RetrogeneDB ID: retro_hsap_1364

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 14:74949917..74950208(+)
• Located in intron of: ENSG00000119655

Retrocopy information

• Ensembl ID: ENSG00000258769
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RAP1A
• Ensembl ID: ENSG00000116473
• Aliases: RAP1A, KREV-1, KREV1, RAP1, SMGP21
• Description: RAP1A, member of RAS oncogene family [Source:HGNC Symbol;Acc:9855]

Sequence

>retro_hsap_1364
CAGTCCACGTTTGACTTACAGGACCTGAGGGAACAGATTTTACTGGTTAAGGACACAGAAGATGTTCCAATGATTTTGGT
TGGCAATAAATGTGACCTGGAAGATGAGTGAGTAGTTGGCAAAGAACAGGGCCAGAATTTAGCATGACAGTGATGGAACT
GTGCCATTTTAGAATAATCTGCAAAGTCAAAGGTCAATGTTAATGAAATATTTTATGACCTGGTCAGACAGATAAATAGA
AAAACACCAGTGGAAAAGAAACAGCCTAAAAAGAAATCATGTCTGCTGCTC

Alignment

ORF - retro_hsap_1364 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.8 %
• Parental protein coverage: 53.26 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QSTFNDLQDLREQILRVKDTEDVPMILVGNKCDLEDERVVGKEQGQNLARQWCNCAFLESSAKSKINVNE
          QSTF.DLQDLREQIL.VKDTEDVPMILVGNKCDLEDE.VVGKEQGQNLA.Q..NCA.LE.SAKSK.NVNE
Retrocopy QSTF-DLQDLREQILLVKDTEDVPMILVGNKCDLEDE*VVGKEQGQNLA*Q*WNCAILE*SAKSKVNVNE

Parental  IFYDLVRQINRKTPVEKKKPKKKSCLLL
          IFYDLVRQINRKTPVEKK.PKKKSCLLL
Retrocopy IFYDLVRQINRKTPVEKKQPKKKSCLLL

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	165.90 RPM
bodymap2_adrenal	0.29 RPM	161.01 RPM
bodymap2_brain	0.02 RPM	123.15 RPM
bodymap2_breast	0.00 RPM	108.70 RPM
bodymap2_colon	0.14 RPM	460.12 RPM
bodymap2_heart	0.02 RPM	137.41 RPM
bodymap2_kidney	0.00 RPM	129.29 RPM
bodymap2_liver	0.00 RPM	53.23 RPM
bodymap2_lung	0.00 RPM	186.53 RPM
bodymap2_lymph_node	0.15 RPM	167.13 RPM
bodymap2_ovary	0.06 RPM	114.74 RPM
bodymap2_prostate	0.00 RPM	383.76 RPM
bodymap2_skeletal_muscle	0.16 RPM	135.12 RPM
bodymap2_testis	0.23 RPM	134.40 RPM
bodymap2_thyroid	0.09 RPM	160.01 RPM
bodymap2_white_blood_cells	0.00 RPM	292.70 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_1364 was not detected

EST

No EST(s) were mapped for retro_hsap_1364 retrocopy.

TSS

No TSS is located nearby retro_hsap_1364 retrocopy 5' end.

Lab

retro_hsap_1364 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1364 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_937
Pongo abelii	retro_pabe_1132
Callithrix jacchus	retro_cjac_728

