RetrogeneDB ID: retro_hsap_3829

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 7:24945753..24946198(-)
• Located in intron of: ENSG00000070882

Retrocopy information

• Ensembl ID: ENSG00000234999
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SNRPC
• Ensembl ID: ENSG00000124562
• Aliases: None
• Description: small nuclear ribonucleoprotein polypeptide C [Source:HGNC Symbol;Acc:11157]

Sequence

>retro_hsap_3829
TGTGACTACTGCAATAAATACCTCACTCATGACTCTTCATCTGTGCAAAAGATACTCTACAGTGATATCTACAAAGAGAA
TATGAAAGACTGCTGTCAGAATGGGGTGGAAGAGCAGCTCAGAGCCTGATGGACGAAACAATGGCTGCACTTCAACAAGG
AAAGGTTCCTCCTACTCCATTCTCTGCCTCTCCCCAGCAGGGGCAATGATCCCACCTCCTCGCAAGTCTCCCGGCTCCTC
TTTGCCCTGGTATGATGCCTGCACCTCCTATAAGTGGCCATCCCATGATGTCAGTGATGGGTTCTCCTCCTCCTGGGATG
ATGCCAGTGGGACCTGCTCCTGGAATGAGGCTGCCATGGGAGGTCACATGCCAATGATGCCTAGGCCTCCAGTGATGGAA
CCTCCTACCTGCTCCGTGATGATGCCTGCTGAGCCCAGAATGACT

Alignment

ORF - retro_hsap_3829 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.53 %
• Parental protein coverage: 94.34 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  CDYCDTYLTHDSPSVRKTHCSGRKHKENVKDYYQKWMEEQ-AQSLIDKTTAAFQQGKIPPTPFSAPP-PA
          CDYC..YLTHDS.SV.K...S....KEN.KD..Q...EEQ.AQSL.D.T.AA.QQGK.PPTPFSA.P.PA
Retrocopy CDYCNKYLTHDSSSVQKILYSDI-YKENMKDCCQNGVEEQ<AQSLMDETMAALQQGKVPPTPFSASP<PA

Parental  GAMIPPP-PSLPGPPRPGMMPAPHMGGPPMMPMMGPPPPGMMPVGPAPGMRPP-MGGHMPMMPGPPMMRP
          GAMIPPP..SLP.P..PGMMPAP...G.PMM..MG.PPPGMMPVGPAPGMR.P.MGGHMPMMP.PP.M.P
Retrocopy GAMIPPP>ASLPAPLCPGMMPAPPISGHPMMSVMGSPPPGMMPVGPAPGMRLP<MGGHMPMMPRPPVMEP

Parental  PARPMMVPTRPGMT
          P....M.P..P.MT
Retrocopy PTCSVMMPAEPRMT

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	16.28 RPM
bodymap2_adrenal	0.08 RPM	31.52 RPM
bodymap2_brain	0.00 RPM	15.14 RPM
bodymap2_breast	0.02 RPM	17.49 RPM
bodymap2_colon	0.00 RPM	19.55 RPM
bodymap2_heart	0.00 RPM	37.37 RPM
bodymap2_kidney	0.17 RPM	21.86 RPM
bodymap2_liver	0.00 RPM	20.30 RPM
bodymap2_lung	0.00 RPM	18.11 RPM
bodymap2_lymph_node	0.00 RPM	26.79 RPM
bodymap2_ovary	0.06 RPM	20.88 RPM
bodymap2_prostate	0.00 RPM	32.53 RPM
bodymap2_skeletal_muscle	0.00 RPM	28.50 RPM
bodymap2_testis	0.00 RPM	49.11 RPM
bodymap2_thyroid	0.00 RPM	29.04 RPM
bodymap2_white_blood_cells	0.00 RPM	27.72 RPM

ChIP-Seq

RNA Polymerase II actvity may be related with retro_hsap_3829 in 2 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF002CJZ	POLR2A	7:24947066..24947616
ENCFF002CMI	POLR2A	7:24947166..24947464

EST

No EST(s) were mapped for retro_hsap_3829 retrocopy.

