RetrogeneDB ID: retro_hsap_2075

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 2:11397333..11397875(+)
• Located in intron of: ENSG00000134318

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: RP11-159G9.5
• Ensembl ID: ENSG00000229729
• Aliases: None
• Description: None

Sequence

>retro_hsap_2075
ATGGCGGAGGAAGACAGCGATCAAAAGGCCGAACGCCTCAGAGAAGAGCTTGTGGCCACTGTGGAGTCCCTGCTGGCCCT
GTGGGGCTTAGAGCTGCGGGCGACGGCAGAGGCGGTGCTGGCAGCTGCAGTGGCGGCGTCACGATCAGCTGTCGGGGTTA
CTGCTGACGCTTCTGTCAGGTGGTTGAAGATTACGTTGGAAGATGGCAGGTCCCTTTGCCACAGCTTCAGGTTCTTCAGA
CTGTACTTTGTTGTTTTACAACAGCCAGTGCATCATTCCCAGATGAATGTGAGCACGTACAACATGTTTTGAGTAGCCTT
GCTGTGAGTTTCTTCGAGTTGCTGCTGTTCTTTGGAAGAGGTGAGTTTTATGAAGAGCCCTTAAAGGATATTCTTGGATC
ATTCCAGGAATACCAGAATCACCTCCGCAGATATGGAAATGTGAATCTGGAACTGGTGACTCGAATCATTAGAGATGGCG
GCCCATGGGAAGATCCAGTGTTGCAAGCTGTCCTTAAAGCTCAGCCAGCATCTCAGGAGATA

Alignment

ORF - retro_hsap_2075 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.22 %
• Parental protein coverage: 51.12 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAEEESDQEAERLGEELVAIVES-PLGPVGLRAAGDGRGGAGSGNCGGGVGISSRDYCRRFCQVVEDYAG
          MAEE.SDQ.AERL.EELVA.VES.P.GPVGLRAAGDGRGGAGS..C.GGV.IS.R.YC.RFCQVVEDY.G
Retrocopy MAEEDSDQKAERLREELVATVES<PAGPVGLRAAGDGRGGAGS--CSGGVTISCRGYC*RFCQVVEDYVG

Parental  RWQVPLPQLQVLQTALCCFTTASASFPDECEHVQYVLSSLAVSFFELLLFFGRDEFYEEPLKDILGSFQE
          RWQVPLPQLQVLQT.LCCFTTASASFPDECEHVQ.VLSSLAVSFFELLLFFGR.EFYEEPLKDILGSFQE
Retrocopy RWQVPLPQLQVLQTVLCCFTTASASFPDECEHVQHVLSSLAVSFFELLLFFGRGEFYEEPLKDILGSFQE

Parental  CQNHLRRYGNVNLELVTRIIRDGGPWEDPVLQAVLKAQPASQEI
          .QNHLRRYGNVNLELVTRIIRDGGPWEDPVLQAVLKAQPASQEI
Retrocopy YQNHLRRYGNVNLELVTRIIRDGGPWEDPVLQAVLKAQPASQEI

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	0.26 RPM	3.18 RPM
bodymap2_adrenal	0.00 RPM	1.92 RPM
bodymap2_brain	0.05 RPM	3.31 RPM
bodymap2_breast	0.00 RPM	2.55 RPM
bodymap2_colon	0.00 RPM	2.49 RPM
bodymap2_heart	0.00 RPM	2.84 RPM
bodymap2_kidney	0.00 RPM	1.94 RPM
bodymap2_liver	0.00 RPM	1.01 RPM
bodymap2_lung	0.07 RPM	1.83 RPM
bodymap2_lymph_node	0.05 RPM	3.98 RPM
bodymap2_ovary	0.00 RPM	3.51 RPM
bodymap2_prostate	0.00 RPM	2.74 RPM
bodymap2_skeletal_muscle	0.00 RPM	2.16 RPM
bodymap2_testis	0.02 RPM	5.24 RPM
bodymap2_thyroid	0.00 RPM	4.71 RPM
bodymap2_white_blood_cells	0.00 RPM	7.38 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_2075 was not detected

EST

No EST(s) were mapped for retro_hsap_2075 retrocopy.

TSS

No TSS is located nearby retro_hsap_2075 retrocopy 5' end.

Lab

retro_hsap_2075 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2075 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1527

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000229729	1 retrocopy	retro_hsap_2075 ,
Nomascus leucogenys	ENSNLEG00000011752	1 retrocopy	retro_nleu_2375,
Pan troglodytes	ENSPTRG00000042169	1 retrocopy	retro_ptro_1527,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.00 RPM
CEU_NA11843	0.00 RPM
CEU_NA11930	0.03 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	0.03 RPM
FIN_HG00321	0.03 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	0.02 RPM
GBR_HG00099	0.03 RPM
GBR_HG00111	0.00 RPM
GBR_HG00114	0.03 RPM
GBR_HG00119	0.00 RPM
GBR_HG00131	0.00 RPM
GBR_HG00133	0.02 RPM
GBR_HG00134	0.02 RPM
GBR_HG00137	0.00 RPM
GBR_HG00142	0.00 RPM
GBR_HG00143	0.03 RPM
TSI_NA20512	0.03 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	0.02 RPM
TSI_NA20771	0.00 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.00 RPM
YRI_NA18907	0.03 RPM
YRI_NA18916	0.02 RPM
YRI_NA19093	0.03 RPM
YRI_NA19099	0.00 RPM
YRI_NA19114	0.00 RPM
YRI_NA19118	0.02 RPM
YRI_NA19213	0.00 RPM
YRI_NA19214	0.00 RPM
YRI_NA19223	0.00 RPM

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Indel association:

The presence of retro_hsap_2075 across human populations is associated with 1 indel. The percentage values indicate the frequencies of retro_hsap_2075 presence in various populations. Based on Kabza et al. 2015 (PubMed).

#	Indel coordinates	AFR, African			AMR, Ad Mixed American			EUR, European					EAS, East Asian
		ASW	YRI	LWK	MXL	PUR	CLM	CEU	IBS	GBR	FIN	TSI	JPT	CHB	CHS
1.	2:11394742..11400300	97.54	97.16	93.3	100	100	98.33	100	100	100	100	100	100	100	100

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Indel #1, located at the genomic coordinates 2:11394742..11400300.