RetrogeneDB ID: retro_hsap_2772

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 3:37058013..37058478(-)
• Located in intron of: ENSG00000076242

Retrocopy information

• Ensembl ID: ENSG00000224858
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPL29
• Ensembl ID: ENSG00000162244
• Aliases: RPL29, HIP, HUMRPL29, L29, RPL29P10, RPL29_3_370
• Description: ribosomal protein L29 [Source:HGNC Symbol;Acc:10331]

Sequence

>retro_hsap_2772
ATGGCGAAGTCCAAGAACCACACCACACACAACCAGTCCCGAAAATGGCACAGAAATGGTATCAAGAAACCCCGATCACA
AAGATACGAATCTCTTAAGGGGGTGGACCCCAAGTTCCTGAGGAACATGCACTTTGCCAAGAAGCACAACAAGAAGGGCC
TAAAGAAGATGCAGGCCAACAATGCCAAGGCCATGAGTGCACGTGCCGAGGCTATCAAGGCCCTCGTAAAGCCCAAGGAG
GTTAAGCCCAAGATCCCAAAGGGTGTCAGCCGCAAGCTCGATCGACTTGCCTACATTGCCCATCCCAAGCTTGGGAAGCG
TGCTCGTGCCCGTATTGCCAAGGGGCTCAGGCTGTGCCGGCCAAAGGCCAAGGCCAAGGATCAAACCAAGGCCCAGGCTG
CAGCTCCACCTTCAGTTCCAGCTCAGGCTCCCAAAGGTGCCCAGGCCCCTACAAAGGCTTCAGAG

Alignment

ORF - retro_hsap_2772 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.97 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAKSKNHTTHNQSRKWHRNGIKKPRSQRYESLKGVDPKFLRNMRFAKKHNKKGLKKMQANNAKAMSARAE
          MAKSKNHTTHNQSRKWHRNGIKKPRSQRYESLKGVDPKFLRNM.FAKKHNKKGLKKMQANNAKAMSARAE
Retrocopy MAKSKNHTTHNQSRKWHRNGIKKPRSQRYESLKGVDPKFLRNMHFAKKHNKKGLKKMQANNAKAMSARAE

Parental  AIKALVKPKEVKPKIPKGVSRKLDRLAYIAHPKLGKRARARIAKGLRLCRPKAKAKAKAKDQTKAQAAAP
          AIKALVKPKEVKPKIPKGVSRKLDRLAYIAHPKLGKRARARIAKGLRLCRPKAKAK....DQTKAQAAAP
Retrocopy AIKALVKPKEVKPKIPKGVSRKLDRLAYIAHPKLGKRARARIAKGLRLCRPKAKAK----DQTKAQAAAP

Parental  ASVPAQAPKRTQAPTKASE
          .SVPAQAPK..QAPTKASE
Retrocopy PSVPAQAPKGAQAPTKASE

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	0.42 RPM	345.40 RPM
bodymap2_adrenal	0.45 RPM	368.49 RPM
bodymap2_brain	0.23 RPM	44.84 RPM
bodymap2_breast	0.16 RPM	226.07 RPM
bodymap2_colon	0.04 RPM	351.62 RPM
bodymap2_heart	0.09 RPM	82.58 RPM
bodymap2_kidney	0.00 RPM	143.27 RPM
bodymap2_liver	0.00 RPM	120.41 RPM
bodymap2_lung	0.30 RPM	323.61 RPM
bodymap2_lymph_node	0.57 RPM	374.43 RPM
bodymap2_ovary	0.50 RPM	388.74 RPM
bodymap2_prostate	0.17 RPM	379.29 RPM
bodymap2_skeletal_muscle	0.22 RPM	419.30 RPM
bodymap2_testis	0.06 RPM	194.98 RPM
bodymap2_thyroid	0.32 RPM	207.95 RPM
bodymap2_white_blood_cells	0.00 RPM	354.52 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_2772 was not detected

