RetrogeneDB ID: retro_hsap_4136

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 9:15055057..15056047(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000234297
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PSIP1
• Ensembl ID: ENSG00000164985
• Aliases: PSIP1, DFS70, LEDGF, PAIP, PSIP2, p52, p75
• Description: PC4 and SFRS1 interacting protein 1 [Source:HGNC Symbol;Acc:9527]

Sequence

>retro_hsap_4136
ACTCGCGATTTCAAACCTGGAGACCTCATCTTCGCCAAGATGAAAGGTTATCCCCACTGGCCAGCTGGAGTAGATGAAGT
TCTTGATGGAGCTGTAAAGCCACCCACAAACAAACTACCCATTTTCTTTTTTTGGAACTCATGAGACTGCTTTTTTAGGA
CCAAAGGTTATATTTCCTTACTCCGAAAATAAGGAAAAGTATGGCGAACCAAACAAAAGATTTTAACGAAGGTTTATGGG
GACAGATAACAATCCAAAAGTGAAATTTTCAAGTCAACAGGCAGCAACTAAACAATCAAACACATCATCCAATGTTGAAG
TTGAAGAAAAAGAAACTAGTGTTTCAAAGGAAGATACCGACCATGAAGAAAAAGCCAGCAATGAGGGTGTGACTAAAGCA
GTTGACATAACTACTCCAAAAGCTGCCAGAAGAGGGAGAAAGAGAAAGGCAGAAAAACAAGTAGAAACTGAGGAGGCAGG
AGTAGTGACAACAGCAACAGCATCTGTTCATCTAAAAGTGAGTCCTAAAAGAGGACGACCTGCAGCTACGGAAGTCAAGA
TTCCAAAACCAAGAGGCAGACCCAAAATGGTAAAACAGCCCTGTCCTTCAGAGAGTGACATCATTACTGAAGAGGACAAA
AGTAAGAAAAAGGGGCAAGAGGAAAAACAACCTAAAAAGCAGCCTAAGAAGGACAAAGAGGGCCAGAAGGAAGAAGATAA
GCCAAGAAAAGAGCCAGACAAAATAGAGTAGAAGAAAGAAGTTGAGTCAAAAGGAAAAATTTAGCTAACACAGGGGTTAC
ATCAACCTCCGATTCTGAAGAAGAAGGAGATGATCAAGAAGGTGAAAAGAAGAGAAAAGGTGACAGGAACGTTCAGACTG
CTCACAGAAGGAATATGCTGAAAGGCCAAAATGAGAAAGAAGCAGCAGATCGAAAACGCAAGCAGGAAAAACAAGTGGAA
ACTGAGCACCAAACAAGATGTAATCTACAG

Alignment

ORF - retro_hsap_4136 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.32 %
• Parental protein coverage: 99.7 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TRDFKPGDLIFAKMKGYPHWPARVDEVPDGAVKPPTNKLPIF-FFGTHETAFLGPKDIFPYSENKEKYGK
          TRDFKPGDLIFAKMKGYPHWPA.VDEV.DGAVKPPTNKLPIF.FFGTHETAFLGPK.IFPYSENKEKYG.
Retrocopy TRDFKPGDLIFAKMKGYPHWPAGVDEVLDGAVKPPTNKLPIF>FFGTHETAFLGPKVIFPYSENKEKYGE

Parental  PNKRKGFNEGLWEIDNNPKVKFSSQQAATKQSNASSDVEVEEKETSVSKEDTDHEEKASNEDVTKAVDIT
          PNKR..F.......DNNPKVKFSSQQAATKQSN.SS.VEVEEKETSVSKEDTDHEEKASNE.VTKAVDIT
Retrocopy PNKR--F*RRFMGTDNNPKVKFSSQQAATKQSNTSSNVEVEEKETSVSKEDTDHEEKASNEGVTKAVDIT

Parental  TPKAARRGRKRKAEKQVETEEAGVVTTATASVNLKVSPKRGRPAATEVKIPKPRGRPKMVKQPCPSESDI
          TPKAARRGRKRKAEKQVETEEAGVVTTATASV.LKVSPKRGRPAATEVKIPKPRGRPKMVKQPCPSESDI
Retrocopy TPKAARRGRKRKAEKQVETEEAGVVTTATASVHLKVSPKRGRPAATEVKIPKPRGRPKMVKQPCPSESDI

Parental  ITEEDKSKKKGQEEKQPKKQPKKDEEGQKEEDKPRKEPDKKEGKKEVES-KRKNLAKTGVTSTSDSEEEG
          ITEEDKSKKKGQEEKQPKKQPKKD.EGQKEEDKPRKEPDK.E.KKEVES.KRKNLA.TGVTSTSDSEEEG
Retrocopy ITEEDKSKKKGQEEKQPKKQPKKDKEGQKEEDKPRKEPDKIE*KKEVES<KRKNLANTGVTSTSDSEEEG

