RetrogeneDB ID: retro_nleu_1938

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397317.1:14260535..14261535(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM149B1
• Ensembl ID: ENSNLEG00000016575
• Aliases: None
• Description: None

Sequence

>retro_nleu_1938
TCCAGATACACTCGGGAAGGCGGTGCCACAGAGCTTGGAGCTGAAAGGAATAACGAAACATGCTCTTAACCATCATCCCC
CTCCAGAGAAGCTGGAGGAAATTTCCCCCACCAGTGACAGTCATGAGAAAGACACGAGGTCCCAAAGCGAGTCTGACATC
ACAAGAGAATCACCTTTTACATCAGCCGACGCTGGGAATTCACTGTCTGCTTTTCCAAGTGATACAGGCGCAGGGATATC
TACTGAAGGCAGCCCGGACTTCTCCTGGGAATACGGTGAACTCGATCAAAATGCCACTGAAAAGGCCTAGGCAATGTTCA
CAGCCATTGATGAACTCTTGTATGAGCAGAAGTTCAGTGTGCATACCAAGAGTCTACAAGAAGAGCGCCAACAGTGGACA
GCTAGCTTTCCTCACATCAGGATTCTAGGTAGGCAGATAATCACTCCAAGTGAAGGTTATAGATTGTATCCTAGATCCCC
TTCTGCTGTTTCAGCTTCCTATGAAACAACCTTGTCTCAAGAAAGAGATTCTACTATATTTGGTATAAGGGGAAAGAAGT
TACATTTTTCATCTTCGTATGCTCATAAAGCATCTGCTATTGCCAAATCCTCCAGCTTTTGTTCTATGGAAAGAGACGAG
GAAGACTCTATAATCATCTCCAAAGGAATAATTGAGGAATACCTAGCATTCGATCACACAGATACGGAAGAGGGATTTCA
TGGGAAGAAATCAGAAGCAGCTACAGAGAAATAGAAATTAGGATATCCTCCCACTGCTCCGTTTTACTGCATGAAAGAAG
ATGTCCTTGTTTATGTGTTTGACAATGTATGGAGCAAGGTTGTGAGCTTTATGGAGCAGTTGACATGTAGTCACTGGGAA
GGATTTGCCTCTGATGATGAGAGTAATGTTGCAGTTACCAGACCCGATTCAGAAAGTTCCTGTGTGCTGAGTGAGCCACA
TCCTTTGGTGTTACCGCAAGTGCCACAGTCTAAGGTGCTG

Alignment

ORF - retro_nleu_1938 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.92 %
• Parental protein coverage: 57.14 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SRYTR-KAVPQSLELKGITKHALNHHPPPEKLEEISPTSDSHEKDTSSQSKSDITRESSFTSADTGNSLS
          SRYTR.KAVPQSLELKGITKHALNHHPPPEKLEEISPTSDSHEKDT.SQS.SDITRES.FTSAD.GNSLS
Retrocopy SRYTR>KAVPQSLELKGITKHALNHHPPPEKLEEISPTSDSHEKDTRSQSESDITRESPFTSADAGNSLS

Parental  AFPSYTGAGISTEGSLDF-WGYGELDQNATEKVQAMFTAIDELLYEQKLSVHTKSLQEECQQWTASFPHL
          AFPS.TGAGISTEGS.DF.W.YGELDQNATEK..AMFTAIDELLYEQK.SVHTKSLQEE.QQWTASFPH.
Retrocopy AFPSDTGAGISTEGSPDFSWEYGELDQNATEKA*AMFTAIDELLYEQKFSVHTKSLQEERQQWTASFPHI

Parental  RILGRQIITPSEGYRLYPRSPSAVSASYETTLFQERDSTIFGIRGNKLHFSSSYAHKASFIAKSSSFCSM
          RILGRQIITPSEGYRLYPRSPSAVSASYETTL.QERDSTIFGIRG.KLHFSSSYAHKAS.IAKSSSFCSM
Retrocopy RILGRQIITPSEGYRLYPRSPSAVSASYETTLSQERDSTIFGIRGKKLHFSSSYAHKASAIAKSSSFCSM

Parental  ERDEEDSIIVSEGIIEEYLAFDHTDMEEGFRGKKSEAATEKQKLGYPPIAPFYCMKEDVLAYVFDNVWSK
          ERDEEDSII.S.GIIEEYLAFDHTD.EEGF.GKKSEAATEK.KLGYPP.APFYCMKEDVL.YVFDNVWSK
Retrocopy ERDEEDSIIISKGIIEEYLAFDHTDTEEGFHGKKSEAATEK*KLGYPPTAPFYCMKEDVLVYVFDNVWSK

Parental  VVSCMEQLTRSHWEGFASDDESNVAVTRPDSESSCVLSEPHPLVLPRVPQSKVL
          VVS.MEQLT.SHWEGFASDDESNVAVTRPDSESSCVLSEPHPLVLP.VPQSKVL
Retrocopy VVSFMEQLTCSHWEGFASDDESNVAVTRPDSESSCVLSEPHPLVLPQVPQSKVL

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_1938 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
Homo sapiens	ENSG00000138286	1 retrocopy	retro_hsap_1529,
Macaca mulatta	ENSMMUG00000011281	1 retrocopy	retro_mmul_2158,
Nomascus leucogenys	ENSNLEG00000016575	1 retrocopy	retro_nleu_1938 ,
Pan troglodytes	ENSPTRG00000002623	2 retrocopies	retro_ptro_1036, retro_ptro_2950,
Rattus norvegicus	ENSRNOG00000006554	1 retrocopy	retro_rnor_2124,
Ictidomys tridecemlineatus	ENSSTOG00000002142	1 retrocopy	retro_itri_429,