RetrogeneDB ID: retro_nleu_1970

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397320.1:7744589..7745212(+)
• Located in intron of: ENSNLEG00000003177

Retrocopy information

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

Parental gene information

• Parental gene symbol: STRAP
• Ensembl ID: ENSNLEG00000004160
• Aliases: None
• Description: None

Sequence

>retro_nleu_1970
AAAGTGTGGGATGCTATCCCAGGGGATGAACTGATGACCCTGGCTCATAAACACATTATCAAGACTATGGATTTCATGCA
GGATAGTAATTATTTGTGAACCAGGGGACAGGATAAACTGTTTTGCATATATGACTTGAACAAACCCGAAGCAGAACCTG
AGGAAATTAGTGATCACAGCTCTGAGACAAAAAAGGCCCTATGGTGCAGTGAGGATAAAAAGATTCTTTCTTCTGATGAC
AAAACTGTTAGACTTTGGGATCATGTTACTATGACAGAAGTGAAATCTCTAAATTTTATTATGTTGGCTAGTAGTATGGA
ATATATTCCTGAGGGAGAGACTTTGGTAATAACTTATGGCTGATCCAGTGCTTTTGACAGTACAGTAAGTTTGGAACCAA
TTAAATCCTTTCAAGCTCCTGCAACCATTAACTCTGAATCTCTTCACCTTGAGAAAGAATTTCTTGTTGCAGGTGGTGAA
GATGTTAAACTTATAAGTATAATGATAATAGTGGAGAAGAATTAGAATCCTACAAAGGACACTCTGGTCCTATTCACTGT
GTGAGATTTGATCCTGATGGAGAACTCTATGCCAGTGGTTCTGAAGGTGGAACACTGAGACTG

Alignment

ORF - retro_nleu_1970 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.78 %
• Parental protein coverage: 57.3 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KVWDAVSGDELMTLAHKHIVKTVDFTQDSNYLLTGGQDKLLRIYDLNKPEAEPKEISGHTSGIKKALWCS
          KVWDA..GDELMTLAHKHI.KT.DF.QDSNYL.T.GQDKL..IYDLNKPEAEP.EIS.H.S..KKALWCS
Retrocopy KVWDAIPGDELMTLAHKHIIKTMDFMQDSNYL*TRGQDKLFCIYDLNKPEAEPEEISDHSSETKKALWCS

Parental  EDKQILSADDKTVRLWDHATMTEVKSLNFNMSVSSMEYIPEGEILVITYGRSIAFHSAVSLDPIKSFEAP
          EDK.ILS.DDKTVRLWDH.TMTEVKSLNF.M..SSMEYIPEGE.LVITYG.S.AF.S.VSL.PIKSF.AP
Retrocopy EDKKILSSDDKTVRLWDHVTMTEVKSLNFIMLASSMEYIPEGETLVITYG*SSAFDSTVSLEPIKSFQAP

Parental  ATINSASLHPEKEFLVAGGEDFKL-YKYDYNSGEELESYKGHFGPIHCVRFSPDGELYASGSEDGTLRL
          ATINS.SLH.EKEFLVAGGED.KL.YKY..NSGEELESYKGH.GPIHCVRF.PDGELYASGSE.GTLRL
Retrocopy ATINSESLHLEKEFLVAGGEDVKL<YKYNDNSGEELESYKGHSGPIHCVRFDPDGELYASGSEGGTLRL

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_1970 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 12 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007422	2 retrocopies	retro_chof_1098, retro_chof_1620,
Callithrix jacchus	ENSCJAG00000021593	1 retrocopy	retro_cjac_2503,
Homo sapiens	ENSG00000023734	2 retrocopies	retro_hsap_2092, retro_hsap_3723,
Gorilla gorilla	ENSGGOG00000009939	1 retrocopy	retro_ggor_1633,
Macaca mulatta	ENSMMUG00000013307	2 retrocopies	retro_mmul_1695, retro_mmul_985,
Mus musculus	ENSMUSG00000030224	1 retrocopy	retro_mmus_794,
Nomascus leucogenys	ENSNLEG00000002426	2 retrocopies	retro_nleu_1129, retro_nleu_1135,
Nomascus leucogenys	ENSNLEG00000004160	2 retrocopies	retro_nleu_1301, retro_nleu_1970 ,
Ochotona princeps	ENSOPRG00000015211	3 retrocopies	retro_opri_1029, retro_opri_217, retro_opri_541,
Pongo abelii	ENSPPYG00000004334	3 retrocopies	retro_pabe_2005, retro_pabe_3134, retro_pabe_3212,
Pan troglodytes	ENSPTRG00000004734	2 retrocopies	retro_ptro_1538, retro_ptro_2616,
Tursiops truncatus	ENSTTRG00000003466	2 retrocopies	retro_ttru_581, retro_ttru_974,