RetrogeneDB ID: retro_nleu_212

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397261.1:30073138..30073824(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCNB2
• Ensembl ID: ENSNLEG00000011543
• Aliases: None
• Description: None

Sequence

>retro_nleu_212
TCTAAACCTAAGAGTCATGTGACTATTAGGCATAACATTTTAGAAGAAATTGGAAATAGAGTTACAGCCAGAGCAGCACA
AGTAGCTAAGAAAGCTCAGAACACCAAAGGACCAGTTCAACCCAGGGAAACAACAAATGTCAACAAACAACTGAAACCTA
CTGCTTCTGTGAAACAGCACAGATGGAAATGTTGGCTCCAAAGGGTCCTTCTGCCATACCTGAGGATGCCTCCATGAAAG
AAGAGAACACCTGCCAAGCTTTTTCTGATGCCTTGCTCTACAAAATTGAGGATATTGATAACGAAGATTGGAATAACCCT
CAGCTCTGCAGTGACTATGTTAAGGATATCTATCAGTACCTCAGGCAGCTGGAGATTTTGCAGTTCATAAACCCACATGT
CTTAGATGGATGAGATATAAATGGACGTAAGTGTACCATCCTGGTAGACTGGTTGGTGCAAATTCACTCCAAGTTTAGGC
TTCTTCAGGAGACTCTGTATGTGTGTGTTGCCAGTATGGATTGATTTTTACTGGTTCAGCCAGTTTCCCAGAGGAAGCTT
CAACTAGTTTGGATTAGTGCTCTGCTCTTGGCTTCCAAGTATGAGGAGATGTTTTCTCCAAATATTGAAGGCTTTGTTTA
CATTACAGACAATGCTTATACTAGTTTCCAAATCCAAGACATGGAA

Alignment

ORF - retro_nleu_212 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.17 %
• Parental protein coverage: 57.54 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SKVKSHVTIRRTVLEEIGNRVTTRAAQVAKKAQNAKVTVQPTKTTNVNKQLKPTASVKP-VQMEMLAPKG
          SK.KSHVTIR...LEEIGNRVT.RAAQVAKKAQN.K..VQP..TTNVNKQLKPTASVK...QMEMLAPKG
Retrocopy SKPKSHVTIRHNILEEIGNRVTARAAQVAKKAQNTKGPVQPRETTNVNKQLKPTASVKQ<AQMEMLAPKG

Parental  PSPTPEDVSMKEENLCQAFSDALLCKIEDIDNEDWENPQLCSDYVKDIYQYLRQLEVLQSVNPHFLDGRD
          PS..PED.SMKEEN.CQAFSDALL.KIEDIDNEDW.NPQLCSDYVKDIYQYLRQLE.LQ..NPH.LDG.D
Retrocopy PSAIPEDASMKEENTCQAFSDALLYKIEDIDNEDWNNPQLCSDYVKDIYQYLRQLEILQFINPHVLDG*D

Parental  INGRMRAILVDWLVQVHSKFRLLQETLYMCIAIMDRFLQVQPVSRKKLQLVGITALLLASKYEEMFSPNI
          INGR...ILVDWLVQ.HSKFRLLQETLY.C.A.MD.FL.VQPVS..KLQLV.I.ALLLASKYEEMFSPNI
Retrocopy INGRKCTILVDWLVQIHSKFRLLQETLYVCVASMD*FLLVQPVSQRKLQLVWISALLLASKYEEMFSPNI

Parental  EDFVYITDNAYTSSQIREME
          E.FVYITDNAYTS.QI..ME
Retrocopy EGFVYITDNAYTSFQIQDME

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_212 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 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005269	1 retrocopy	retro_btau_1584,
Homo sapiens	ENSG00000157456	1 retrocopy	retro_hsap_3816,
Nomascus leucogenys	ENSNLEG00000011543	1 retrocopy	retro_nleu_212 ,
Otolemur garnettii	ENSOGAG00000012885	2 retrocopies	retro_ogar_1770, retro_ogar_2766,
Pongo abelii	ENSPPYG00000006517	2 retrocopies	retro_pabe_3073, retro_pabe_3074,
Pan troglodytes	ENSPTRG00000007123	1 retrocopy	retro_ptro_2597,
Ictidomys tridecemlineatus	ENSSTOG00000001275	1 retrocopy	retro_itri_229,
Tarsius syrichta	ENSTSYG00000013818	1 retrocopy	retro_tsyr_1402,