RetrogeneDB ID: retro_hsap_455

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 1:153689792..153690296(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000235015
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GEMIN2
• Ensembl ID: ENSG00000092208
• Aliases: GEMIN2, SIP1, SIP1-delta
• Description: gem (nuclear organelle) associated protein 2 [Source:HGNC Symbol;Acc:10884]

Sequence

>retro_hsap_455
AAGTTGAAAAGGAAGCAAGGTGTGAAGGTTTCTCTTTTAGGATGCCAACCTGCCCCTGAAGGTTATTCCCCAATACTTCA
GTGGCAATAGAAAGTGGCACCGTTTTCAACGTAAGACAGAATGTGCACAAACATAGAAGTCACTGCAAATCACGACAGTT
GGATAGTAATGTGACTATGCCAAAATCTAAAGATGAAGAAGGCTAGAAGAAATTTTGTCTGAGTGAAAGTTTATATGCTG
GTGTGGTCACTGACAGCTACAAATGAAAGTCCTAGAATTAATTATGTTCAAATTGGTTTTCCTCCCTTGGTTAGTATTGC
TAGCAGAATGAATCAGACAACAGTAGCTACTGTCTTGGAATATCTGAGTAATTGGTTTGGAGAAAGAGACTTTACTTTGG
ATTTGAGAAGATGGCTTTATGTCTTATTGGCTTGCCTTGAAAAACCTTTATTACATGAGGTTCATTCACTGATTCAGCAG
CTTGCAAGAAGGTGCTCTGAAGTG

Alignment

ORF - retro_hsap_455 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.91 %
• Parental protein coverage: 60.71 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KLKRKQSVNISLSGCQPAPEGYSPTLQWQQQQVAQFST-VRQNVNKHRSHWKSQQLDSNVTMPKSEDEEG
          KLKRKQ.V..SL.GCQPAPEGYSP.LQWQ...VA.FST.VRQNV.KHRSH.KS.QLDSNVTMPKS.DEEG
Retrocopy KLKRKQGVKVSLLGCQPAPEGYSPILQWQ*K-VAPFST<VRQNVHKHRSHCKSRQLDSNVTMPKSKDEEG

Parental  WKKFCLGEKLCADGAVGPA-TNESPGIDYVQIGFPPLLSIVSRMNQATVTSVLEYLSNWFGERDFTPELG
          .KKFCL.E.L.A.G.V....TNESP.I.YVQIGFPPL.SI.SRMNQ.TV..VLEYLSNWFGERDFT..L.
Retrocopy *KKFCLSESLYA-GVVTDS>TNESPRINYVQIGFPPLVSIASRMNQTTVATVLEYLSNWFGERDFTLDLR

Parental  RWLYALLACLEKPLLPEAHSLIRQLARRCSEV
          RWLY.LLACLEKPLL.E.HSLI.QLARRCSEV
Retrocopy RWLYVLLACLEKPLLHEVHSLIQQLARRCSEV

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	5.74 RPM
bodymap2_adrenal	0.10 RPM	8.27 RPM
bodymap2_brain	0.00 RPM	5.46 RPM
bodymap2_breast	0.00 RPM	7.41 RPM
bodymap2_colon	0.00 RPM	6.65 RPM
bodymap2_heart	0.00 RPM	2.82 RPM
bodymap2_kidney	0.00 RPM	6.89 RPM
bodymap2_liver	0.00 RPM	1.77 RPM
bodymap2_lung	0.00 RPM	2.48 RPM
bodymap2_lymph_node	0.00 RPM	7.69 RPM
bodymap2_ovary	0.00 RPM	9.77 RPM
bodymap2_prostate	0.00 RPM	7.72 RPM
bodymap2_skeletal_muscle	0.00 RPM	6.15 RPM
bodymap2_testis	0.00 RPM	10.92 RPM
bodymap2_thyroid	0.00 RPM	6.65 RPM
bodymap2_white_blood_cells	0.00 RPM	5.39 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_455 was not detected

EST

No EST(s) were mapped for retro_hsap_455 retrocopy.

TSS

No TSS is located nearby retro_hsap_455 retrocopy 5' end.

Lab

retro_hsap_455 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_455 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_342
Gorilla gorilla	retro_ggor_438
Pongo abelii	retro_pabe_278

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016248	1 retrocopy	retro_cjac_2630,
Dasypus novemcinctus	ENSDNOG00000018278	1 retrocopy	retro_dnov_1040,
Homo sapiens	ENSG00000092208	1 retrocopy	retro_hsap_455 ,
Gorilla gorilla	ENSGGOG00000016691	2 retrocopies	retro_ggor_1844, retro_ggor_438,
Microcebus murinus	ENSMICG00000004811	1 retrocopy	retro_mmur_1221,
Myotis lucifugus	ENSMLUG00000002619	1 retrocopy	retro_mluc_1005,
Mus musculus	ENSMUSG00000060121	1 retrocopy	retro_mmus_354,
Pongo abelii	ENSPPYG00000005764	1 retrocopy	retro_pabe_278,
Pan troglodytes	ENSPTRG00000006291	1 retrocopy	retro_ptro_342,

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	0.03 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).