TSS

No TSS is located nearby retro_hsap_3829 retrocopy 5' end.

Lab

retro_hsap_3829 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3829 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2606
Gorilla gorilla	retro_ggor_2577
Pongo abelii	retro_pabe_3066
Macaca mulatta	retro_mmul_1626
Callithrix jacchus	retro_cjac_3056

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 48 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000024549	1 retrocopy	retro_btau_1636,
Canis familiaris	ENSCAFG00000001231	3 retrocopies	retro_cfam_348, retro_cfam_402, retro_cfam_409,
Callithrix jacchus	ENSCJAG00000015321	16 retrocopies	retro_cjac_1009, retro_cjac_1015, retro_cjac_1064, retro_cjac_1750, retro_cjac_1937, retro_cjac_2014, retro_cjac_2395, retro_cjac_2456, retro_cjac_2785, retro_cjac_3056, retro_cjac_3110, retro_cjac_400, retro_cjac_4010, retro_cjac_617, retro_cjac_770, retro_cjac_873,
Homo sapiens	ENSG00000124562	6 retrocopies	retro_hsap_1531, retro_hsap_1866, retro_hsap_2865, retro_hsap_3195, retro_hsap_3829 , retro_hsap_4241,
Loxodonta africana	ENSLAFG00000013534	2 retrocopies	retro_lafr_621, retro_lafr_878,
Monodelphis domestica	ENSMODG00000013904	1 retrocopy	retro_mdom_22,
Nomascus leucogenys	ENSNLEG00000008392	2 retrocopies	retro_nleu_2129, retro_nleu_99,
Oryctolagus cuniculus	ENSOCUG00000026668	3 retrocopies	retro_ocun_1019, retro_ocun_184, retro_ocun_196,
Otolemur garnettii	ENSOGAG00000008755	9 retrocopies	retro_ogar_1040, retro_ogar_130, retro_ogar_1763, retro_ogar_183, retro_ogar_2434, retro_ogar_3064, retro_ogar_3322, retro_ogar_3377, retro_ogar_697,
Pongo abelii	ENSPPYG00000017272	4 retrocopies	retro_pabe_1271, retro_pabe_3066, retro_pabe_3225, retro_pabe_915,
Sarcophilus harrisii	ENSSHAG00000000945	1 retrocopy	retro_shar_112,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.00 RPM
CEU_NA11843	0.06 RPM
CEU_NA11930	0.03 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.04 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	0.08 RPM
FIN_HG00277	0.04 RPM
FIN_HG00315	0.00 RPM
FIN_HG00321	0.03 RPM
FIN_HG00328	0.05 RPM
FIN_HG00338	0.02 RPM
FIN_HG00349	0.00 RPM
FIN_HG00375	0.05 RPM
FIN_HG00377	0.00 RPM
FIN_HG00378	0.02 RPM
GBR_HG00099	0.06 RPM
GBR_HG00111	0.04 RPM
GBR_HG00114	0.08 RPM
GBR_HG00119	0.10 RPM
GBR_HG00131	0.14 RPM
GBR_HG00133	0.05 RPM
GBR_HG00134	0.02 RPM
GBR_HG00137	0.11 RPM
GBR_HG00142	0.03 RPM
GBR_HG00143	0.10 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.10 RPM
TSI_NA20518	0.00 RPM
TSI_NA20532	0.14 RPM
TSI_NA20538	0.09 RPM
TSI_NA20756	0.03 RPM
TSI_NA20765	0.00 RPM
TSI_NA20771	0.00 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.03 RPM
YRI_NA18870	0.07 RPM
YRI_NA18907	0.10 RPM
YRI_NA18916	0.00 RPM
YRI_NA19093	0.03 RPM
YRI_NA19099	0.03 RPM
YRI_NA19114	0.03 RPM
YRI_NA19118	0.04 RPM
YRI_NA19213	0.02 RPM
YRI_NA19214	0.00 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).