RetrogeneDB ID: retro_hsap_2316

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 2:130970445..130971063(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000230756
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RHOQ
• Ensembl ID: ENSG00000119729
• Aliases: None
• Description: ras homolog family member Q [Source:HGNC Symbol;Acc:17736]

Sequence

>retro_hsap_2316
GTGGCTCACGGGCCTGGCGCGCTGATGCTCAAGTGCGTGGTGGTCGGCGACGGGGCGGTGGGCAAGACGTGCCCACTCAT
GAGCTATGCCAACGAAGCCTTCCCGGAGGAGTACGTGCCCACCGTCTTCGACCACTAAGCAGTCAGCGTCACTGTGGGGG
GCAAGTAGTACCTCCTAGGACTCTATGACACGGCCGGACAGGAAGACTATGACTGTCTGAGGCCTTTATCTTACCCAGTG
ACCGACGTCTTCCTTATATGCTTCTCGGTGGTAAATCCAGCCTCATTTCAAAATGTGAAAGAGGAGTGGGTACCGGAACT
TAAGGAATACGCACCAAATGTACCCTTTTTATTAATAAGAACTCAGATTGATCTCCGAGATGACCCCAAAACTTTAGCAA
GACTGAATGATATGAAAGAAAAACCTATATGTGTGGAACAAGGACAGAAACTAGCAAAAGAGATAGGAGCATGCTGCTAT
GTGGAATGTTCAGCTTTAACCCAGAAGGGATTGAAGACTGTTTTTGATGAGGCTATCATAGCCATTTTAACTCCAAAGAA
ACACACTGTAAAAAAAAAAAGAATAGGATCAAGATGTATAAACTGTTGTTTAATTACG

Alignment

ORF - retro_hsap_2316 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.69 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAHGPGALMLKCVVVGDGAVGKTCLLMSYANDAFPEEYVPTVFDHYAVSVTVGGKQYLLGLYDTAGQEDY
          .AHGPGALMLKCVVVGDGAVGKTC.LMSYAN.AFPEEYVPTVFDH.AVSVTVGGK.YLLGLYDTAGQEDY
Retrocopy VAHGPGALMLKCVVVGDGAVGKTCPLMSYANEAFPEEYVPTVFDH*AVSVTVGGK*YLLGLYDTAGQEDY

Parental  DRLRPLSYPMTDVFLICFSVVNPASFQNVKEEWVPELKEYAPNVPFLLIGTQIDLRDDPKTLARLNDMKE
          D.LRPLSYP.TDVFLICFSVVNPASFQNVKEEWVPELKEYAPNVPFLLI.TQIDLRDDPKTLARLNDMKE
Retrocopy DCLRPLSYPVTDVFLICFSVVNPASFQNVKEEWVPELKEYAPNVPFLLIRTQIDLRDDPKTLARLNDMKE

Parental  KPICVEQGQKLAKEIGACCYVECSALTQKGLKTVFDEAIIAILTPKKHT-VKKRIGSRCINCCLIT
          KPICVEQGQKLAKEIGACCYVECSALTQKGLKTVFDEAIIAILTPKKHT.....IGSRCINCCLIT
Retrocopy KPICVEQGQKLAKEIGACCYVECSALTQKGLKTVFDEAIIAILTPKKHTXXXXXIGSRCINCCLIT

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	0.02 RPM	155.90 RPM
bodymap2_adrenal	0.04 RPM	75.55 RPM
bodymap2_brain	0.05 RPM	72.38 RPM
bodymap2_breast	0.31 RPM	302.16 RPM
bodymap2_colon	0.10 RPM	144.05 RPM
bodymap2_heart	0.15 RPM	302.02 RPM
bodymap2_kidney	0.04 RPM	77.34 RPM
bodymap2_liver	0.00 RPM	19.35 RPM
bodymap2_lung	0.09 RPM	151.11 RPM
bodymap2_lymph_node	0.00 RPM	86.67 RPM
bodymap2_ovary	0.12 RPM	84.18 RPM
bodymap2_prostate	0.02 RPM	204.17 RPM
bodymap2_skeletal_muscle	0.04 RPM	148.10 RPM
bodymap2_testis	0.21 RPM	70.38 RPM
bodymap2_thyroid	0.08 RPM	100.73 RPM
bodymap2_white_blood_cells	0.00 RPM	84.19 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_2316 was not detected

