RetrogeneDB ID: retro_hsap_3708

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 7:20866944..20867365(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000219451
• Aliases: RPL23P8, RPL23_4_790
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPL23
• Ensembl ID: ENSG00000125691
• Aliases: None
• Description: ribosomal protein L23 [Source:HGNC Symbol;Acc:10316]

Sequence

>retro_hsap_3708
ATGTGGAAGCGAGGACGTGGTGGGTCCTCTGGTGTGAACTTCCGGATTTCTGTGGGTCTTCCGGTAGGAGCTGTGATCAA
CTGTGCTGACAACACAGGAGCCAAAAACCTGTATATCATCTCCGTGAAGGGGATCAAGGGACGGCTGAACAGACTTCCCG
CTGCTGGTGTGGGTGACATGGGGATGGCTACAGTCAAGAAAGGGAAACTAGAGCTCAGAAAAAAGGTACATCCAGCAGTG
GTCATTTGACAATGAAAGTCATACCAGAGAAAAGATGGCGTGTTTCTTTCTTTTGAAGATAATGCAGTGGTCATAGTGGG
CAATAAAGGCCAGATGAAAGGTTCTGCCATTACAGGACCAGTAGCAAAGGAGTGTGCAGACTTGTGGCCCCCGGATTGTG
TCCGATGCTGGCAGCATTGCG

Alignment

ORF - retro_hsap_3708 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.65 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSKRGRGGSSGAKFRISLGLPVGAVINCADNTGAKNLYIISVKGIKGRLNRLPAAGVGDMVMATVKKGKP
          M.KRGRGGSSG..FRIS.GLPVGAVINCADNTGAKNLYIISVKGIKGRLNRLPAAGVGDM.MATVKKGK.
Retrocopy MWKRGRGGSSGVNFRISVGLPVGAVINCADNTGAKNLYIISVKGIKGRLNRLPAAGVGDMGMATVKKGKL

Parental  ELRKKVHPAVVIRQRKSYRRKDGVFLYFEDNAGVIVNNKGEMKGSAITGPVAKECADLW-PRIASNAGSI
          ELRKKVHPAVVI.Q.KSY.RKDGVFL.FEDNA.VIV.NKG.MKGSAITGPVAKECADLW.PRI.S.AGSI
Retrocopy ELRKKVHPAVVI*Q*KSYQRKDGVFLSFEDNAVVIVGNKGQMKGSAITGPVAKECADLW>PRIVSDAGSI

Parental  A
          A
Retrocopy A

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	0.76 RPM	648.40 RPM
bodymap2_adrenal	1.23 RPM	671.03 RPM
bodymap2_brain	0.16 RPM	181.66 RPM
bodymap2_breast	1.01 RPM	478.08 RPM
bodymap2_colon	0.33 RPM	795.05 RPM
bodymap2_heart	0.06 RPM	211.75 RPM
bodymap2_kidney	0.06 RPM	330.39 RPM
bodymap2_liver	0.02 RPM	243.03 RPM
bodymap2_lung	0.18 RPM	749.49 RPM
bodymap2_lymph_node	0.04 RPM	752.78 RPM
bodymap2_ovary	1.25 RPM	891.59 RPM
bodymap2_prostate	0.17 RPM	911.16 RPM
bodymap2_skeletal_muscle	0.02 RPM	556.95 RPM
bodymap2_testis	0.32 RPM	483.20 RPM
bodymap2_thyroid	0.40 RPM	340.24 RPM
bodymap2_white_blood_cells	0.14 RPM	835.22 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_3708 was not detected

EST

No EST(s) were mapped for retro_hsap_3708 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_173764	532 libraries	615 libraries	631 libraries	50 libraries	1 library

The graphical summary, for retro_hsap_3708 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_3708 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3708 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2512
Pongo abelii	retro_pabe_3147
Macaca mulatta	retro_mmul_1705