Parental  DDQEGEKKRKGGRNFQTAHRRNMLKGQHEKEAADRKRKQEEQMETEHQTTCNLQ
          DDQEGEKKRKG.RN.QTAHRRNMLKGQ.EKEAADRKRKQE.Q.ETEHQT.CNLQ
Retrocopy DDQEGEKKRKGDRNVQTAHRRNMLKGQNEKEAADRKRKQEKQVETEHQTRCNLQ

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	66.51 RPM
bodymap2_adrenal	0.02 RPM	117.52 RPM
bodymap2_brain	0.33 RPM	272.37 RPM
bodymap2_breast	0.00 RPM	63.31 RPM
bodymap2_colon	0.10 RPM	150.65 RPM
bodymap2_heart	0.02 RPM	39.64 RPM
bodymap2_kidney	0.00 RPM	70.58 RPM
bodymap2_liver	0.00 RPM	15.08 RPM
bodymap2_lung	0.00 RPM	75.67 RPM
bodymap2_lymph_node	0.00 RPM	105.11 RPM
bodymap2_ovary	0.17 RPM	266.00 RPM
bodymap2_prostate	0.00 RPM	146.27 RPM
bodymap2_skeletal_muscle	0.00 RPM	37.21 RPM
bodymap2_testis	0.19 RPM	249.86 RPM
bodymap2_thyroid	0.02 RPM	106.66 RPM
bodymap2_white_blood_cells	0.00 RPM	134.66 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_4136 was not detected

EST

1 EST(s) were mapped to retro_hsap_4136 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
CB331920	15055592	15055695	97	100	0	99

TSS

No TSS is located nearby retro_hsap_4136 retrocopy 5' end.

Lab

retro_hsap_4136 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_4136 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2811

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012471	1 retrocopy	retro_cjac_4069,
Homo sapiens	ENSG00000143321	1 retrocopy	retro_hsap_33,
Homo sapiens	ENSG00000164985	1 retrocopy	retro_hsap_4136 ,
Mus musculus	ENSMUSG00000028484	1 retrocopy	retro_mmus_2896,
Pan troglodytes	ENSPTRG00000020786	1 retrocopy	retro_ptro_2811,
Tupaia belangeri	ENSTBEG00000000715	1 retrocopy	retro_tbel_364,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.28 RPM
CEU_NA11843	0.11 RPM
CEU_NA11930	0.23 RPM
CEU_NA12004	0.11 RPM
CEU_NA12400	0.07 RPM
CEU_NA12751	0.05 RPM
CEU_NA12760	0.18 RPM
CEU_NA12827	0.24 RPM
CEU_NA12872	0.19 RPM
CEU_NA12873	0.10 RPM
FIN_HG00183	0.16 RPM
FIN_HG00277	0.15 RPM
FIN_HG00315	0.17 RPM
FIN_HG00321	0.15 RPM
FIN_HG00328	0.14 RPM
FIN_HG00338	0.19 RPM
FIN_HG00349	0.40 RPM
FIN_HG00375	0.07 RPM
FIN_HG00377	0.10 RPM
FIN_HG00378	0.23 RPM
GBR_HG00099	0.09 RPM
GBR_HG00111	0.06 RPM
GBR_HG00114	0.13 RPM
GBR_HG00119	0.14 RPM
GBR_HG00131	0.14 RPM
GBR_HG00133	0.12 RPM
GBR_HG00134	0.09 RPM
GBR_HG00137	0.16 RPM
GBR_HG00142	0.39 RPM
GBR_HG00143	0.10 RPM
TSI_NA20512	0.11 RPM
TSI_NA20513	0.24 RPM
TSI_NA20518	0.22 RPM
TSI_NA20532	0.24 RPM
TSI_NA20538	0.09 RPM
TSI_NA20756	0.20 RPM
TSI_NA20765	0.02 RPM
TSI_NA20771	0.17 RPM
TSI_NA20786	0.13 RPM
TSI_NA20798	0.25 RPM
YRI_NA18870	0.20 RPM
YRI_NA18907	0.07 RPM
YRI_NA18916	0.17 RPM
YRI_NA19093	0.05 RPM
YRI_NA19099	0.05 RPM
YRI_NA19114	0.13 RPM
YRI_NA19118	0.15 RPM
YRI_NA19213	0.14 RPM
YRI_NA19214	0.10 RPM
YRI_NA19223	0.18 RPM

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Indel association:

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