EST

No EST(s) were mapped for retro_hsap_2772 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_134414	504 libraries	865 libraries	450 libraries	9 libraries	1 library

The graphical summary, for retro_hsap_2772 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_2772 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2772 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_1929

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 186 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009163	6 retrocopies	retro_amel_1373, retro_amel_1740, retro_amel_345, retro_amel_379, retro_amel_686, retro_amel_913,
Callithrix jacchus	ENSCJAG00000005951	9 retrocopies	retro_cjac_135, retro_cjac_160, retro_cjac_241, retro_cjac_29, retro_cjac_331, retro_cjac_348, retro_cjac_358, retro_cjac_73, retro_cjac_96,
Felis catus	ENSFCAG00000001762	9 retrocopies	retro_fcat_1032, retro_fcat_1132, retro_fcat_1753, retro_fcat_1774, retro_fcat_1897, retro_fcat_249, retro_fcat_485, retro_fcat_687, retro_fcat_952,
Homo sapiens	ENSG00000162244	23 retrocopies	retro_hsap_1098, retro_hsap_1146, retro_hsap_123, retro_hsap_1283, retro_hsap_1406, retro_hsap_1587, retro_hsap_170, retro_hsap_1759, retro_hsap_2053, retro_hsap_2358, retro_hsap_263, retro_hsap_2772 , retro_hsap_2899, retro_hsap_3201, retro_hsap_3289, retro_hsap_3316, retro_hsap_3511, retro_hsap_3562, retro_hsap_3951, retro_hsap_3998, retro_hsap_4304, retro_hsap_863, retro_hsap_882,
Gorilla gorilla	ENSGGOG00000024691	16 retrocopies	retro_ggor_1007, retro_ggor_1090, retro_ggor_1205, retro_ggor_1315, retro_ggor_1330, retro_ggor_142, retro_ggor_1480, retro_ggor_1929, retro_ggor_224, retro_ggor_2247, retro_ggor_254, retro_ggor_2684, retro_ggor_312, retro_ggor_715, retro_ggor_863, retro_ggor_892,
Microcebus murinus	ENSMICG00000002705	9 retrocopies	retro_mmur_192, retro_mmur_198, retro_mmur_303, retro_mmur_446, retro_mmur_508, retro_mmur_519, retro_mmur_657, retro_mmur_816, retro_mmur_938,
Myotis lucifugus	ENSMLUG00000015088	14 retrocopies	retro_mluc_1086, retro_mluc_1160, retro_mluc_134, retro_mluc_1377, retro_mluc_1699, retro_mluc_1955, retro_mluc_2228, retro_mluc_2522, retro_mluc_2523, retro_mluc_2575, retro_mluc_297, retro_mluc_421, retro_mluc_889, retro_mluc_915,
Macaca mulatta	ENSMMUG00000019248	2 retrocopies	retro_mmul_1352, retro_mmul_218,
Monodelphis domestica	ENSMODG00000028750	17 retrocopies	retro_mdom_1013, retro_mdom_1187, retro_mdom_1201, retro_mdom_1328, retro_mdom_1445, retro_mdom_1452, retro_mdom_1505, retro_mdom_1532, retro_mdom_1604, retro_mdom_1665, retro_mdom_1904, retro_mdom_35, retro_mdom_504, retro_mdom_589, retro_mdom_612, retro_mdom_639, retro_mdom_995,
Mustela putorius furo	ENSMPUG00000011734	6 retrocopies	retro_mputfur_137, retro_mputfur_187, retro_mputfur_370, retro_mputfur_467, retro_mputfur_816, retro_mputfur_970,
