RetrogeneDB ID: retro_hsap_2802

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 3:73231654..73232430(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000182921
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GPATCH11
• Ensembl ID: ENSG00000152133
• Aliases: GPATCH11, CCDC75, CENP-Y, CENPY
• Description: G patch domain containing 11 [Source:HGNC Symbol;Acc:26768]

Sequence

>retro_hsap_2802
ATGGCAGAAGAAGAGGACTAACGTCTGATTCCTTCATTAATGTCCAAGAAGATATCAGACCAGGCTTGCCAATGCTAAGG
CAAATCCGGGAAGCCCGTGGAAAAGAAGAAAAGCAACAGGAAGCTAACTTGAAACATAGGCAGAAGAGTTTAAAAGAAGA
AGAACAAAAAAGACGTAACATTGGGTTGAAGAATGCACTAGGCTATGAAAACAAAGGGTTTGCCTTGCTCCAAAAGATGG
GCTATAAAAGTGGTCAGGCACTTGGCAAGGGTAGGGGTGGTATTGTTGAACCCATTCCTCTCAATATCAAAACAGGGAAA
AGTGGCATTTGGTCATAAGGCATCATTAAAACGGAAAGCAGAGGAAAAATTAGAAAGCTACGGAAAAAAGATTCACATGA
TGAATAACCAAGCTGAAGAAAAAGCTGCAGACCAGTTTCGAATGCGACTTAAAAATAAGCAAGATGAAATGAAGCTAGAA
GGAGATCACAGAAGAAGCCAGCAAGTCTGTCAACAATTGGACACCCAGAAAAATATTCAGGTTCCCAGGGAAGCATGGTA
CTGGTTGAGGCTTGAAAAGGAGACTGAAGATGAAGAAGAAAAAGAACAGGATGAAGATGAATATAAGAGTGAAGATTTAA
GTGTACTGGAAAAATTACAAATATTGACTAGTTATTTAAGAGAAGAACTTCTGTATAGTATTTGGTGTGGAACAGCCTAT
GAAGATAAAGAAGACCTATCTTCAAATTGTCCAGGACCAACTTCGCAGATCATGAC

Alignment

ORF - retro_hsap_2802 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.49 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAEEED-YMSDSFINVQEDIRPGLPMLRQIREARRKEEKQQEANLKNRQKSLKEEEQERRDIGLKNALGC
          MAEEED...SDSFINVQEDIRPGLPMLRQIREAR.KEEKQQEANLK.RQKSLKEEEQ.RR.IGLKNALG.
Retrocopy MAEEED<LTSDSFINVQEDIRPGLPMLRQIREARGKEEKQQEANLKHRQKSLKEEEQKRRNIGLKNALGY

Parental  ENKGFALLQKMGYKSGQALGKSGGGIVEPIPLNIKTGKSGI-GHEASLKRKAEEKLESYRKKIH-MKNQA
          ENKGFALLQKMGYKSGQALGK..GGIVEPIPLNIKTGKSGI.GH.ASLKRKAEEKLESY.KKIH.M.NQA
Retrocopy ENKGFALLQKMGYKSGQALGKGRGGIVEPIPLNIKTGKSGI>GHKASLKRKAEEKLESYGKKIHMMNNQA

Parental  EEKAAEQFRMRLKNKQDEMKLEGDLRRSQRACQQLDVQKNIQVPREAWYWLRLEEETEEDEEEKEQDEDE
          EEKAA.QFRMRLKNKQDEMKLEGD.RRSQ..CQQLD.QKNIQVPREAWYWLRLE.ET.EDEEEKEQDEDE
Retrocopy EEKAADQFRMRLKNKQDEMKLEGDHRRSQQVCQQLDTQKNIQVPREAWYWLRLEKET-EDEEEKEQDEDE

Parental  YKSEDLSVLEKLQILTSYLREEHLYCIWCGTAYEDKEDLSSNCPGPTS-ADHD
          YKSEDLSVLEKLQILTSYLREE.LY.IWCGTAYEDKEDLSSNCPGPTS.ADHD
Retrocopy YKSEDLSVLEKLQILTSYLREELLYSIWCGTAYEDKEDLSSNCPGPTS<ADHD

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	0.02 RPM	24.97 RPM
bodymap2_adrenal	0.00 RPM	17.67 RPM
bodymap2_brain	0.00 RPM	31.93 RPM
bodymap2_breast	0.00 RPM	53.23 RPM
bodymap2_colon	0.00 RPM	19.01 RPM
bodymap2_heart	0.00 RPM	9.78 RPM
bodymap2_kidney	0.00 RPM	18.24 RPM
bodymap2_liver	0.00 RPM	7.73 RPM
bodymap2_lung	0.00 RPM	7.61 RPM
bodymap2_lymph_node	0.00 RPM	22.93 RPM
bodymap2_ovary	0.00 RPM	12.45 RPM
bodymap2_prostate	0.00 RPM	16.59 RPM
bodymap2_skeletal_muscle	0.00 RPM	5.91 RPM
bodymap2_testis	0.04 RPM	36.18 RPM
bodymap2_thyroid	0.00 RPM	17.40 RPM
bodymap2_white_blood_cells	0.00 RPM	42.21 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_2802 was not detected

EST

No EST(s) were mapped for retro_hsap_2802 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_137447	791 libraries	758 libraries	269 libraries	9 libraries	2 libraries

The graphical summary, for retro_hsap_2802 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_2802 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2802 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1899

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000006041	1 retrocopy	retro_cfam_708,
Choloepus hoffmanni	ENSCHOG00000004377	3 retrocopies	retro_chof_1420, retro_chof_2292, retro_chof_398,
Homo sapiens	ENSG00000152133	1 retrocopy	retro_hsap_2802 ,
Monodelphis domestica	ENSMODG00000015289	1 retrocopy	retro_mdom_1855,
Nomascus leucogenys	ENSNLEG00000027017	1 retrocopy	retro_nleu_1542,
Pan troglodytes	ENSPTRG00000011832	1 retrocopy	retro_ptro_1899,

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	0.03 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	0.03 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).