RetrogeneDB ID: retro_hsap_2925

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 4:42473826..42474183(+)
• Located in intron of: ENSG00000124406

Retrocopy information

• Ensembl ID: ENSG00000240167
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPS7
• Ensembl ID: ENSG00000171863
• Aliases: RPS7, DBA8, S7
• Description: ribosomal protein S7 [Source:HGNC Symbol;Acc:10440]

Sequence

>retro_hsap_2925
ATGTTCATTTCAAGCACCAAGACTGTGAAGCCCAACAGCGAGACGCCAAACGAGTTAAGAGTCCGGCATCTTTCAGGCTC
TTCTGGAGCTGGAGATAAACTCGGACCTCAAGGCTCAGCTCAGGAAGCTGAGTATTACAGCAGCCAAAGAGCCTAAGTTG
GTGGTGTCCAGAAAGCTATCATAATCTTTGTTCCTGTTCCTCAACTGAAATCTTTCCAGAAAATCCAACTCTGGCTAGTA
CGTGAATTGGAGAAAAAGTTCAGTGGGAAGCATGCTGTCTTTATTGCTCAGAGGAGAATTCTGCCTAAGCCAGCTTGAAA
AAGCCATACAAAAAATAAGCAAAAACATCCTAGGAGC

Alignment

ORF - retro_hsap_2925 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.17 %
• Parental protein coverage: 61.34 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MFSSSAKIVKPNGEKPDEF-ESGISQALLELEMNSDLKAQLRELNITAAKEIE-VGGGRKAIIIFVPVPQ
          MF.SS.K.VKPN.E.P.E..ESGI.QALLELE.NSDLKAQLR.L.ITAAKE...VGG..KAIIIFVPVPQ
Retrocopy MFISSTKTVKPNSETPNEL>ESGIFQALLELEINSDLKAQLRKLSITAAKEPK<VGGVQKAIIIFVPVPQ

Parental  LKSFQKIQVRLVRELEKKFSGKHVVFIAQRRILPKPTRKSRTKNKQKRPRS
          LKSFQKIQ..LVRELEKKFSGKH.VFIAQRRILPKP..KS.TKNKQK.PRS
Retrocopy LKSFQKIQLWLVRELEKKFSGKHAVFIAQRRILPKPA*KSHTKNKQKHPRS

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	175.50 RPM
bodymap2_adrenal	0.00 RPM	361.59 RPM
bodymap2_brain	0.00 RPM	61.53 RPM
bodymap2_breast	0.06 RPM	167.10 RPM
bodymap2_colon	0.00 RPM	318.25 RPM
bodymap2_heart	0.00 RPM	125.79 RPM
bodymap2_kidney	0.00 RPM	187.12 RPM
bodymap2_liver	0.00 RPM	209.80 RPM
bodymap2_lung	0.14 RPM	502.62 RPM
bodymap2_lymph_node	0.00 RPM	539.69 RPM
bodymap2_ovary	0.00 RPM	308.45 RPM
bodymap2_prostate	0.00 RPM	603.61 RPM
bodymap2_skeletal_muscle	0.00 RPM	151.58 RPM
bodymap2_testis	0.00 RPM	215.28 RPM
bodymap2_thyroid	0.19 RPM	178.44 RPM
bodymap2_white_blood_cells	0.00 RPM	583.74 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_2925 was not detected

EST

No EST(s) were mapped for retro_hsap_2925 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_143975	1641 libraries	167 libraries	14 libraries	2 libraries	5 libraries

The graphical summary, for retro_hsap_2925 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_hsap_2925 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2925 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_2028

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 54 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000171863	14 retrocopies	retro_hsap_111, retro_hsap_112, retro_hsap_1242, retro_hsap_1737, retro_hsap_1837, retro_hsap_2907, retro_hsap_2925 , retro_hsap_329, retro_hsap_3635, retro_hsap_404, retro_hsap_4711, retro_hsap_4760, retro_hsap_528, retro_hsap_703,
Loxodonta africana	ENSLAFG00000015087	11 retrocopies	retro_lafr_1223, retro_lafr_160, retro_lafr_217, retro_lafr_318, retro_lafr_319, retro_lafr_413, retro_lafr_514, retro_lafr_720, retro_lafr_786, retro_lafr_964, retro_lafr_970,
Myotis lucifugus	ENSMLUG00000006121	1 retrocopy	retro_mluc_1118,
Macaca mulatta	ENSMMUG00000011870	7 retrocopies	retro_mmul_1831, retro_mmul_1846, retro_mmul_1929, retro_mmul_23, retro_mmul_2403, retro_mmul_2540, retro_mmul_357,
Monodelphis domestica	ENSMODG00000014495	2 retrocopies	retro_mdom_662, retro_mdom_810,
Mus musculus	ENSMUSG00000061477	2 retrocopies	retro_mmus_271, retro_mmus_53,
Oryctolagus cuniculus	ENSOCUG00000008507	2 retrocopies	retro_ocun_203, retro_ocun_230,
Otolemur garnettii	ENSOGAG00000028165	1 retrocopy	retro_ogar_133,
Pongo abelii	ENSPPYG00000025872	12 retrocopies	retro_pabe_1033, retro_pabe_1555, retro_pabe_2506, retro_pabe_2982, retro_pabe_2983, retro_pabe_31, retro_pabe_313, retro_pabe_360, retro_pabe_3659, retro_pabe_3803, retro_pabe_499, retro_pabe_524,
Rattus norvegicus	ENSRNOG00000008551	2 retrocopies	retro_rnor_39, retro_rnor_391,

Population studies

Expression level across human populations :

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

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Indel association:

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