RetrogeneDB ID: retro_hsap_4263

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 9:46918103..46918437(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000236825
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RAB28
• Ensembl ID: ENSG00000157869
• Aliases: RAB28, CORD18
• Description: RAB28, member RAS oncogene family [Source:HGNC Symbol;Acc:9768]

Sequence

>retro_hsap_4263
GATGGGTACATTGTACTGAAGAAAGTGAGCGAAGAGTCAGAAGCTTTGCTACTGGTTGCCTTGGTGAGCAATAAAATTTA
TTTGGAGCACATGGAAACAGTAAAACCTGAAAAACACTTATGGTTTTGCCAGGAAAATGGTTTTAGTAGCCACTTTATCT
CAGCCAAGACAGGAGACTGTCTTCCTGTATTTTCAGAAAGTTGCTAATGAAATCCTTGGACTCAAATTAAACAAAGCAGA
AAAATAGAAGAGTCAGAGAGTGGTGAAGGCAGGTATTGGAAACTACAACCAGGCCCCCAGAATGGTGACTCTTCCTACAA
GCTCTATGTCTGCA

Alignment

ORF - retro_hsap_4263 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.38 %
• Parental protein coverage: 51.58 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DWYTVVKKVSEESETQPLVALVGNKIDLEHMRTIKPEKHLRFCQENGFSSHFVSAKTGDSV-FLCFQKVA
          D.Y.V.KKVSEESE...LVALV.NKI.LEHM.T.KPEKHL.FCQENGFSSHF.SAKTGD......F.K..
Retrocopy DGYIVLKKVSEESEALLLVALVSNKIYLEHMETVKPEKHLWFCQENGFSSHFISAKTGDCL<SCIFRKLL

Parental  AEIL-GIKLNKAEIEQSQRVVKADIVNYNQEPMSRTVNPPRSSMCA
          ...L.G.KLNKAE...SQRVVKA.I.NYNQ.P..R.V..P.SSM.A
Retrocopy MKSL<GLKLNKAEK*KSQRVVKAGIGNYNQAP--RMVTLPTSSMSA

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
bodymap2_adipose	0.00 RPM	14.67 RPM
bodymap2_adrenal	0.00 RPM	14.02 RPM
bodymap2_brain	0.00 RPM	20.72 RPM
bodymap2_breast	0.00 RPM	17.24 RPM
bodymap2_colon	0.00 RPM	17.42 RPM
bodymap2_heart	0.00 RPM	15.67 RPM
bodymap2_kidney	0.00 RPM	17.85 RPM
bodymap2_liver	0.00 RPM	5.20 RPM
bodymap2_lung	0.00 RPM	24.05 RPM
bodymap2_lymph_node	0.00 RPM	17.93 RPM
bodymap2_ovary	0.00 RPM	29.67 RPM
bodymap2_prostate	0.00 RPM	20.94 RPM
bodymap2_skeletal_muscle	0.00 RPM	6.00 RPM
bodymap2_testis	0.00 RPM	48.40 RPM
bodymap2_thyroid	0.00 RPM	19.09 RPM
bodymap2_white_blood_cells	0.00 RPM	19.33 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_4263 was not detected

EST

No EST(s) were mapped for retro_hsap_4263 retrocopy.

TSS

No TSS is located nearby retro_hsap_4263 retrocopy 5' end.

Lab

retro_hsap_4263 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_4263 has 0 orthologous retrocopies within eutheria group .

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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,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.00 RPM
CEU_NA11843	0.00 RPM
CEU_NA11930	0.00 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.00 RPM
CEU_NA12751	0.00 RPM
CEU_NA12760	0.00 RPM
CEU_NA12827	0.00 RPM
CEU_NA12872	0.00 RPM
CEU_NA12873	0.00 RPM
FIN_HG00183	0.00 RPM
FIN_HG00277	0.00 RPM
FIN_HG00315	0.00 RPM
FIN_HG00321	0.00 RPM
FIN_HG00328	0.00 RPM
FIN_HG00338	0.00 RPM
FIN_HG00349	0.00 RPM
FIN_HG00375	0.00 RPM
FIN_HG00377	0.00 RPM
FIN_HG00378	0.00 RPM
GBR_HG00099	0.00 RPM
GBR_HG00111	0.00 RPM
GBR_HG00114	0.00 RPM
GBR_HG00119	0.00 RPM
GBR_HG00131	0.00 RPM
GBR_HG00133	0.00 RPM
GBR_HG00134	0.00 RPM
GBR_HG00137	0.00 RPM
GBR_HG00142	0.00 RPM
GBR_HG00143	0.00 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.00 RPM
TSI_NA20518	0.00 RPM
TSI_NA20532	0.00 RPM
TSI_NA20538	0.00 RPM
TSI_NA20756	0.00 RPM
TSI_NA20765	0.00 RPM
TSI_NA20771	0.00 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.00 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.00 RPM
YRI_NA19093	0.00 RPM
YRI_NA19099	0.00 RPM
YRI_NA19114	0.00 RPM
YRI_NA19118	0.00 RPM
YRI_NA19213	0.00 RPM
YRI_NA19214	0.00 RPM
YRI_NA19223	0.00 RPM

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Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).