RetrogeneDB ID: retro_nleu_1984

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397321.1:561308..561705(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SHISA5
• Ensembl ID: ENSNLEG00000006485
• Aliases: None
• Description: shisa homolog 5 (Xenopus laevis) [Source:HGNC Symbol;Acc:30376]

Sequence

>retro_nleu_1984
GGGTTCGGAGCTATGGGTGGCCATCAGCCTGACCATCTTTGTGCTGTCTGTCATCACTATCATCACCTGCTTCACCTGCT
GCCTGTACAAGATGTGCCGCCGACCATGTCCGGTTGTCACCAGCATCACGTTAACCACTGTGGTGCACGCCCCTTACACT
CAGCCTCCAAGTATGCCGCCCAGCTACCCTGGATCGAGCTACCAGGGCTACTACCCCATGCTCCCCCAGCCAGGGATGCC
AGCAGCACCCTATCCAACATAGTACCCACCACCTTACTCGGCCCAGCCCATGGGCCCGCAGGCCTACCACGAGACCCTGG
CTGGAGGAGCAACCGCGCCATACCCCAAGAGCCAGCCTCCTTACAACCCAGCCTACATATATGCCCTGAAGGCGGCT

Alignment

ORF - retro_nleu_1984 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.68 %
• Parental protein coverage: 57.69 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GFGAT-LAIGLTIFVLSVVTIIICFTCSCCCLYKTCRRPRPVVTTTTSTTVVHAPYPQPPSVPPSYPGPS
          GFGA...AI.LTIFVLSV.TII.CFT...CCLYK.CRRP.PVVT..T.TTVVHAPY.QPPS.PPSYPG.S
Retrocopy GFGAM>VAISLTIFVLSVITIITCFT---CCLYKMCRRPCPVVTSITLTTVVHAPYTQPPSMPPSYPGSS

Parental  YQGYHTMPPQPGMPAAPYPMQYPPPYPAQPMGPPAYHETLAGGAAAPYPASQPPYNPAYMDAPKAA
          YQGY..M.PQPGMPAAPYP..YPPPY.AQPMGP.AYHETLAGGA.APYP.SQPPYNPAY..A.KAA
Retrocopy YQGYYPMLPQPGMPAAPYPT*YPPPYSAQPMGPQAYHETLAGGATAPYPKSQPPYNPAYIYALKAA

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_1984 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 7 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002915	2 retrocopies	retro_cjac_4077, retro_cjac_4152,
Homo sapiens	ENSG00000164054	2 retrocopies	retro_hsap_4706, retro_hsap_4812,
Gorilla gorilla	ENSGGOG00000028207	2 retrocopies	retro_ggor_2996, retro_ggor_86,
Macaca mulatta	ENSMMUG00000010062	1 retrocopy	retro_mmul_2565,
Nomascus leucogenys	ENSNLEG00000006485	1 retrocopy	retro_nleu_1984 ,
Pongo abelii	ENSPPYG00000013902	3 retrocopies	retro_pabe_2120, retro_pabe_3653, retro_pabe_3739,
Pan troglodytes	ENSPTRG00000014888	1 retrocopy	retro_ptro_3128,