RetrogeneDB ID: retro_ggor_2192

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 5:85893336..85893713(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGGOG00000027517
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: EIF3K
• Ensembl ID: ENSGGOG00000016808
• Aliases: None
• Description: None

Sequence

>retro_ggor_2192
CATCAAGAAGAGTGGCCATCTGACAGATTTTGTATCTCAAGGACCTGCTGGAGACCAGCCTCTTTCAGGCCTTCTGGGAA
GCCCTGGATGAAAACGTGGACCTCTTGGAAGGTATAACTGGCTTTGAAGACTCTGTCCGAATGTGTATCTGCCCTGTCGT
GGGTATCACTTACCAGCACATCGACCACTGGCTGCTGGCCGAGATGCCTGGGTATCTGTCGGACAGCCAGCTGAAGGTGT
GGATGAGAAAATACACCTGGAGGGCTGACGAGTCCCGGCAGATCTTCATCTGTAGCCAGGAAGAGAACATTAAGCCCAAG
AACCCTGTGGAGAAGATAGATTTCGACAGTGTGTCCAGCATCATGGCCTTCTTCCAG

Alignment

ORF - retro_ggor_2192 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.89 %
• Parental protein coverage: 58.06 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NQEERP-IRQILYLGDLLETCHFQAFWQALDENMDLLEGITGFEDSVRKFICHVVGITYQHIDRWLLAEM
          .QEE.P.I.QILYL.DLLET..FQAFW.ALDEN.DLLEGITGFEDSVR..IC.VVGITYQHID.WLLAEM
Retrocopy HQEEWP<I*QILYLKDLLETSLFQAFWEALDENVDLLEGITGFEDSVRMCICPVVGITYQHIDHWLLAEM

Parental  LGDLSDSQLKVWMSKYGWSADESGQIFICSQEESIKPKNIVEKIDFDSVSSIMASSQ
          .G.LSDSQLKVWM.KY.W.ADES.QIFICSQEE.IKPKN.VEKIDFDSVSSIMA..Q
Retrocopy PGYLSDSQLKVWMRKYTWRADESRQIFICSQEENIKPKNPVEKIDFDSVSSIMAFFQ

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	51.93 RPM
SRP007412_cerebellum	0.12 RPM	51.34 RPM
SRP007412_heart	0.09 RPM	34.40 RPM
SRP007412_kidney	0.12 RPM	70.25 RPM
SRP007412_liver	0.03 RPM	57.19 RPM
SRP007412_testis	0.00 RPM	41.23 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_2192 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2192 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3224
Pan troglodytes	retro_ptro_2176
Pongo abelii	retro_pabe_2673
Macaca mulatta	retro_mmul_2029
Macaca mulatta	retro_mmul_2098

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000007594	3 retrocopies	retro_etel_1653, retro_etel_1868, retro_etel_5,
Homo sapiens	ENSG00000178982	2 retrocopies	retro_hsap_2616, retro_hsap_3224,
Gorilla gorilla	ENSGGOG00000016808	1 retrocopy	retro_ggor_2192 ,
Myotis lucifugus	ENSMLUG00000010217	1 retrocopy	retro_mluc_645,
Macaca mulatta	ENSMMUG00000028767	2 retrocopies	retro_mmul_1478, retro_mmul_2029,
Monodelphis domestica	ENSMODG00000013314	3 retrocopies	retro_mdom_1235, retro_mdom_1929, retro_mdom_781,
Otolemur garnettii	ENSOGAG00000026260	1 retrocopy	retro_ogar_413,
Pongo abelii	ENSPPYG00000025857	4 retrocopies	retro_pabe_2342, retro_pabe_2555, retro_pabe_2610, retro_pabe_2673,
Pan troglodytes	ENSPTRG00000010934	2 retrocopies	retro_ptro_1763, retro_ptro_2176,
Rattus norvegicus	ENSRNOG00000020495	3 retrocopies	retro_rnor_1128, retro_rnor_2039, retro_rnor_513,
Sarcophilus harrisii	ENSSHAG00000005313	1 retrocopy	retro_shar_689,
Tarsius syrichta	ENSTSYG00000007001	1 retrocopy	retro_tsyr_1964,