RetrogeneDB ID: retro_hsap_3265

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 5:168043356..168043998(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000233913
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPL10
• Ensembl ID: ENSG00000147403
• Aliases: RPL10, AUTSX5, DXS648, DXS648E, L10, NOV, QM
• Description: ribosomal protein L10 [Source:HGNC Symbol;Acc:10298]

Sequence

>retro_hsap_3265
ATGGGCCGCCGCCCCGCCTGTTGTTACCGGTATTGTAAGAACAAGCCGTACCCAAAGTCTCGCTTCTGCCGAGGTGTCCC
TGATGCCAAGATTCGCATTTTTGACCTGGGGCGGAAAAAGGCAAAAGTGGATGAGTTTCCACTTTGTGGCCACATGGTGT
CAGATGAATATGAGCAGCTGTCCTCTGAAGCCCTGGAGGCTGCCCGAATTTGTGCCAATAAGTACATGGTAAAAAGTTGT
GGCAAAGATGGCTTCCATATCCGGGTGCGGCTCCACTCCTTCCACGTCATCCGCATCAACAAGATGTTGTCCTGTGCTGG
GGCTGACAGGCTCCAAACAGGCATGCGAGGTGCCTTTGGAAAGCCCCAGGGCACTTTGGCCAGGGTTCACACTGGCCAAG
TTATCATGTCCATCCGCACCAAGCTGCAGAACAAGGAGCATGTGATTGAGGCCCTGGGCAGGGCCAAGTTCAAGTTTCCT
GGCCGCCAGAAGATCCACATCTCAAAGAAGTGGGGCTTCACCAAGTTCAATGCTGATGAATTTGAAGACATGGTGGCTGA
AAAGCGGCTCATCCCAGATGGCTGTGGGGTCAAGTACATCCCCAATCGTGGCCCTCTGGACAAGTGGCGGGCCCTGCACT
CA

Alignment

ORF - retro_hsap_3265 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.66 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGRRPARCYRYCKNKPYPKSRFCRGVPDAKIRIFDLGRKKAKVDEFPLCGHMVSDEYEQLSSEALEAARI
          MGRRPA.CYRYCKNKPYPKSRFCRGVPDAKIRIFDLGRKKAKVDEFPLCGHMVSDEYEQLSSEALEAARI
Retrocopy MGRRPACCYRYCKNKPYPKSRFCRGVPDAKIRIFDLGRKKAKVDEFPLCGHMVSDEYEQLSSEALEAARI

Parental  CANKYMVKSCGKDGFHIRVRLHPFHVIRINKMLSCAGADRLQTGMRGAFGKPQGTVARVHIGQVIMSIRT
          CANKYMVKSCGKDGFHIRVRLH.FHVIRINKMLSCAGADRLQTGMRGAFGKPQGT.ARVH.GQVIMSIRT
Retrocopy CANKYMVKSCGKDGFHIRVRLHSFHVIRINKMLSCAGADRLQTGMRGAFGKPQGTLARVHTGQVIMSIRT

Parental  KLQNKEHVIEALRRAKFKFPGRQKIHISKKWGFTKFNADEFEDMVAEKRLIPDGCGVKYIPNRGPLDKWR
          KLQNKEHVIEAL.RAKFKFPGRQKIHISKKWGFTKFNADEFEDMVAEKRLIPDGCGVKYIPNRGPLDKWR
Retrocopy KLQNKEHVIEALGRAKFKFPGRQKIHISKKWGFTKFNADEFEDMVAEKRLIPDGCGVKYIPNRGPLDKWR

Parental  ALHS
          ALHS
Retrocopy ALHS

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	0.62 RPM	465.66 RPM
bodymap2_adrenal	0.86 RPM	522.26 RPM
bodymap2_brain	0.05 RPM	102.06 RPM
bodymap2_breast	0.49 RPM	310.82 RPM
bodymap2_colon	0.44 RPM	703.36 RPM
bodymap2_heart	0.17 RPM	249.13 RPM
bodymap2_kidney	0.25 RPM	366.37 RPM
bodymap2_liver	0.57 RPM	302.00 RPM
bodymap2_lung	0.79 RPM	1014.17 RPM
bodymap2_lymph_node	1.06 RPM	1033.94 RPM
bodymap2_ovary	1.54 RPM	739.54 RPM
bodymap2_prostate	1.89 RPM	1347.95 RPM
bodymap2_skeletal_muscle	1.04 RPM	691.03 RPM
bodymap2_testis	0.49 RPM	282.25 RPM
bodymap2_thyroid	0.55 RPM	300.94 RPM
bodymap2_white_blood_cells	0.85 RPM	1398.58 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_3265 was not detected

EST

No EST(s) were mapped for retro_hsap_3265 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_151901	5 libraries	0 libraries	0 libraries	0 libraries	1824 libraries

The graphical summary, for retro_hsap_3265 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_3265 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3265 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007454	2 retrocopies	retro_btau_140, retro_btau_99,
Homo sapiens	ENSG00000147403	3 retrocopies	retro_hsap_2030, retro_hsap_3265 , retro_hsap_3437,
Macropus eugenii	ENSMEUG00000013163	3 retrocopies	retro_meug_1839, retro_meug_5, retro_meug_547,
Myotis lucifugus	ENSMLUG00000014337	3 retrocopies	retro_mluc_1592, retro_mluc_191, retro_mluc_275,
Monodelphis domestica	ENSMODG00000008731	2 retrocopies	retro_mdom_177, retro_mdom_829,
Mus musculus	ENSMUSG00000008682	1 retrocopy	retro_mmus_71,
Pongo abelii	ENSPPYG00000020874	5 retrocopies	retro_pabe_173, retro_pabe_1854, retro_pabe_2036, retro_pabe_2843, retro_pabe_2955,