RetrogeneDB ID: retro_ggor_263

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 1:91795831..91796482(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CAPNS1
• Ensembl ID: ENSGGOG00000003699
• Aliases: None
• Description: None

Sequence

>retro_ggor_263
GGCAGAAGAGGTGGCAGAGTGGCCGTGTGCTTCCTAGGTGGAATCATTAGCTCCATCATAGAGGTGGCTACACAGCACAA
CCTGGAGCCCCTGCCTCAACACACACATTGCTCCAACACTGAGGCCAACAAGAGTGAGGAGGTCCATCATTTCTGGAGGC
TCTTTGCCCGGTTGGCTGGAGATGACATCGAGGTCAGCGGCACAGAACTCATGAATGTTGTCAACAAGGTTGTGATCAGT
AGGACTGAACTGAAGACTCATGGTTTTGGCATTGATACATGTCAAAGCATGGTGGCCATGATGGATAGTGACACCACAGG
CAGGCTGGACTTTGAGGAATTCAAGTACCTGTGGAACAACATCAAAAAGTGACAGACAATATACAAGCAGTTTGATGTTG
ACCGATCCGGAACCATTTGCAGCAGTGAACTTGCAGAGGCCTTTGAGGCAGCAGGGTTCCACCTGAATGAACAACTCTAC
AACATAATATTCTGACACTACTTGCATGAAGGACAGAACATGGATTTTGGCAGCTTTATCAGCTGCTTGGTCAGGCCAGA
TGCTTCGTTTCATGCCTTGAAATCTCTTTACAAAGATGACACTAGACCATTCTAAGTGAATATCCAAGAGTGGCTGCAGC
TGACAATGTAT

Alignment

ORF - retro_ggor_263 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.59 %
• Parental protein coverage: 81.58 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GGGGGGTAMRILGGVISAISEAAAQYNPEPPPPRTHYSNIEANESEEVRQFRRLFAQLAGDDMEVSATEL
          G..GG..A...LGG.IS.I.E.A.Q.N.EP.P..TH.SN.EAN.SEEV..F.RLFA.LAGDD.EVS.TEL
Retrocopy GRRGGRVAVCFLGGIISSIIEVATQHNLEPLPQHTHCSNTEANKSEEVHHFWRLFARLAGDDIEVSGTEL

Parental  MNILNKVVTRHPDLKTDGFGIDTCRSMVAVMDSDTTGKLGFEEFKYLWNNIKRWQAIYKQFDTDRSGTIC
          MN..NKVV.....LKT.GFGIDTC.SMVA.MDSDTTG.L.FEEFKYLWNNIK..Q.IYKQFD.DRSGTIC
Retrocopy MNVVNKVVISRTELKTHGFGIDTCQSMVAMMDSDTTGRLDFEEFKYLWNNIKK*QTIYKQFDVDRSGTIC

Parental  SSELPGAFEAAGFHLNEHLYNMIIRRYSDESGNMDFDNFISCLVRLDAMFRAFKSLDRDGTGQIQVNIQE
          SSEL..AFEAAGFHLNE.LYN.I...Y..E..NMDF..FISCLVR.DA.F.A.KSL..D.T....VNIQE
Retrocopy SSELAEAFEAAGFHLNEQLYNIIF*HYLHEGQNMDFGSFISCLVRPDASFHALKSLYKDDTRPF*VNIQE

Parental  WLQLTMY
          WLQLTMY
Retrocopy WLQLTMY

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	178.58 RPM
SRP007412_cerebellum	0.04 RPM	106.61 RPM
SRP007412_heart	0.00 RPM	129.14 RPM
SRP007412_kidney	0.00 RPM	210.86 RPM
SRP007412_liver	0.00 RPM	93.56 RPM
SRP007412_testis	0.00 RPM	272.36 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_263 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_263 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 25 parental genes, and 35 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000000511	1 retrocopy	retro_acar_205,
Ailuropoda melanoleuca	ENSAMEG00000001024	1 retrocopy	retro_amel_136,
Bos taurus	ENSBTAG00000014872	2 retrocopies	retro_btau_1126, retro_btau_692,
Canis familiaris	ENSCAFG00000031314	1 retrocopy	retro_cfam_942,
Callithrix jacchus	ENSCJAG00000009594	1 retrocopy	retro_cjac_2940,
Cavia porcellus	ENSCPOG00000000115	1 retrocopy	retro_cpor_1131,
Equus caballus	ENSECAG00000012210	1 retrocopy	retro_ecab_707,
Felis catus	ENSFCAG00000014149	1 retrocopy	retro_fcat_1691,
Homo sapiens	ENSG00000126247	1 retrocopy	retro_hsap_98,
Gorilla gorilla	ENSGGOG00000003699	2 retrocopies	retro_ggor_1241, retro_ggor_263 ,
Myotis lucifugus	ENSMLUG00000024944	1 retrocopy	retro_mluc_2336,
Macaca mulatta	ENSMMUG00000000249	2 retrocopies	retro_mmul_1334, retro_mmul_1567,
Monodelphis domestica	ENSMODG00000014179	1 retrocopy	retro_mdom_410,
Mustela putorius furo	ENSMPUG00000005617	1 retrocopy	retro_mputfur_444,
Mus musculus	ENSMUSG00000001794	1 retrocopy	retro_mmus_80,
Nomascus leucogenys	ENSNLEG00000011712	2 retrocopies	retro_nleu_1328, retro_nleu_992,
Pongo abelii	ENSPPYG00000009898	2 retrocopies	retro_pabe_1359, retro_pabe_448,
Pelodiscus sinensis	ENSPSIG00000012793	1 retrocopy	retro_psin_45,
Pan troglodytes	ENSPTRG00000010887	2 retrocopies	retro_ptro_1112, retro_ptro_168,
Pteropus vampyrus	ENSPVAG00000012885	3 retrocopies	retro_pvam_1375, retro_pvam_639, retro_pvam_737,
Rattus norvegicus	ENSRNOG00000045747	2 retrocopies	retro_rnor_1447, retro_rnor_2145,
Sorex araneus	ENSSARG00000004266	1 retrocopy	retro_sara_215,
Sus scrofa	ENSSSCG00000030149	2 retrocopies	retro_sscr_495, retro_sscr_73,
Ictidomys tridecemlineatus	ENSSTOG00000026235	1 retrocopy	retro_itri_342,
Vicugna pacos	ENSVPAG00000008074	1 retrocopy	retro_vpac_64,