RetrogeneDB ID: retro_ggor_2966

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: X:134438486..134439131(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGGOG00000027459
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RAB28
• Ensembl ID: ENSGGOG00000024190
• Aliases: None
• Description: None

Sequence

>retro_ggor_2966
ATGTAGGACTCTAAGGAAGAGAGCCAGGACCAGCACTGAAAATCATTGTGCTAGGGAACAGCACCTCCCGGAAGACCTCC
TTAGCTACAGATTTTGCTCAAAAAACTTTCAGGAACCAGTACAAACTATAGGACTGGATTTCGTTTGAGAAGGATAACAT
TGCCAGGAAACTTGAATGTTACTCTCTAGTTTGGGATACAGGAGGCCAGACAATAGGAAGCAAAATGTTGGACAGATCCA
TCTATGGAGCACAGGAAATCATCTTGGTATATGGTATTACGAGTTATCAAAGCTTTGAGAATTTTTAGAAGATTAGTGAA
GAAAGTGAGTGAAGAGTCAGAAACTCAGCCACTGGTTACCTTAGTGGGCAATAAAATTGATTTGGAGCACAATCGAACAG
TAAAACCTGAAAAACACTTACGGTTTTGCCAGGAAAATGGTTTTAATAGCCACTTTGTTTCAGCCAAGGCAAGAGACTCT
GTCTTCCTGTGTTTTCAAAAAGTTGTTGCTGAAATCCTTGGAATCAAATTAAACAAAGCAGAAATAGAACAGTCACAGAG
GGTGGTAAAGGCAGATATTGTAAACTACAACCAGGAACCTATGGCAAGAGCTGTTAACCCTTCTAGAAGCTGTGTGTGTG
CAGTT

Alignment

ORF - retro_ggor_2966 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.33 %
• Parental protein coverage: 99.55 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MSDSEEESQDRQ-LKIVVLGDGASGKTSLTTC-FAQETFGKQYKQTIGLDFF-LRRITLPGNLNVTL-QI
          M.DS.EESQD...LKI.VLG...S.KTSL.T..F....F.....QTIGLDF..LRRITLPGNLNVTL...
Retrocopy M*DSKEESQDQH<LKIIVLGNSTSRKTSLATD<FCSKNF-QEPVQTIGLDFV<LRRITLPGNLNVTL<LV

Parental  WDIGGQTIGGKMLDKYIYGAQGVLLVYDITNYQSFENLEDWYTV-VKKVSEESETQPLVALVGNKIDLEH
          WD.GGQTIG.KMLD..IYGAQ...LVY.IT...S....E......VKKVSEESETQPLV.LVGNKIDLEH
Retrocopy WDTGGQTIGSKMLDRSIYGAQEIILVYGIT---SYQSFENF*KI>VKKVSEESETQPLVTLVGNKIDLEH

Parental  MRTIKPEKHLRFCQENGFSSHFVSAKTGDSVFLCFQKVAAEILGIKLNKAEIEQSQRVVKADIVNYNQEP
          .RT.KPEKHLRFCQENGF.SHFVSAK..DSVFLCFQKV.AEILGIKLNKAEIEQSQRVVKADIVNYNQEP
Retrocopy NRTVKPEKHLRFCQENGFNSHFVSAKARDSVFLCFQKVVAEILGIKLNKAEIEQSQRVVKADIVNYNQEP

Parental  MSRTVNPPRSSMCAV
          M.R.VNP.RS..CAV
Retrocopy MARAVNPSRSCVCAV

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	0.82 RPM	24.79 RPM
SRP007412_cerebellum	1.54 RPM	24.15 RPM
SRP007412_heart	0.38 RPM	5.32 RPM
SRP007412_kidney	0.82 RPM	13.74 RPM
SRP007412_liver	0.40 RPM	8.34 RPM
SRP007412_testis	0.31 RPM	62.89 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_2966 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2966 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4762
Pongo abelii	retro_pabe_3707

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001523	1 retrocopy	retro_chof_1365,
Callithrix jacchus	ENSCJAG00000012136	2 retrocopies	retro_cjac_2713, retro_cjac_4126,
Dasypus novemcinctus	ENSDNOG00000007750	4 retrocopies	retro_dnov_1426, retro_dnov_1771, retro_dnov_2419, retro_dnov_381,
Dipodomys ordii	ENSDORG00000012378	1 retrocopy	retro_dord_682,
Homo sapiens	ENSG00000157869	7 retrocopies	retro_hsap_4166, retro_hsap_4259, retro_hsap_4261, retro_hsap_4263, retro_hsap_4265, retro_hsap_4317, retro_hsap_4762,
Gorilla gorilla	ENSGGOG00000024190	1 retrocopy	retro_ggor_2966 ,
Macropus eugenii	ENSMEUG00000006792	4 retrocopies	retro_meug_1079, retro_meug_1182, retro_meug_1510, retro_meug_913,
Macaca mulatta	ENSMMUG00000022025	1 retrocopy	retro_mmul_1172,
Nomascus leucogenys	ENSNLEG00000016243	1 retrocopy	retro_nleu_2292,
Pongo abelii	ENSPPYG00000014610	1 retrocopy	retro_pabe_3707,
Pan troglodytes	ENSPTRG00000015920	2 retrocopies	retro_ptro_2893, retro_ptro_3171,
Rattus norvegicus	ENSRNOG00000017074	1 retrocopy	retro_rnor_1075,
Sarcophilus harrisii	ENSSHAG00000009274	1 retrocopy	retro_shar_602,
Sus scrofa	ENSSSCG00000022358	2 retrocopies	retro_sscr_482, retro_sscr_514,
Ictidomys tridecemlineatus	ENSSTOG00000004135	1 retrocopy	retro_itri_27,
Tarsius syrichta	ENSTSYG00000010939	2 retrocopies	retro_tsyr_1450, retro_tsyr_1750,