RetrogeneDB ID: retro_hsap_238

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 1:159728959..159729376(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000235226
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPL27
• Ensembl ID: ENSG00000131469
• Aliases: RPL27, L27
• Description: ribosomal protein L27 [Source:HGNC Symbol;Acc:10328]

Sequence

>retro_hsap_238
ATGGGCAAGTTCATAAAACCTGGGAAAGTAGTGTTGGTCCAGGCCAGACACTACACCGGATGCTACTCTGGATGCAAAAC
CATCATCGTGAAGAACATTGATGATGGCACCTTAGAATGCCCCGTCAGCTGTTCTCTGGTGGCTGGAATTGACTGTTATC
CTTGCAAGGTGACAGCTGCCATGGGCAAGAAGAGCACCCAGAGGTCAAAGACCAAGTCTTTTGTGAAAGTTTATAACTAC
AATCATCTCATGCCCACAAGGCACTCTGTGGATACCCCCTTGGACAAAACTGTCATCAACAAGGATGTCTTCAGAGACCC
TGCTCTTAAACACAAGGCCCAAAGGAAGGCCAAAGTCAAAATCAAAGAGAGGTAAAACCTGGGCAAGAACAAGTGGCTCT
TCCAAAAGCTGTGGTTT

Alignment

ORF - retro_hsap_238 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.29 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGKFMKPGKVVLVLA----GRYSGRKAVIVKNIDDGTSDRPYSHALVAGIDRYPRKVTAAMGKKKIAKRS
          MGKF.KPGKVVLV.A....G.YSG.K..IVKNIDDGT...P.S..LVAGID.YP.KVTAAMGKK....RS
Retrocopy MGKFIKPGKVVLVQARHYTGCYSGCKTIIVKNIDDGTLECPVSCSLVAGIDCYPCKVTAAMGKKS-TQRS

Parental  KIKSFVKVYNYNHLMPTRYSVDIPLDKTVVNKDVFRDPALKRKARREAKVKFEERYKTGKNKWFFQKLRF
          K.KSFVKVYNYNHLMPTR.SVD.PLDKTV.NKDVFRDPALK.KA.R.AKVK..ER...GKNKW.FQKL.F
Retrocopy KTKSFVKVYNYNHLMPTRHSVDTPLDKTVINKDVFRDPALKHKAQRKAKVKIKER*NLGKNKWLFQKLWF

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	241.08 RPM
bodymap2_adrenal	0.00 RPM	363.66 RPM
bodymap2_brain	0.00 RPM	121.72 RPM
bodymap2_breast	0.10 RPM	201.25 RPM
bodymap2_colon	0.00 RPM	427.75 RPM
bodymap2_heart	0.00 RPM	164.32 RPM
bodymap2_kidney	0.00 RPM	141.79 RPM
bodymap2_liver	0.04 RPM	160.56 RPM
bodymap2_lung	0.00 RPM	512.69 RPM
bodymap2_lymph_node	0.00 RPM	489.64 RPM
bodymap2_ovary	0.00 RPM	349.24 RPM
bodymap2_prostate	0.00 RPM	572.27 RPM
bodymap2_skeletal_muscle	0.00 RPM	321.43 RPM
bodymap2_testis	0.00 RPM	320.22 RPM
bodymap2_thyroid	0.00 RPM	193.10 RPM
bodymap2_white_blood_cells	0.00 RPM	603.00 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_238 was not detected

EST

No EST(s) were mapped for retro_hsap_238 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_84285	515 libraries	813 libraries	488 libraries	12 libraries	1 library

The graphical summary, for retro_hsap_238 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_238 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_238 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_208
Gorilla gorilla	retro_ggor_298
Macaca mulatta	retro_mmul_418
Callithrix jacchus	retro_cjac_1630