Mus musculus	ENSMUSG00000048758	3 retrocopies	retro_mmus_203, retro_mmus_231, retro_mmus_86,
Otolemur garnettii	ENSOGAG00000013766	2 retrocopies	retro_ogar_290, retro_ogar_31,
Ochotona princeps	ENSOPRG00000008821	10 retrocopies	retro_opri_1166, retro_opri_277, retro_opri_373, retro_opri_535, retro_opri_607, retro_opri_69, retro_opri_700, retro_opri_877, retro_opri_983, retro_opri_99,
Pongo abelii	ENSPPYG00000013818	21 retrocopies	retro_pabe_1062, retro_pabe_1162, retro_pabe_1306, retro_pabe_1503, retro_pabe_1714, retro_pabe_1882, retro_pabe_2125, retro_pabe_2131, retro_pabe_2398, retro_pabe_2718, retro_pabe_2952, retro_pabe_3254, retro_pabe_3284, retro_pabe_3504, retro_pabe_3525, retro_pabe_404, retro_pabe_459, retro_pabe_491, retro_pabe_673, retro_pabe_687, retro_pabe_911,
Rattus norvegicus	ENSRNOG00000011138	15 retrocopies	retro_rnor_1045, retro_rnor_1158, retro_rnor_1161, retro_rnor_1422, retro_rnor_1702, retro_rnor_184, retro_rnor_1951, retro_rnor_2207, retro_rnor_2222, retro_rnor_2356, retro_rnor_2561, retro_rnor_338, retro_rnor_397, retro_rnor_63, retro_rnor_928,
Sorex araneus	ENSSARG00000013572	8 retrocopies	retro_sara_108, retro_sara_309, retro_sara_329, retro_sara_347, retro_sara_400, retro_sara_53, retro_sara_637, retro_sara_669,
Sarcophilus harrisii	ENSSHAG00000006854	2 retrocopies	retro_shar_355, retro_shar_444,
Ictidomys tridecemlineatus	ENSSTOG00000020488	14 retrocopies	retro_itri_1345, retro_itri_1433, retro_itri_1482, retro_itri_1586, retro_itri_1664, retro_itri_1667, retro_itri_194, retro_itri_482, retro_itri_520, retro_itri_592, retro_itri_622, retro_itri_874, retro_itri_934, retro_itri_942,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.26 RPM
CEU_NA11843	0.28 RPM
CEU_NA11930	0.33 RPM
CEU_NA12004	0.27 RPM
CEU_NA12400	0.28 RPM
CEU_NA12751	0.36 RPM
CEU_NA12760	0.27 RPM
CEU_NA12827	0.38 RPM
CEU_NA12872	0.41 RPM
CEU_NA12873	0.45 RPM
FIN_HG00183	0.69 RPM
FIN_HG00277	0.26 RPM
FIN_HG00315	0.39 RPM
FIN_HG00321	0.39 RPM
FIN_HG00328	0.28 RPM
FIN_HG00338	0.21 RPM
FIN_HG00349	0.28 RPM
FIN_HG00375	0.34 RPM
FIN_HG00377	0.10 RPM
FIN_HG00378	0.34 RPM
GBR_HG00099	0.17 RPM
GBR_HG00111	0.17 RPM
GBR_HG00114	0.08 RPM
GBR_HG00119	0.22 RPM
GBR_HG00131	0.29 RPM
GBR_HG00133	0.19 RPM
GBR_HG00134	0.26 RPM
GBR_HG00137	0.36 RPM
GBR_HG00142	0.36 RPM
GBR_HG00143	0.13 RPM
TSI_NA20512	0.31 RPM
TSI_NA20513	0.24 RPM
TSI_NA20518	0.36 RPM
TSI_NA20532	0.24 RPM
TSI_NA20538	0.28 RPM
TSI_NA20756	0.20 RPM
TSI_NA20765	0.23 RPM
TSI_NA20771	0.31 RPM
TSI_NA20786	0.18 RPM
TSI_NA20798	0.37 RPM
YRI_NA18870	0.51 RPM
YRI_NA18907	0.17 RPM
YRI_NA18916	0.15 RPM
YRI_NA19093	0.13 RPM
YRI_NA19099	0.19 RPM
YRI_NA19114	0.29 RPM
YRI_NA19118	0.25 RPM
YRI_NA19213	0.33 RPM
YRI_NA19214	0.15 RPM
YRI_NA19223	0.16 RPM

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Indel association:

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