RetrogeneDB ID: retro_ggor_1254

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 16:4808659..4809039(-)
• Located in intron of: ENSGGOG00000004639

Retrocopy information

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

Parental gene information

• Parental gene symbol: SUB1
• Ensembl ID: ENSGGOG00000027033
• Aliases: None
• Description: None

Sequence

>retro_ggor_1254
ATGCCTAAAGCAAAGGAACTTGTTTCTTCAAACTCTTCTGGCAGTGATTCTGACAGTGAGGTTGACAAAAAGTTAAAGAG
GAAAAAGCAAGTTGCTCCAGAAAAACCTGTAAAGAAGCAAAAGACAGGCGAAACTTGGAGAGTTCTGTCATCTTCCGACA
GAGGAGCAGCAGCAGAGATGGTAACATGTTTCAGACTGGGAAAATGAGGTACGTTGGTGTTCAAGATTTTAAAGGCAAAG
TGCTAATTGATACTGGAGAATATTGGATGGATCCTGAAGGTGAAATGAAACCAGGAAGAAAAGGTATTTCTTTAAATCCA
GAACAATGGAGCCAGCTGACGGAACAGATTTCTGACATTGATGATACAGTAAAAAACCTG

Alignment

ORF - retro_ggor_1254 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.41 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPKSKELVSSSSSGSDSDSEVDKKL-KEK--GCNLPEIPFFKKKKMRSSRILVSSSFSSRPQFLLQIGKM
          MPK.KELVSS.SSGSDSDSEVDKKL.KE....C........K......S........SSR.....Q.GKM
Retrocopy MPKAKELVSSNSSGSDSDSEVDKKL<KEEKASCSRKTCKEAKDRRNLESSVIFRQRSSSRDGNMFQTGKM

Parental  RYVSVRDFKGKVLIDIREYWMDPEGEMKPGRKGISLNPEQWSQLKEQISDIDDAVRKL
          RYV.V.DFKGKVLID..EYWMDPEGEMKPGRKGISLNPEQWSQL.EQISDIDD.V..L
Retrocopy RYVGVQDFKGKVLIDTGEYWMDPEGEMKPGRKGISLNPEQWSQLTEQISDIDDTVKNL

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	3.07 RPM	21.10 RPM
SRP007412_cerebellum	1.46 RPM	11.31 RPM
SRP007412_heart	0.78 RPM	3.91 RPM
SRP007412_kidney	3.11 RPM	30.54 RPM
SRP007412_liver	2.93 RPM	19.94 RPM
SRP007412_testis	1.76 RPM	19.58 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_1254 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1254 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1662
Pongo abelii	retro_pabe_1371

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Parental genes homology:

Parental genes homology involve 25 parental genes, and 83 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006238	2 retrocopies	retro_amel_1331, retro_amel_794,
Canis familiaris	ENSCAFG00000018879	5 retrocopies	retro_cfam_1266, retro_cfam_1536, retro_cfam_1916, retro_cfam_2010, retro_cfam_215,
Callithrix jacchus	ENSCJAG00000018718	2 retrocopies	retro_cjac_1908, retro_cjac_484,
Cavia porcellus	ENSCPOG00000005584	4 retrocopies	retro_cpor_1114, retro_cpor_1481, retro_cpor_834, retro_cpor_854,
Dasypus novemcinctus	ENSDNOG00000007611	5 retrocopies	retro_dnov_1230, retro_dnov_161, retro_dnov_1822, retro_dnov_2156, retro_dnov_400,
Dipodomys ordii	ENSDORG00000013916	2 retrocopies	retro_dord_85, retro_dord_98,
Felis catus	ENSFCAG00000006012	2 retrocopies	retro_fcat_1052, retro_fcat_1313,
Homo sapiens	ENSG00000113387	2 retrocopies	retro_hsap_1662, retro_hsap_3934,
Gorilla gorilla	ENSGGOG00000027033	3 retrocopies	retro_ggor_1063, retro_ggor_1254 , retro_ggor_2645,
Loxodonta africana	ENSLAFG00000011006	1 retrocopy	retro_lafr_19,
Macropus eugenii	ENSMEUG00000007770	4 retrocopies	retro_meug_1155, retro_meug_1820, retro_meug_2038, retro_meug_500,
Microcebus murinus	ENSMICG00000014535	2 retrocopies	retro_mmur_1115, retro_mmur_17,
Myotis lucifugus	ENSMLUG00000013685	6 retrocopies	retro_mluc_1649, retro_mluc_1696, retro_mluc_1785, retro_mluc_226, retro_mluc_2346, retro_mluc_621,
Macaca mulatta	ENSMMUG00000011470	2 retrocopies	retro_mmul_2318, retro_mmul_993,
Monodelphis domestica	ENSMODG00000020410	3 retrocopies	retro_mdom_840, retro_mdom_841, retro_mdom_895,