RetrogeneDB ID: retro_nleu_2071

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397326.1:5929041..5929992(+)
• Located in intron of: ENSNLEG00000006128

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNX5
• Ensembl ID: ENSNLEG00000009714
• Aliases: None
• Description: None

Sequence

>retro_nleu_2071
CTGCAGATTCCGCCTGCTCCTACGAAGCCTGACTTCGATGGTCTTTGAGAGAAGATGCAGAAACTGGGAGAAGGTGAAGG
GTCTATGACCAAAGAAGAATTTGCCAAGATGAAATAAGAACTGGAAGCTGAGTATCTCGCTGTTTATAAGAAGACTGTGT
CCTCCCATGAAGCCTTTCTTTAGTGGCTTTCTTCTCACCCTGTTCTCAGTACAGATCGCAACTTTCATGTTTTCCTGGAA
TATGATCAGGATCTAAGTGTTAGGTGGAAAAATACTAAAGAGATGTTTGGTGGCTTCTTCAAAAGTGTGGTGAAAGTGCT
GATGCAGTCCTTTTTACTGGAGTTAAGGAGGTAGATGACTTCTTTGAGCAAGAGAATGACTTCCTTATTAACTATTACAA
TAGGATCAAAGATTCTTGTGTGAAAGCTGACAAAATGACCAGCTCTCATAAAAATGTTGCTGATGACTATATTCACACCG
CAGCCTGCTTACATAGCCTGGCTTTAGAAGAGCCTACAGTCATCAAAAAGTATCTATTGAAGGTTGCTGAGCTATTTGAA
AAACTTATGAAAGTAGAGGGTGGAATCTCATCAGATGAAGATTTAAAGCTAACAGAGCTCCTCCGATACTACATGCTCAA
CATCGAAGCTGCTAAGGATCTCTTACACAGATGCACCAAAGCCCTCACTGACTATGAAAAATCAAACAAAGCTCTGGATA
AGGCCCAGTTTAAAGAGCAAAGATGTCAAGTTGGCTAAGGTACACTAGCAGGAGTGCTGCCAGAAATTTGAATAGCTTTC
CAAATCTGCAAAAGAAGAACTGATAAATTTCAAACGGAAGAAAGTGGCAGCATTTAGAAAGAATCTAATTGAAATGTCTG
AACTGGAAATAAAACATGCGAGGAACAGTGTCTCTCTTTTGCAGAGCTGTATTGACTTGTTCGAGAATAAC

Alignment

ORF - retro_nleu_2071 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.66 %
• Parental protein coverage: 78.47 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LIIPPAPTKPDFDGPREKMQKLGEGEGSMTKEEFAKMKQELEAEYLAVFKKTVSSHEVFLQRLSSHPVLS
          L.IPPAPTKPDFDG..EKMQKLGEGEGSMTKEEFAKMK.ELEAEYLAV.KKTVSSHE.FL..LSSHPVLS
Retrocopy LQIPPAPTKPDFDGL*EKMQKLGEGEGSMTKEEFAKMK*ELEAEYLAVYKKTVSSHEAFL*WLSSHPVLS

Parental  KDRNFHVFLEYDQDLSVRRKNTKEMFGGFFKSVVK-SADEVLFTGVKEVDDFFEQEKNFLINYYNRIKDS
          .DRNFHVFLEYDQDLSVR.KNTKEMFGGFFKSVVK.SAD.VLFTGVKEVDDFFEQE..FLINYYNRIKDS
Retrocopy TDRNFHVFLEYDQDLSVRWKNTKEMFGGFFKSVVK<SADAVLFTGVKEVDDFFEQENDFLINYYNRIKDS

Parental  CVKADKMTRSHKNVADDYIHTAACLHSLALEEPTVIKKYLLKVAELFEKLRKVEGRVSSDEDLKLTELLR
          CVKADKMT.SHKNVADDYIHTAACLHSLALEEPTVIKKYLLKVAELFEKL.KVEG..SSDEDLKLTELLR
Retrocopy CVKADKMTSSHKNVADDYIHTAACLHSLALEEPTVIKKYLLKVAELFEKLMKVEGGISSDEDLKLTELLR

Parental  YYMLNIEAAKDLLYRRTKALIDYENSNKALDKAR-LKSRDVKLAEAHQQECCQKFEQLSESAKEELINFK
          YYMLNIEAAKDLL.R.TKAL.DYE.SNKALDKA..LKS.DVKLA..H.QECCQKFE.LS.SAKEELINFK
Retrocopy YYMLNIEAAKDLLHRCTKALTDYEKSNKALDKAQ>LKSKDVKLAKVH*QECCQKFE*LSKSAKEELINFK

Parental  RKRVAAFRKNLIEMSELEIKHARNNVSLLQSCIDLFKNN
          RK.VAAFRKNLIEMSELEIKHARN.VSLLQSCIDLF.NN
Retrocopy RKKVAAFRKNLIEMSELEIKHARNSVSLLQSCIDLFENN

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_2071 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 15 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010128	2 retrocopies	retro_chof_1478, retro_chof_2166,
Callithrix jacchus	ENSCJAG00000004947	2 retrocopies	retro_cjac_2192, retro_cjac_3243,
Homo sapiens	ENSG00000089006	2 retrocopies	retro_hsap_1051, retro_hsap_2945,
Gorilla gorilla	ENSGGOG00000008953	1 retrocopy	retro_ggor_829,
Macropus eugenii	ENSMEUG00000009110	1 retrocopy	retro_meug_475,
Macaca mulatta	ENSMMUG00000011476	2 retrocopies	retro_mmul_1746, retro_mmul_832,
Nomascus leucogenys	ENSNLEG00000003310	1 retrocopy	retro_nleu_3063,
Nomascus leucogenys	ENSNLEG00000009714	1 retrocopy	retro_nleu_2071 ,
Oryctolagus cuniculus	ENSOCUG00000017072	1 retrocopy	retro_ocun_1323,
Otolemur garnettii	ENSOGAG00000006157	1 retrocopy	retro_ogar_1203,
Pongo abelii	ENSPPYG00000010730	2 retrocopies	retro_pabe_2442, retro_pabe_877,
Pan troglodytes	ENSPTRG00000013278	2 retrocopies	retro_ptro_2052, retro_ptro_717,
Sus scrofa	ENSSSCG00000007088	1 retrocopy	retro_sscr_593,
Ictidomys tridecemlineatus	ENSSTOG00000015416	1 retrocopy	retro_itri_1176,
Tursiops truncatus	ENSTTRG00000016432	1 retrocopy	retro_ttru_410,