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 47 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005384	1 retrocopy	retro_amel_1764,
Canis familiaris	ENSCAFG00000013686	1 retrocopy	retro_cfam_696,
Callithrix jacchus	ENSCJAG00000013392	7 retrocopies	retro_cjac_1671, retro_cjac_2218, retro_cjac_3376, retro_cjac_3707, retro_cjac_3843, retro_cjac_3844, retro_cjac_728,
Dasypus novemcinctus	ENSDNOG00000007809	5 retrocopies	retro_dnov_101, retro_dnov_1617, retro_dnov_1764, retro_dnov_628, retro_dnov_94,
Equus caballus	ENSECAG00000016434	1 retrocopy	retro_ecab_99,
Erinaceus europaeus	ENSEEUG00000010446	2 retrocopies	retro_eeur_306, retro_eeur_361,
Echinops telfairi	ENSETEG00000016893	2 retrocopies	retro_etel_1196, retro_etel_176,
Homo sapiens	ENSG00000006451	2 retrocopies	retro_hsap_1136, retro_hsap_3707,
Homo sapiens	ENSG00000116473	1 retrocopy	retro_hsap_1364 ,
Homo sapiens	ENSG00000127314	2 retrocopies	retro_hsap_3338, retro_hsap_4234,
Homo sapiens	ENSG00000133703	1 retrocopy	retro_hsap_3474,
Myotis lucifugus	ENSMLUG00000010571	3 retrocopies	retro_mluc_2311, retro_mluc_2312, retro_mluc_2313,
Monodelphis domestica	ENSMODG00000001323	3 retrocopies	retro_mdom_1327, retro_mdom_139, retro_mdom_1777,
Mus musculus	ENSMUSG00000068798	2 retrocopies	retro_mmus_1963, retro_mmus_3027,
Nomascus leucogenys	ENSNLEG00000004018	1 retrocopy	retro_nleu_1069,
Ochotona princeps	ENSOPRG00000003999	3 retrocopies	retro_opri_321, retro_opri_460, retro_opri_875,
Pongo abelii	ENSPPYG00000001028	1 retrocopy	retro_pabe_1132,
Pan troglodytes	ENSPTRG00000001102	1 retrocopy	retro_ptro_937,
Rattus norvegicus	ENSRNOG00000032463	3 retrocopies	retro_rnor_1147, retro_rnor_1494, retro_rnor_1639,
Ictidomys tridecemlineatus	ENSSTOG00000027847	1 retrocopy	retro_itri_81,
Tarsius syrichta	ENSTSYG00000004521	3 retrocopies	retro_tsyr_1546, retro_tsyr_1829, retro_tsyr_2140,
Vicugna pacos	ENSVPAG00000010033	1 retrocopy	retro_vpac_491,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.02 RPM
CEU_NA11843	0.03 RPM
CEU_NA11930	0.00 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.07 RPM
CEU_NA12751	0.05 RPM
CEU_NA12760	0.04 RPM
CEU_NA12827	0.14 RPM
CEU_NA12872	0.05 RPM
CEU_NA12873	0.03 RPM
FIN_HG00183	0.05 RPM
FIN_HG00277	0.15 RPM
FIN_HG00315	0.06 RPM
FIN_HG00321	0.06 RPM
FIN_HG00328	0.05 RPM
FIN_HG00338	0.00 RPM
FIN_HG00349	0.00 RPM
FIN_HG00375	0.02 RPM
FIN_HG00377	0.00 RPM
FIN_HG00378	0.04 RPM
GBR_HG00099	0.03 RPM
GBR_HG00111	0.02 RPM
GBR_HG00114	0.08 RPM
GBR_HG00119	0.05 RPM
GBR_HG00131	0.00 RPM
GBR_HG00133	0.00 RPM
GBR_HG00134	0.07 RPM
GBR_HG00137	0.03 RPM
GBR_HG00142	0.08 RPM
GBR_HG00143	0.00 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.07 RPM
TSI_NA20518	0.11 RPM
TSI_NA20532	0.10 RPM
TSI_NA20538	0.05 RPM
TSI_NA20756	0.00 RPM
TSI_NA20765	0.04 RPM
TSI_NA20771	0.06 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.06 RPM
YRI_NA18870	0.03 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.02 RPM
YRI_NA19093	0.05 RPM
YRI_NA19099	0.03 RPM
YRI_NA19114	0.00 RPM
YRI_NA19118	0.06 RPM
YRI_NA19213	0.14 RPM
YRI_NA19214	0.05 RPM
YRI_NA19223	0.02 RPM

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Indel association:

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