGTACCCAACGGAAGATAGAAATGACCGGTTAAGAGATTCTTATTTCTTTACCTGTGAGTGCCAGGAGTGCACCACCAA
GGACAAGGATAAGGCCAAGGTGGAAATCCGGAAGCTCAGCGATCCCCCAAAGGCAGAAGCCATCCGAGACATGGTCAGGT
ATGCATGCAACATCATTGAAGAGTTCCGGAGGGCCAAGCACTATAAATCCCCTAGTGAGCTGCTGGAGATCTGTGAGCTC
AGCCAGGAGAAGATGAGCTCCGTGTTTGAGGACAGTAACGTGTACATGTTGCACATGATGTACCCGGCCATGGGTGTCTG
CTTGTACATGCAGGACTGGGAAGGAGCCCTGCAATATGTACAGAAAATCATTAAGCCCTACAGTAAGCACTATCCTTTGT
ACTCCCTCAACGTGGCCTCCATGTGGTTGAAGCTAGGGAGACTCTACATGGGCCTGGAACACAAAGCTGCAGGGGAGAAA
GCCCTGAAGAAAGCCATTGCAATCATGGAAGTAGCTCACGGCAAAGATCATCCATATATTTCTGAGATCAAACAGGAAAT
TGAAAGCCAC

Alignment

ORF - retro_nleu_1279 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.29 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EGLGGMERFCSPGKG-PGAAGSAA-FQVGDLLFSCPAYAYVLTVNERGNHCEYCFARKEGLSKCGRCKQA
          .GLGG.ERFCSPGKG.PG..GSAA.FQVGDLLFSCP..AYVL.VNERGNHCEYCFAR.EGLSKCGRCKQA
Retrocopy KGLGGLERFCSPGKG<PGTVGSAA>FQVGDLLFSCPPCAYVLMVNERGNHCEYCFAR*EGLSKCGRCKQA

Parental  FYCNVECQKEDWPMHKLECSPMVVFGENWNPSETVRLTARILAKQKIYPERTPSEKLLAVKEFESHLDKL
          FYCNVECQKEDWPMHKLECSPMVVFGENWNPSETVRLTARILAKQKI.PERTPSEKLLAVKEFESHL.KL
Retrocopy FYCNVECQKEDWPMHKLECSPMVVFGENWNPSETVRLTARILAKQKIHPERTPSEKLLAVKEFESHLNKL

Parental  DNEKKDLIQSDIAALHHFYSKHLEFPDNDSLVVLFAQVNCNGFTIEDEELSHLGSAIFPDVALMNHSCCP
          DNE.KDLIQSDIAALHHFYSKHL.FPDNDSLVVLFAQVNCNGFTIEDEELSHLGSAIFPDV.LMNHSCCP
Retrocopy DNERKDLIQSDIAALHHFYSKHLKFPDNDSLVVLFAQVNCNGFTIEDEELSHLGSAIFPDVTLMNHSCCP

Parental  NVIVTYKGTLAEVRAVQEIKTGEEVFTSYIDLLYPTEDRNDRLRDSYFFTCECQECTTKDKDKAKVEIRK
          NVIVTYKGTLAEVRAVQEIK.GEEVFTSYIDLLYPTEDRNDRLRDSYFFTCECQECTTKDKDKAKVEIRK
Retrocopy NVIVTYKGTLAEVRAVQEIKPGEEVFTSYIDLLYPTEDRNDRLRDSYFFTCECQECTTKDKDKAKVEIRK

Parental  LSDPPKAEAIRDMVRYARNVIEEGNERKSHSPPSELLEICELSQEKMSSVFEDSNVYMLHMMYQAMGVCL
          LSDPPKAEAIRDMVRYA.N.IEE....K....PSELLEICELSQEKMSSVFEDSNVYMLHMMY.AMGVCL
Retrocopy LSDPPKAEAIRDMVRYACNIIEEFRRAKHYKSPSELLEICELSQEKMSSVFEDSNVYMLHMMYPAMGVCL

Parental  YMQDWEGALQYGQKIIKPYSKHYPLYSLNVASMWLKLGRLYMGLEYKAAGEKALKKAIAIMEVAHGKDHP
          YMQDWEGALQY.QKIIKPYSKHYPLYSLNVASMWLKLGRLYMGLE.KAAGEKALKKAIAIMEVAHGKDHP
Retrocopy YMQDWEGALQYVQKIIKPYSKHYPLYSLNVASMWLKLGRLYMGLEHKAAGEKALKKAIAIMEVAHGKDHP

Parental  YISEIKQEIESH
          YISEIKQEIESH
Retrocopy YISEIKQEIESH

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_1279 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000014059	1 retrocopy	retro_dnov_805,
Nomascus leucogenys	ENSNLEG00000014428	1 retrocopy	retro_nleu_1279 ,