EST

1 EST(s) were mapped to retro_hsap_2316 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AA969277	130970494	130970603	100	108	0	107

TSS

No TSS is located nearby retro_hsap_2316 retrocopy 5' end.

Lab

retro_hsap_2316 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2316 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_22

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000549	3 retrocopies	retro_chof_2030, retro_chof_457, retro_chof_914,
Callithrix jacchus	ENSCJAG00000000685	1 retrocopy	retro_cjac_2403,
Erinaceus europaeus	ENSEEUG00000015226	1 retrocopy	retro_eeur_129,
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,
Loxodonta africana	ENSLAFG00000004327	1 retrocopy	retro_lafr_316,
Microcebus murinus	ENSMICG00000009124	1 retrocopy	retro_mmur_29,
Otolemur garnettii	ENSOGAG00000033272	1 retrocopy	retro_ogar_742,
Pongo abelii	ENSPPYG00000012439	2 retrocopies	retro_pabe_1107, retro_pabe_2195,
Pteropus vampyrus	ENSPVAG00000013691	1 retrocopy	retro_pvam_611,
Rattus norvegicus	ENSRNOG00000015415	1 retrocopy	retro_rnor_473,
Sus scrofa	ENSSSCG00000008439	1 retrocopy	retro_sscr_102,
Tarsius syrichta	ENSTSYG00000002837	1 retrocopy	retro_tsyr_1609,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.06 RPM
CEU_NA11843	0.00 RPM
CEU_NA11930	0.07 RPM
CEU_NA12004	0.04 RPM
CEU_NA12400	0.00 RPM
CEU_NA12751	0.05 RPM
CEU_NA12760	0.04 RPM
CEU_NA12827	0.09 RPM
CEU_NA12872	0.03 RPM
CEU_NA12873	0.10 RPM
FIN_HG00183	0.00 RPM
FIN_HG00277	0.07 RPM
FIN_HG00315	0.03 RPM
FIN_HG00321	0.12 RPM
FIN_HG00328	0.02 RPM
FIN_HG00338	0.02 RPM
FIN_HG00349	0.00 RPM
FIN_HG00375	0.02 RPM
FIN_HG00377	0.05 RPM
FIN_HG00378	0.00 RPM
GBR_HG00099	0.09 RPM
GBR_HG00111	0.06 RPM
GBR_HG00114	0.00 RPM
GBR_HG00119	0.02 RPM
GBR_HG00131	0.00 RPM
GBR_HG00133	0.05 RPM
GBR_HG00134	0.02 RPM
GBR_HG00137	0.00 RPM
GBR_HG00142	0.08 RPM
GBR_HG00143	0.00 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.00 RPM
TSI_NA20518	0.08 RPM
TSI_NA20532	0.00 RPM
TSI_NA20538	0.00 RPM
TSI_NA20756	0.00 RPM
TSI_NA20765	0.06 RPM
TSI_NA20771	0.09 RPM
TSI_NA20786	0.05 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.00 RPM
YRI_NA18907	0.03 RPM
YRI_NA18916	0.02 RPM
YRI_NA19093	0.08 RPM
YRI_NA19099	0.03 RPM
YRI_NA19114	0.10 RPM
YRI_NA19118	0.04 RPM
YRI_NA19213	0.02 RPM
YRI_NA19214	0.05 RPM
YRI_NA19223	0.08 RPM

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Indel association:

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