RetrogeneDB ID: retro_ggor_1958

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 3:92881922..92882197(-)
• Located in intron of: ENSGGOG00000009491

Retrocopy information

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

Parental gene information

• Parental gene symbol: HSPE1
• Ensembl ID: ENSGGOG00000027944
• Aliases: None
• Description: None

Sequence

>retro_ggor_1958
TTCTGCTCTTTGACCGAGTGTTGTTTGGCTGAAAGTGGTGCAGCCAAAACCGTAACCAAAGAAGGCATTATGCTTCCAGA
AAAGTCTCAGGAAAAGCATTGCAAGCAACAGTAGTAGCTGTTCGATTGGGCCCTAAAGGAAAGGGATTCAAGCAGTCAGT
GTGAAAGCTGGAGATAAAGTACTTCTCTCAGAATATGGAGGCACCAAAGTAATTCTAGACCACAAGGATTATTTTTTTAT
TTAGAGATTGTGACATTCTTGGAAAGTAGGTAGAC

Alignment

ORF - retro_ggor_1958 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.16 %
• Parental protein coverage: 92.16 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  FLPLFDRVLVERSAAETVTKGGIMLPEKSQ-GKVLQATVVAVGSGSKG-KGGEIQPVSVKVGDKVLLPEY
          F..L....L.E..AA.TVTK.GIMLPEKSQ.GK.LQATVVAV..G.KG.KG..IQ.VSVK.GDKVLL.EY
Retrocopy FCSLTECCLAESGAAKTVTKEGIMLPEKSQ<GKALQATVVAVRLGPKG<KG--IQAVSVKAGDKVLLSEY

Parental  GGTKVVLDDKDY-FLFRDGDILGKYVD
          GGTKV.LD.KDY.FLFRD.DILGK.VD
Retrocopy GGTKVILDHKDY>FLFRDCDILGK*VD

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	0.00 RPM	66.03 RPM
SRP007412_cerebellum	0.00 RPM	33.29 RPM
SRP007412_heart	0.00 RPM	38.15 RPM
SRP007412_kidney	0.00 RPM	204.49 RPM
SRP007412_liver	0.05 RPM	113.82 RPM
SRP007412_testis	0.00 RPM	58.53 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_1958 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1958 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1908

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 87 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007417	17 retrocopies	retro_chof_1048, retro_chof_1160, retro_chof_143, retro_chof_1476, retro_chof_1561, retro_chof_1755, retro_chof_1880, retro_chof_2052, retro_chof_2053, retro_chof_226, retro_chof_303, retro_chof_414, retro_chof_420, retro_chof_86, retro_chof_907, retro_chof_91, retro_chof_940,
Callithrix jacchus	ENSCJAG00000004008	1 retrocopy	retro_cjac_254,
Dasypus novemcinctus	ENSDNOG00000013246	27 retrocopies	retro_dnov_1088, retro_dnov_1117, retro_dnov_1214, retro_dnov_1375, retro_dnov_1391, retro_dnov_1405, retro_dnov_1412, retro_dnov_1428, retro_dnov_1445, retro_dnov_1546, retro_dnov_1647, retro_dnov_1652, retro_dnov_1686, retro_dnov_1821, retro_dnov_2176, retro_dnov_2291, retro_dnov_2413, retro_dnov_2569, retro_dnov_2625, retro_dnov_2652, retro_dnov_418, retro_dnov_481, retro_dnov_483, retro_dnov_490, retro_dnov_524, retro_dnov_554, retro_dnov_966,
Erinaceus europaeus	ENSEEUG00000005040	6 retrocopies	retro_eeur_132, retro_eeur_278, retro_eeur_474, retro_eeur_611, retro_eeur_657, retro_eeur_698,
Gorilla gorilla	ENSGGOG00000027944	17 retrocopies	retro_ggor_1051, retro_ggor_117, retro_ggor_1243, retro_ggor_1545, retro_ggor_157, retro_ggor_1676, retro_ggor_1821, retro_ggor_1956, retro_ggor_1957, retro_ggor_1958 , retro_ggor_2331, retro_ggor_2391, retro_ggor_2476, retro_ggor_2492, retro_ggor_775, retro_ggor_841, retro_ggor_897,
Mus musculus	ENSMUSG00000073676	11 retrocopies	retro_mmus_1005, retro_mmus_1719, retro_mmus_1750, retro_mmus_1934, retro_mmus_2483, retro_mmus_2485, retro_mmus_301, retro_mmus_3077, retro_mmus_386, retro_mmus_872, retro_mmus_877,
Procavia capensis	ENSPCAG00000009541	1 retrocopy	retro_pcap_330,
Sus scrofa	ENSSSCG00000016078	7 retrocopies	retro_sscr_103, retro_sscr_1059, retro_sscr_106, retro_sscr_1088, retro_sscr_294, retro_sscr_298, retro_sscr_401,