RetrogeneDB ID: retro_hsap_276

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 1:192685312..192685780(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000231767
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPS27A
• Ensembl ID: ENSG00000143947
• Aliases: RPS27A, CEP80, HEL112, S27A, UBA80, UBC, UBCEP1, UBCEP80
• Description: ribosomal protein S27a [Source:HGNC Symbol;Acc:10417]

Sequence

>retro_hsap_276
ATGCAGATTTTCGTGAAAACCCTTATGGGGAAGACCATCACCCTCGAGGTTGAACTCTCGGATACAATAGATAATGTAAA
GGCCAAGATCCAGGATAAGGAAGGAATTCCTCCTGATCAGCAGAGACTGATCTTTGCTGGCAAGCAGTTGGAAGATGGAC
GTACTTTGTCTGACTACAATATTCAAAAGGAGTCTACTCTTCATCTTGTGTTGAGACTTCGTGGTGGTGCTAAGAAAAGG
AAGAAGAAGTCTTACACCACTCCCAGGAAGAATAAGCACAAGAGAAAGAAGGTTAAGCTGGCTCTCCTGAAATATTATAA
GGTGGATGAGAATGGCAAAATTAGTTGCCTTCATCGAGAGTGCCCTTCTGATGAATGTGGTGCTGGGGTGTTTATGGCAA
GCCACTTTGACAGACATTATTGTGGCAAATGTTGTCTGACTTACTGTTTCAACAAACCAGAAGACAAG

Alignment

ORF - retro_hsap_276 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.51 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLV
          MQIFVKTL.GKTITLEVE.SDTI.NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLV
Retrocopy MQIFVKTLMGKTITLEVELSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLV

Parental  LRLRGGAKKRKKKSYTTPKKNKHKRKKVKLAVLKYYKVDENGKISRLRRECPSDECGAGVFMASHFDRHY
          LRLRGGAKKRKKKSYTTP.KNKHKRKKVKLA.LKYYKVDENGKIS.L.RECPSDECGAGVFMASHFDRHY
Retrocopy LRLRGGAKKRKKKSYTTPRKNKHKRKKVKLALLKYYKVDENGKISCLHRECPSDECGAGVFMASHFDRHY

Parental  CGKCCLTYCFNKPEDK
          CGKCCLTYCFNKPEDK
Retrocopy CGKCCLTYCFNKPEDK

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	0.32 RPM	241.34 RPM
bodymap2_adrenal	0.55 RPM	445.31 RPM
bodymap2_brain	0.16 RPM	168.49 RPM
bodymap2_breast	0.27 RPM	255.72 RPM
bodymap2_colon	0.50 RPM	539.62 RPM
bodymap2_heart	0.07 RPM	135.97 RPM
bodymap2_kidney	0.23 RPM	283.70 RPM
bodymap2_liver	0.06 RPM	197.57 RPM
bodymap2_lung	0.37 RPM	575.35 RPM
bodymap2_lymph_node	0.11 RPM	651.95 RPM
bodymap2_ovary	0.67 RPM	554.21 RPM
bodymap2_prostate	0.24 RPM	709.26 RPM
bodymap2_skeletal_muscle	0.11 RPM	147.09 RPM
bodymap2_testis	0.23 RPM	329.65 RPM
bodymap2_thyroid	0.38 RPM	244.64 RPM
bodymap2_white_blood_cells	0.61 RPM	847.09 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_276 was not detected

EST

No EST(s) were mapped for retro_hsap_276 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_87138	418 libraries	639 libraries	743 libraries	28 libraries	1 library

The graphical summary, for retro_hsap_276 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_276 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_276 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 19 parental genes, and 92 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004017	5 retrocopies	retro_amel_1565, retro_amel_175, retro_amel_598, retro_amel_661, retro_amel_844,
Canis familiaris	ENSCAFG00000023471	3 retrocopies	retro_cfam_1048, retro_cfam_640, retro_cfam_81,
Callithrix jacchus	ENSCJAG00000010052	5 retrocopies	retro_cjac_200, retro_cjac_229, retro_cjac_344, retro_cjac_74, retro_cjac_88,
Felis catus	ENSFCAG00000023939	1 retrocopy	retro_fcat_1542,
Homo sapiens	ENSG00000143947	10 retrocopies	retro_hsap_1694, retro_hsap_1715, retro_hsap_2217, retro_hsap_2416, retro_hsap_276 , retro_hsap_3344, retro_hsap_3508, retro_hsap_4272, retro_hsap_4649, retro_hsap_4650,
Loxodonta africana	ENSLAFG00000023133	2 retrocopies	retro_lafr_1122, retro_lafr_185,
Macropus eugenii	ENSMEUG00000008917	13 retrocopies	retro_meug_107, retro_meug_1184, retro_meug_1460, retro_meug_1514, retro_meug_1544, retro_meug_1657, retro_meug_183, retro_meug_1866, retro_meug_209, retro_meug_521, retro_meug_594, retro_meug_937, retro_meug_94,
Myotis lucifugus	ENSMLUG00000017064	10 retrocopies	retro_mluc_1201, retro_mluc_1255, retro_mluc_1298, retro_mluc_1646, retro_mluc_1730, retro_mluc_1865, retro_mluc_1867, retro_mluc_2264, retro_mluc_37, retro_mluc_380,
Myotis lucifugus	ENSMLUG00000029449	1 retrocopy	retro_mluc_1585,
Macaca mulatta	ENSMMUG00000015563	8 retrocopies	retro_mmul_1198, retro_mmul_193, retro_mmul_2189, retro_mmul_222, retro_mmul_2470, retro_mmul_282, retro_mmul_606, retro_mmul_73,
Monodelphis domestica	ENSMODG00000001819	3 retrocopies	retro_mdom_1367, retro_mdom_1751, retro_mdom_205,
Mustela putorius furo	ENSMPUG00000010468	6 retrocopies	retro_mputfur_1512, retro_mputfur_242, retro_mputfur_319, retro_mputfur_332, retro_mputfur_499, retro_mputfur_777,
Oryctolagus cuniculus	ENSOCUG00000003613	10 retrocopies	retro_ocun_1087, retro_ocun_1163, retro_ocun_1209, retro_ocun_1259, retro_ocun_1268, retro_ocun_1339, retro_ocun_164, retro_ocun_288, retro_ocun_381, retro_ocun_851,
Pongo abelii	ENSPPYG00000025871	1 retrocopy	retro_pabe_117,
Pan troglodytes	ENSPTRG00000011928	1 retrocopy	retro_ptro_32,
Rattus norvegicus	ENSRNOG00000004426	2 retrocopies	retro_rnor_117, retro_rnor_161,
Sus scrofa	ENSSSCG00000022357	1 retrocopy	retro_sscr_145,
Ictidomys tridecemlineatus	ENSSTOG00000009566	5 retrocopies	retro_itri_1583, retro_itri_1765, retro_itri_26, retro_itri_635, retro_itri_962,
Tursiops truncatus	ENSTTRG00000013947	5 retrocopies	retro_ttru_1199, retro_ttru_1279, retro_ttru_533, retro_ttru_705, retro_ttru_838,