RetrogeneDB ID: retro_nleu_1103

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397281.1:10162635..10163144(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL35
• Ensembl ID: ENSNLEG00000002756
• Aliases: None
• Description: None

Sequence

>retro_nleu_1103
ATGGCTGCCTCTGCCTTTGCTGGTGCGATGAGAGCGGCTTCAGGAATCTATGGCTCCTGAATATTTTTGCATCTCCAGCC
CACCGAAACTGTGCCAGGAATACCTCTTGTATTTCTGCATTGTCTACTGGACGTTTTAGTCATATTCGGACACCATTCGT
TTCCTCCACTCCCAGGCTTATCACATCTGTCAGAAACCTGACATGTGGGCATACTGCAGTAATCCCCAACAGAGTGGCCC
CCTTGCTTCCAAGTGTCCTGAAGCTGCCAGTCAGAACTGTAATATACATCAGTACACAAAAAGGCAAGAGAGAGACTGTG
AAAGCTGTCATCTATAGGTTTCTTCGACTTCATTCTGGCCTTTGGGTGAGGAAAAAGGCTGGTCATAAGAAAAAATTCTG
GAAAAAGACACCTGCAAGAAAAAAGCGATTGAGGGAATTTGTGTTCTGCAATAAAACCCAGAGTAAACTCTTAGATAAAA
TGACAATGTCCTTCTGGAAGAGGTGAAAC

Alignment

ORF - retro_nleu_1103 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.53 %
• Parental protein coverage: 81.73 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAASAFAGAVRAASGI-LRPLNILASSTYRNCVKNASLISAWSTGRFSHIQTPVVSSTPRLTTSERNLTC
          MAASAFAGA.RAASGI.L..LNI.AS...RNC..N.S.ISA.STGRFSHI.TP.VSSTPRL.TS.RNLTC
Retrocopy MAASAFAGAMRAASGI<LWLLNIFASPAHRNCARNTSCISALSTGRFSHIRTPFVSSTPRLITSVRNLTC

Parental  GHTSAILNRVAPVLPSVVKLPVRFLTYFSARKGKRKTVKAVIYRFLRLHCGLWVRRKAGYKKKLWKKTPA
          GHT..I.NRVAP.LPSV.KLPVR...Y.S..KGKR.TVKAVIYRFLRLH.GLWVR.KAG.KKK.WKKTPA
Retrocopy GHTAVIPNRVAPLLPSVLKLPVRTVIYISTQKGKRETVKAVIYRFLRLHSGLWVRKKAGHKKKFWKKTPA

Parental  RKKRLREFVFCNKTQSKLLDKMTTSFWKRRN
          RKKRLREFVFCNKTQSKLLDKMT.SFWKR.N
Retrocopy RKKRLREFVFCNKTQSKLLDKMTMSFWKR*N

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_1103 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 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019467	1 retrocopy	retro_cjac_203,
Dasypus novemcinctus	ENSDNOG00000008329	1 retrocopy	retro_dnov_404,
Macropus eugenii	ENSMEUG00000004773	1 retrocopy	retro_meug_1703,
Mus musculus	ENSMUSG00000052962	1 retrocopy	retro_mmus_1777,
Nomascus leucogenys	ENSNLEG00000002756	4 retrocopies	retro_nleu_1103 , retro_nleu_1362, retro_nleu_2217, retro_nleu_781,
Otolemur garnettii	ENSOGAG00000004048	1 retrocopy	retro_ogar_2600,
Pongo abelii	ENSPPYG00000012214	5 retrocopies	retro_pabe_1817, retro_pabe_2837, retro_pabe_3724, retro_pabe_541, retro_pabe_595,
Rattus norvegicus	ENSRNOG00000008546	1 retrocopy	retro_rnor_1399,
Tupaia belangeri	ENSTBEG00000015366	10 retrocopies	retro_tbel_1143, retro_tbel_146, retro_tbel_2647, retro_tbel_289, retro_tbel_2892, retro_tbel_3789, retro_tbel_3828, retro_tbel_428, retro_tbel_4379, retro_tbel_627,
Tarsius syrichta	ENSTSYG00000007713	2 retrocopies	retro_tsyr_1128, retro_tsyr_264,