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 112 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000200	3 retrocopies	retro_amel_122, retro_amel_37, retro_amel_674,
Bos taurus	ENSBTAG00000017441	6 retrocopies	retro_btau_1113, retro_btau_129, retro_btau_1565, retro_btau_1855, retro_btau_338, retro_btau_394,
Canis familiaris	ENSCAFG00000014630	6 retrocopies	retro_cfam_1193, retro_cfam_2109, retro_cfam_339, retro_cfam_364, retro_cfam_947, retro_cfam_959,
Callithrix jacchus	ENSCJAG00000013067	9 retrocopies	retro_cjac_1345, retro_cjac_1350, retro_cjac_1543, retro_cjac_1630, retro_cjac_2210, retro_cjac_275, retro_cjac_2828, retro_cjac_369, retro_cjac_776,
Felis catus	ENSFCAG00000013142	6 retrocopies	retro_fcat_1026, retro_fcat_1184, retro_fcat_1824, retro_fcat_228, retro_fcat_698, retro_fcat_78,
Homo sapiens	ENSG00000131469	6 retrocopies	retro_hsap_1161, retro_hsap_1312, retro_hsap_2112, retro_hsap_2204, retro_hsap_238 , retro_hsap_3787,
Gorilla gorilla	ENSGGOG00000026039	6 retrocopies	retro_ggor_1741, retro_ggor_1852, retro_ggor_2546, retro_ggor_2630, retro_ggor_298, retro_ggor_907,
Loxodonta africana	ENSLAFG00000014220	3 retrocopies	retro_lafr_443, retro_lafr_739, retro_lafr_965,
Microcebus murinus	ENSMICG00000014214	5 retrocopies	retro_mmur_1340, retro_mmur_1498, retro_mmur_1542, retro_mmur_673, retro_mmur_695,
Myotis lucifugus	ENSMLUG00000004119	1 retrocopy	retro_mluc_359,
Macaca mulatta	ENSMMUG00000008090	7 retrocopies	retro_mmul_1646, retro_mmul_1997, retro_mmul_418, retro_mmul_478, retro_mmul_52, retro_mmul_680, retro_mmul_925,
Monodelphis domestica	ENSMODG00000015128	1 retrocopy	retro_mdom_1141,
Mus musculus	ENSMUSG00000063316	2 retrocopies	retro_mmus_223, retro_mmus_277,
Nomascus leucogenys	ENSNLEG00000011901	2 retrocopies	retro_nleu_334, retro_nleu_45,
Oryctolagus cuniculus	ENSOCUG00000003872	1 retrocopy	retro_ocun_263,
Otolemur garnettii	ENSOGAG00000003940	14 retrocopies	retro_ogar_1091, retro_ogar_1297, retro_ogar_1478, retro_ogar_1692, retro_ogar_1887, retro_ogar_2189, retro_ogar_2354, retro_ogar_2625, retro_ogar_2687, retro_ogar_2915, retro_ogar_3207, retro_ogar_3294, retro_ogar_3381, retro_ogar_618,
Pan troglodytes	ENSPTRG00000009232	6 retrocopies	retro_ptro_127, retro_ptro_1673, retro_ptro_208, retro_ptro_2569, retro_ptro_794, retro_ptro_900,
Pteropus vampyrus	ENSPVAG00000008817	4 retrocopies	retro_pvam_1084, retro_pvam_1231, retro_pvam_25, retro_pvam_509,
Rattus norvegicus	ENSRNOG00000020674	8 retrocopies	retro_rnor_1150, retro_rnor_125, retro_rnor_1257, retro_rnor_1968, retro_rnor_2594, retro_rnor_2989, retro_rnor_386, retro_rnor_414,
Sarcophilus harrisii	ENSSHAG00000012042	4 retrocopies	retro_shar_10, retro_shar_253, retro_shar_730, retro_shar_741,
Tarsius syrichta	ENSTSYG00000003167	12 retrocopies	retro_tsyr_1032, retro_tsyr_1154, retro_tsyr_1711, retro_tsyr_2036, retro_tsyr_381, retro_tsyr_476, retro_tsyr_602, retro_tsyr_787, retro_tsyr_816, retro_tsyr_822, retro_tsyr_95, retro_tsyr_989,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.00 RPM
CEU_NA11843	0.00 RPM
CEU_NA11930	0.00 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.00 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	0.00 RPM
FIN_HG00277	0.00 RPM
FIN_HG00315	0.00 RPM
FIN_HG00321	0.00 RPM
FIN_HG00328	0.00 RPM
FIN_HG00338	0.00 RPM
FIN_HG00349	0.00 RPM
FIN_HG00375	0.00 RPM
FIN_HG00377	0.00 RPM
FIN_HG00378	0.00 RPM
GBR_HG00099	0.00 RPM
GBR_HG00111	0.00 RPM
GBR_HG00114	0.00 RPM
GBR_HG00119	0.00 RPM
GBR_HG00131	0.00 RPM
GBR_HG00133	0.00 RPM
GBR_HG00134	0.00 RPM
GBR_HG00137	0.00 RPM
GBR_HG00142	0.00 RPM
GBR_HG00143	0.00 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.00 RPM
TSI_NA20518	0.00 RPM
TSI_NA20532	0.00 RPM
TSI_NA20538	0.00 RPM
TSI_NA20756	0.00 RPM
TSI_NA20765	0.00 RPM
TSI_NA20771	0.00 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.00 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.00 RPM
YRI_NA19093	0.00 RPM
YRI_NA19099	0.00 RPM
YRI_NA19114	0.00 RPM
YRI_NA19118	0.00 RPM
YRI_NA19213	0.00 RPM
YRI_NA19214	0.00 RPM
YRI_NA19223	0.00 RPM

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Indel association:

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