RetrogeneDB ID: retro_ggor_293

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 1:131366928..131367223(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGGOG00000024846
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: HMGN3
• Ensembl ID: ENSGGOG00000006910
• Aliases: None
• Description: None

Sequence

>retro_ggor_293
ATGCAGAAGAGAAAGTCTCCAGAGAATACAGAGGGCAAAGATGGCTCTAAAGTAACTAAACAGGAGCCCACAAGATGGTC
TCCCAAATTGTCAGCAAAACCTCCTCCACCAAAGCCTGGACCCAAACCAAGAAAAACATCTGCTAAGAAAGAACCTGGAG
CAAAGGTTAGCAGAGGTGCTAAAGAGAAGAAAGGAAAAGTAGGAAGCTGGAAAGGAAGGTACTGCACCAGCTGAAAATGA
TGAAACTAAAGCTGAAGAGGCACAGAAAACTGAATCTGGAGATAACCAGGGAGAA

Alignment

ORF - retro_ggor_293 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68. %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPKRKSPENTEGKDGSKVTKQEPTRRSARLSAKPAPPKP-EPKPRKTSAKKEPGAKISRGAKGKKEEKQE
          M.KRKSPENTEGKDGSKVTKQEPTR.S..LSAKP.PPKP..P...K....K..........K..KE.K.E
Retrocopy MQKRKSPENTEGKDGSKVTKQEPTRWSPKLSAKPPPPKP>DPNQEKHLLRKNLEQRLAEVLKRRKE-K*E

Parental  AGKEGTAPSENGETKAEEAQKTESVDNEGE
          AGKEGTAP.EN.ETKAEEAQKTES.DN.GE
Retrocopy AGKEGTAPAENDETKAEEAQKTESGDNQGE

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	32.70 RPM
SRP007412_cerebellum	0.00 RPM	44.99 RPM
SRP007412_heart	0.00 RPM	40.74 RPM
SRP007412_kidney	0.00 RPM	76.67 RPM
SRP007412_liver	0.00 RPM	39.96 RPM
SRP007412_testis	0.00 RPM	32.74 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_293 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_293 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007015	1 retrocopy	retro_chof_2241,
Cavia porcellus	ENSCPOG00000012407	2 retrocopies	retro_cpor_1399, retro_cpor_147,
Felis catus	ENSFCAG00000028793	1 retrocopy	retro_fcat_1400,
Homo sapiens	ENSG00000118418	1 retrocopy	retro_hsap_231,
Gorilla gorilla	ENSGGOG00000006910	1 retrocopy	retro_ggor_293 ,
Macaca mulatta	ENSMMUG00000004351	1 retrocopy	retro_mmul_414,
Nomascus leucogenys	ENSNLEG00000012377	2 retrocopies	retro_nleu_68, retro_nleu_851,
Otolemur garnettii	ENSOGAG00000016487	1 retrocopy	retro_ogar_190,
Ochotona princeps	ENSOPRG00000009611	1 retrocopy	retro_opri_799,
Pan troglodytes	ENSPTRG00000018366	2 retrocopies	retro_ptro_1427, retro_ptro_200,
Ictidomys tridecemlineatus	ENSSTOG00000014353	1 retrocopy	retro_itri_251,
Tupaia belangeri	ENSTBEG00000015468	3 retrocopies	retro_tbel_1912, retro_tbel_4714, retro_tbel_615,
Tarsius syrichta	ENSTSYG00000005238	3 retrocopies	retro_tsyr_1569, retro_tsyr_268, retro_tsyr_976,