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 89 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004268	6 retrocopies	retro_amel_1791, retro_amel_226, retro_amel_308, retro_amel_880, retro_amel_918, retro_amel_990,
Callithrix jacchus	ENSCJAG00000008311	9 retrocopies	retro_cjac_1129, retro_cjac_1483, retro_cjac_2283, retro_cjac_2598, retro_cjac_2639, retro_cjac_2772, retro_cjac_2885, retro_cjac_3128, retro_cjac_3831,
Dipodomys ordii	ENSDORG00000001372	3 retrocopies	retro_dord_366, retro_dord_475, retro_dord_530,
Felis catus	ENSFCAG00000014502	10 retrocopies	retro_fcat_1022, retro_fcat_1431, retro_fcat_1707, retro_fcat_1708, retro_fcat_1959, retro_fcat_242, retro_fcat_296, retro_fcat_716, retro_fcat_756, retro_fcat_859,
Homo sapiens	ENSG00000125691	9 retrocopies	retro_hsap_2211, retro_hsap_2213, retro_hsap_2522, retro_hsap_3581, retro_hsap_3708 , retro_hsap_3710, retro_hsap_4042, retro_hsap_4106, retro_hsap_556,
Latimeria chalumnae	ENSLACG00000004430	1 retrocopy	retro_lcha_16,
Macaca mulatta	ENSMMUG00000004502	9 retrocopies	retro_mmul_1598, retro_mmul_1705, retro_mmul_1955, retro_mmul_2366, retro_mmul_2391, retro_mmul_384, retro_mmul_928, retro_mmul_930, retro_mmul_935,
Nomascus leucogenys	ENSNLEG00000000642	7 retrocopies	retro_nleu_1506, retro_nleu_181, retro_nleu_2056, retro_nleu_2337, retro_nleu_2988, retro_nleu_574, retro_nleu_8,
Oryctolagus cuniculus	ENSOCUG00000013915	6 retrocopies	retro_ocun_1027, retro_ocun_1196, retro_ocun_1270, retro_ocun_1919, retro_ocun_251, retro_ocun_482,
Otolemur garnettii	ENSOGAG00000012445	7 retrocopies	retro_ogar_1050, retro_ogar_1645, retro_ogar_1695, retro_ogar_2250, retro_ogar_277, retro_ogar_3145, retro_ogar_539,
Ochotona princeps	ENSOPRG00000001957	10 retrocopies	retro_opri_1079, retro_opri_1216, retro_opri_137, retro_opri_14, retro_opri_178, retro_opri_202, retro_opri_224, retro_opri_481, retro_opri_639, retro_opri_684,
Rattus norvegicus	ENSRNOG00000004107	10 retrocopies	retro_rnor_1195, retro_rnor_1539, retro_rnor_1622, retro_rnor_2445, retro_rnor_2483, retro_rnor_2688, retro_rnor_2981, retro_rnor_347, retro_rnor_498, retro_rnor_941,
Ictidomys tridecemlineatus	ENSSTOG00000014279	2 retrocopies	retro_itri_122, retro_itri_1577,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.19 RPM
CEU_NA11843	0.17 RPM
CEU_NA11930	0.20 RPM
CEU_NA12004	0.08 RPM
CEU_NA12400	0.11 RPM
CEU_NA12751	0.17 RPM
CEU_NA12760	0.13 RPM
CEU_NA12827	0.09 RPM
CEU_NA12872	0.14 RPM
CEU_NA12873	0.32 RPM
FIN_HG00183	0.19 RPM
FIN_HG00277	0.22 RPM
FIN_HG00315	0.19 RPM
FIN_HG00321	0.09 RPM
FIN_HG00328	0.07 RPM
FIN_HG00338	0.26 RPM
FIN_HG00349	0.17 RPM
FIN_HG00375	0.10 RPM
FIN_HG00377	0.10 RPM
FIN_HG00378	0.17 RPM
GBR_HG00099	0.06 RPM
GBR_HG00111	0.02 RPM
GBR_HG00114	0.11 RPM
GBR_HG00119	0.17 RPM
GBR_HG00131	0.06 RPM
GBR_HG00133	0.05 RPM
GBR_HG00134	0.17 RPM
GBR_HG00137	0.05 RPM
GBR_HG00142	0.06 RPM
GBR_HG00143	0.03 RPM
TSI_NA20512	0.14 RPM
TSI_NA20513	0.05 RPM
TSI_NA20518	0.11 RPM
TSI_NA20532	0.27 RPM
TSI_NA20538	0.37 RPM
TSI_NA20756	0.12 RPM
TSI_NA20765	0.17 RPM
TSI_NA20771	0.03 RPM
TSI_NA20786	0.05 RPM
TSI_NA20798	0.03 RPM
YRI_NA18870	0.07 RPM
YRI_NA18907	0.03 RPM
YRI_NA18916	0.13 RPM
YRI_NA19093	0.08 RPM
YRI_NA19099	0.03 RPM
YRI_NA19114	0.13 RPM
YRI_NA19118	0.08 RPM
YRI_NA19213	0.00 RPM
YRI_NA19214	0.07 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).