RetrogeneDB ID: retro_hsap_4910

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: X:136523419..136523995(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000237584
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RAC1
• Ensembl ID: ENSG00000136238
• Aliases: RAC1, Rac-1, TC-25, p21-Rac1
• Description: ras-related C3 botulinum toxin substrate 1 (rho family, small GTP binding protein Rac1) [Source:HGNC Symbol;Acc:9801]

Sequence

>retro_hsap_4910
ATGCAGGCCATCAAGGGTGTGGTGGTGGGAGACGGAGCTGTAGGTAAAACTTGCCTACTGATCAGTTACACAACCAACGC
ATTTCCTGGAGAAGATATCCCTACTGCCTTTGACAATTATTCTGCCAATGTTATGGTAGATGGAAAACTGGTGAATCTGG
GCTTATGGAATACAGCTGGACAAGAAGATTATGACAGATTACGCCCCCTATCCTATCCGCAAGCAGATGTGTTCTTAATT
TGCTTTTCGCTTGTGAGTCCTGCATCATTTGAAAATGTCCTTGCAAAGTGGTATCCTGAGGTGCAGCACCACTGTCCCAA
CACTCCCATTATCCTAGTGGGAACTAAACTTGATCTTAGGGATGATAAAGACAGGATCCAGAAACTGAAGGAGAAGAAGC
TAACTCCCATCACCTATCCGCAGGGTCTAGCCATGGCTAAGGAGATGGGTGCTGTAAAATACCTGGAGTGCTTGGCCCTC
ACAAGGCGAGGCCTCAAGACAGTGTTTGACGAAGCGATCCGAGCTGTCCTCTGCCCACCTCCCGTGAAGAAGAGGAAGAG
AAAATGCCTGCAGTTG

Alignment

ORF - retro_hsap_4910 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.71 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MQAIKCVVVGDGAVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPVNLGLWDTAGQEDYDRLRPL
          MQAIK.VVVGDGAVGKTCLLISYTTNAFPGE.IPT.FDNYSANVMVDGK.VNLGLW.TAGQEDYDRLRPL
Retrocopy MQAIKGVVVGDGAVGKTCLLISYTTNAFPGEDIPTAFDNYSANVMVDGKLVNLGLWNTAGQEDYDRLRPL

Parental  SYPQTDVFLICFSLVSPASFENVRAKWYPEVRHHCPNTPIILVGTKLDLRDDKDTIEKLKEKKLTPITYP
          SYPQ.DVFLICFSLVSPASFENV.AKWYPEV.HHCPNTPIILVGTKLDLRDDKD.I.KLKEKKLTPITYP
Retrocopy SYPQADVFLICFSLVSPASFENVLAKWYPEVQHHCPNTPIILVGTKLDLRDDKDRIQKLKEKKLTPITYP

Parental  QGLAMAKEIGAVKYLECSALTQRGLKTVFDEAIRAVLCPPPVKKRKRKCLLL
          QGLAMAKE.GAVKYLEC.ALT.RGLKTVFDEAIRAVLCPPPVKKRKRKCL.L
Retrocopy QGLAMAKEMGAVKYLECLALTRRGLKTVFDEAIRAVLCPPPVKKRKRKCLQL

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	299.08 RPM
bodymap2_adrenal	0.00 RPM	316.19 RPM
bodymap2_brain	0.02 RPM	421.92 RPM
bodymap2_breast	0.02 RPM	323.35 RPM
bodymap2_colon	0.00 RPM	312.24 RPM
bodymap2_heart	0.00 RPM	153.30 RPM
bodymap2_kidney	0.00 RPM	226.02 RPM
bodymap2_liver	0.00 RPM	109.86 RPM
bodymap2_lung	0.00 RPM	367.58 RPM
bodymap2_lymph_node	0.00 RPM	226.96 RPM
bodymap2_ovary	0.00 RPM	345.11 RPM
bodymap2_prostate	0.00 RPM	336.25 RPM
bodymap2_skeletal_muscle	0.02 RPM	296.79 RPM
bodymap2_testis	0.00 RPM	223.28 RPM
bodymap2_thyroid	0.00 RPM	299.27 RPM
bodymap2_white_blood_cells	0.00 RPM	226.06 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_4910 was not detected

EST

No EST(s) were mapped for retro_hsap_4910 retrocopy.

TSS

No TSS is located nearby retro_hsap_4910 retrocopy 5' end.

Lab

retro_hsap_4910 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_4910 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_3274
Gorilla gorilla	retro_ggor_217
Pongo abelii	retro_pabe_3818
Macaca mulatta	retro_mmul_2642

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000070831	6 retrocopies	retro_hsap_2775, retro_hsap_2968, retro_hsap_3028, retro_hsap_3404, retro_hsap_3848, retro_hsap_4013,
Homo sapiens	ENSG00000119729	3 retrocopies	retro_hsap_1333, retro_hsap_2158, retro_hsap_2316,
Homo sapiens	ENSG00000136238	6 retrocopies	retro_hsap_1256, retro_hsap_1925, retro_hsap_28, retro_hsap_3036, retro_hsap_3072, retro_hsap_4910 ,
Gorilla gorilla	ENSGGOG00000026733	2 retrocopies	retro_ggor_2110, retro_ggor_217,
Mus musculus	ENSMUSG00000001847	2 retrocopies	retro_mmus_1372, retro_mmus_234,
Pan troglodytes	ENSPTRG00000018910	4 retrocopies	retro_ptro_1288, retro_ptro_3044, retro_ptro_3274, retro_ptro_36,
Rattus norvegicus	ENSRNOG00000001068	1 retrocopy	retro_rnor_230,
Ictidomys tridecemlineatus	ENSSTOG00000006784	1 retrocopy	retro_itri_1503,
Tupaia belangeri	ENSTBEG00000007272	4 retrocopies	retro_tbel_1796, retro_tbel_2564, retro_tbel_4296, retro_tbel_9,
Tarsius syrichta	ENSTSYG00000001618	2 retrocopies	retro_tsyr_2027, retro_tsyr_2068,
Xenopus tropicalis	ENSXETG00000027593	1 retrocopy	retro_xtro_1,

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	0.03 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).