RetrogeneDB ID: retro_ggor_829

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 12:100318275..100319227(+)
• Located in intron of: ENSGGOG00000000193

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNX5
• Ensembl ID: ENSGGOG00000008953
• Aliases: None
• Description: None

Sequence

>retro_ggor_829
CTGCAGATTCCGCCTGCTCCTACGAAGGCTGACCTCAATGGTCCTTGAGAGAAGATGCAGAAACTGGGAGAAGGTAAAGG
GTCTTTGACCAAAGAAGAATTTGCCAAGATGAAATAAGAACTGGAAGCTGAGTATCTCGCTGTTTTTAAGAAGACTGTGT
CCTCCCATGAAGCCTTTCTTTAGTGGCTTTCTTCTCACCCTGTTCTCAGTAAAGATCGCAACTTTCATATTTTCCTGGAA
TATGATCAGGATCTAAGTGTTAGGTGGAAAAATACTAGAGAGATGTTTGGTGGCTTCTTCAAAAGTGTGGTGAAAGTGCT
GATGCAGTCCTTTTTACTGGAGTTAAGGAGGTAGATGACTTCTTTGAGCAAGAGAATGACTTCCTTATTAACTATTAGAG
TAGGATCAAAGATTCTTGTGTGAAAGCTGGCAAAATGACCAGATGTCATAAAAATGTTGCCGATGACTATATTCACACTG
CAGCCTGCTTACATAGCCTGGCTTTAGAAGAGCCCACAGTCATCAAAAAGTATCTATTGAAGGTTGCTGAGCTATTTGAA
AAACTTAGGAAAGTAGAGGGTTGAATCTCATCAGATGAAGATTTAAAGCTAACAGAGCTCCTCCGATACTACATGCTCAA
CATAGAAGCTGCTAAGGATCTCTTACACAGATGCACCAAAGCCCTCATTGACTATGAAAAATCAAACAAAGCTCTGGATA
AGGCCCAGTTTAAAGAGCAAATATGTCAAGTTGGCTAAGGTACACTAGGAGGAGTGCTGCCAGAAATTTGAATAGCTTTC
CAAATCTGCAAAGGAAGAACTGATAAATTTCAAACGGAAGAAAGTGGCAGCATTTAGAAAGAATCTAATTGAAATGTCTG
AACTGGAAATAAAACATTGCGAGGAACAGTGTCTCCCTTTTGCAGAGCTGTATTGACTTGTTCAAGAATAAC

Alignment

ORF - retro_ggor_829 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.5 %
• Parental protein coverage: 78.47 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LIIPPAPTKPDFDGPREKMQKLGEGEGSMTKEEFAKMKQELEAEYLAVFKKTVSSHEVFLQRLSSHPVLS
          L.IPPAPTK.D..GP.EKMQKLGEG.GS.TKEEFAKMK.ELEAEYLAVFKKTVSSHE.FL..LSSHPVLS
Retrocopy LQIPPAPTKADLNGP*EKMQKLGEGKGSLTKEEFAKMK*ELEAEYLAVFKKTVSSHEAFL*WLSSHPVLS

Parental  KDRNFHVFLEYDQDLSVRRKNTKEMFGGFFKSVVK-SADEVLFTGVKEVDDFFEQEKNFLINYYNRIKDS
          KDRNFH.FLEYDQDLSVR.KNT.EMFGGFFKSVVK.SAD.VLFTGVKEVDDFFEQE..FLINY..RIKDS
Retrocopy KDRNFHIFLEYDQDLSVRWKNTREMFGGFFKSVVK<SADAVLFTGVKEVDDFFEQENDFLINY*SRIKDS

Parental  CVKADKMTRSHKNVADDYIHTAACLHSLALEEPTVIKKYLLKVAELFEKLRKVEGRVSSDEDLKLTELLR
          CVKA.KMTR.HKNVADDYIHTAACLHSLALEEPTVIKKYLLKVAELFEKLRKVEG..SSDEDLKLTELLR
Retrocopy CVKAGKMTRCHKNVADDYIHTAACLHSLALEEPTVIKKYLLKVAELFEKLRKVEG*ISSDEDLKLTELLR

Parental  YYMLNIEAAKDLLYRRTKALIDYENSNKALDKAR-LKSKDVKLAEAHQQECCQKFEQLSESAKEELINFK
          YYMLNIEAAKDLL.R.TKALIDYE.SNKALDKA..LKSK.VKLA..H..ECCQKFE.LS.SAKEELINFK
Retrocopy YYMLNIEAAKDLLHRCTKALIDYEKSNKALDKAQ>LKSKYVKLAKVH*EECCQKFE*LSKSAKEELINFK

Parental  RKRMAAFRKNLIEMSELEIKH-ARNNVSLLQSCIDLFKNN
          RK..AAFRKNLIEMSELEIKH.ARN.VSLLQSCIDLFKNN
Retrocopy RKKVAAFRKNLIEMSELEIKH>ARNSVSLLQSCIDLFKNN

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.05 RPM	35.20 RPM
SRP007412_cerebellum	0.00 RPM	24.70 RPM
SRP007412_heart	0.00 RPM	10.32 RPM
SRP007412_kidney	0.04 RPM	201.34 RPM
SRP007412_liver	0.03 RPM	63.12 RPM
SRP007412_testis	0.00 RPM	53.87 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_829 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_829 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1051
Pan troglodytes	retro_ptro_717
Pongo abelii	retro_pabe_877
Macaca mulatta	retro_mmul_832
Callithrix jacchus	retro_cjac_3243

---

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 ,
Gorilla gorilla	ENSGGOG00000010801	1 retrocopy	retro_ggor_1473,
Macropus eugenii	ENSMEUG00000009110	1 retrocopy	retro_meug_475,
Macaca mulatta	ENSMMUG00000011476	2 retrocopies	retro_mmul_1746, retro_mmul_832,
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,