RetrogeneDB ID: retro_nleu_428

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397265.1:2338630..2339052(+)
• Located in intron of: ENSNLEG00000011752

Retrocopy information

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

Parental gene information

• Parental gene symbol: CBX5
• Ensembl ID: ENSNLEG00000017671
• Aliases: None
• Description: None

Sequence

>retro_nleu_428
ATGGGAAAGAAAACCAAGCACACAGCTGACAGTTCACTAGAGAATGAAGAGGAGTACACTGTGGAGAAGATGCTAGACAG
GCATGTGGTTAAGGGGCAAGTGGAGTATCTACTGAAGTGGAAAGGCTTTTCTGAGGAGCACAATACTTGGGAATCTAAGA
AAAAGTTGGATTGCCTTTAGTTCATTTCTTAGTTTACGAAAAAGTTTAAGATGATGAAGGAGGGTTAAAATAACAAGCCT
GGGGAGAAGTCAGAAAGTAGCAAGGAAATCCAATTTCTCAAACTGTGCTGACAGTATCAAGTCCAAAAAAGAGAACAGAG
CGATGATATTGCTCGCGGCTTCAAGATAAGACTAGAACCAGAAAAGATCATTGGGGCAACAGATTCCTGTGGCGATTTAT
GTTTTTAATGAAATGGAAAGAC

Alignment

ORF - retro_nleu_428 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.97 %
• Parental protein coverage: 75.39 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGKKTKRTADSSSSEDEEEYVVEKVLDRRVVKGQVEYLLKWKGFSEEHNTWEPEKNLDCPELISEFMKKY
          MGKKTK.TADSS..E.EEEY.VEK.LDR.VVKGQVEYLLKWKGFSEEHNTWE..K.LDC...IS.F.KK.
Retrocopy MGKKTKHTADSSL-ENEEEYTVEKMLDRHVVKGQVEYLLKWKGFSEEHNTWESKKKLDCL*FIS*FTKKF

Parental  KKMKEGENNKPREKSESNKRKSNFSNSADDIKSKKKREQSNDIARGFERGLEPEKIIGATDSCGDL-MFL
          K.MKEG.NNKP.EKSES.K....F..........K.......IARGF...LEPEKIIGATDSCGDL.MFL
Retrocopy KMMKEG*NNKPGEKSESSK-EIQFLKLC*QYQVQKREQSDD-IARGFKIRLEPEKIIGATDSCGDL<MFL

Parental  MKWKD
          MKWKD
Retrocopy MKWKD

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_428 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 10 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018847	1 retrocopy	retro_cjac_2020,
Echinops telfairi	ENSETEG00000001220	1 retrocopy	retro_etel_678,
Homo sapiens	ENSG00000094916	1 retrocopy	retro_hsap_2811,
Gorilla gorilla	ENSGGOG00000000041	1 retrocopy	retro_ggor_1955,
Nomascus leucogenys	ENSNLEG00000002435	4 retrocopies	retro_nleu_1089, retro_nleu_1105, retro_nleu_1955, retro_nleu_2961,
Nomascus leucogenys	ENSNLEG00000014931	9 retrocopies	retro_nleu_141, retro_nleu_1685, retro_nleu_2462, retro_nleu_373, retro_nleu_397, retro_nleu_511, retro_nleu_676, retro_nleu_944, retro_nleu_964,
Nomascus leucogenys	ENSNLEG00000017671	1 retrocopy	retro_nleu_428 ,
Pongo abelii	ENSPPYG00000004599	1 retrocopy	retro_pabe_2307,
Pan troglodytes	ENSPTRG00000005034	1 retrocopy	retro_ptro_1905,
Tursiops truncatus	ENSTTRG00000004524	1 retrocopy	retro_ttru_1859,