RetrogeneDB ID: retro_hsap_3780

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 7:124985024..124985428(+)
• Located in intron of: ENSG00000237764

Retrocopy information

• Ensembl ID: ENSG00000234071
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MTX2
• Ensembl ID: ENSG00000128654
• Aliases: None
• Description: metaxin 2 [Source:HGNC Symbol;Acc:7506]

Sequence

>retro_hsap_3780
TTGTATCTTCAGTGGTTTGATGAAGCTAAATCTGGGAGATCACTCATTCTAGGTATGGATCTCCTTACCCTTGGCCTCTG
CATCATATTTTGGCCTATCAGAAATGGTGAAAAGTCAAATGTAAGATGAAAGCTATCAGATGGCGTAAGAAAACTCTGGA
CCAGGTCTTAGAAGATATAGACCAGTGCTGTCAAGCTCTCTCTAAAAGTCTGGTAACACAACCATATTTTTTTAATAAGC
AGCTTCCTGAATTTGATACACTGGTATTTGGCCATTTGTACACCATTCTTACCACACGATTGATGAATGATAAACTTTCT
GAGGTGAAAAACTACAGCAACCTTCTTGCTCTCTGCAGAAGAATTGAAAGGCACTATTTTGACGATTGTGATAAAGGCAG
ATTG

Alignment

ORF - retro_hsap_3780 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.83 %
• Parental protein coverage: 51.71 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LYLQWCDEATVG-EITHARYGSPYPWPLNHILAYQKQWEVKRKMKAIGWGKKTLDQVLEDVDQCCQALSQ
          LYLQW.DEA..G.EITH.RYGSPYPWPL.HILAYQK...VK.KMKAI.W.KKTLDQVLED.DQCCQALS.
Retrocopy LYLQWFDEAKSG<EITHSRYGSPYPWPLHHILAYQKW*KVKCKMKAIRWRKKTLDQVLEDIDQCCQALSK

Parental  RLGTQPYFFNKQPTELDALVFGHLYTILTTQLTNDELSEKVKNYSNLLAFCRRIEQHYFEDRGKGRL
          .L.TQPYFFNKQ..E.D.LVFGHLYTILTT.L.ND.LSE.VKNYSNLLA.CRRIE.HYF.D..KGRL
Retrocopy SLVTQPYFFNKQLPEFDTLVFGHLYTILTTRLMNDKLSE-VKNYSNLLALCRRIERHYFDDCDKGRL

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	13.52 RPM
bodymap2_adrenal	0.00 RPM	21.96 RPM
bodymap2_brain	0.02 RPM	30.19 RPM
bodymap2_breast	0.00 RPM	26.93 RPM
bodymap2_colon	0.00 RPM	20.71 RPM
bodymap2_heart	0.00 RPM	32.75 RPM
bodymap2_kidney	0.00 RPM	40.55 RPM
bodymap2_liver	0.00 RPM	12.23 RPM
bodymap2_lung	0.00 RPM	10.88 RPM
bodymap2_lymph_node	0.00 RPM	14.45 RPM
bodymap2_ovary	0.00 RPM	23.27 RPM
bodymap2_prostate	0.00 RPM	30.02 RPM
bodymap2_skeletal_muscle	0.00 RPM	13.73 RPM
bodymap2_testis	0.00 RPM	64.52 RPM
bodymap2_thyroid	0.00 RPM	20.51 RPM
bodymap2_white_blood_cells	0.00 RPM	8.15 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_3780 was not detected

EST

No EST(s) were mapped for retro_hsap_3780 retrocopy.

TSS

No TSS is located nearby retro_hsap_3780 retrocopy 5' end.

Lab

retro_hsap_3780 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3780 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2561
Macaca mulatta	retro_mmul_1643

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000009655	1 retrocopy	retro_chof_2429,
Cavia porcellus	ENSCPOG00000011099	1 retrocopy	retro_cpor_218,
Dipodomys ordii	ENSDORG00000003848	2 retrocopies	retro_dord_159, retro_dord_192,
Homo sapiens	ENSG00000128654	1 retrocopy	retro_hsap_3780 ,
Macaca mulatta	ENSMMUG00000010185	1 retrocopy	retro_mmul_1643,
Nomascus leucogenys	ENSNLEG00000006020	1 retrocopy	retro_nleu_1117,
Pan troglodytes	ENSPTRG00000012674	1 retrocopy	retro_ptro_2561,
Sarcophilus harrisii	ENSSHAG00000016381	1 retrocopy	retro_shar_162,

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	0.00 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:

The presence of retro_hsap_3780 across human populations is associated with 1 indel. The percentage values indicate the frequencies of retro_hsap_3780 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.	7:124982594..124988000	100	100	100	100	100	98.33	100	100	100	100	100	100	100	100

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Indel #1, located at the genomic coordinates 7:124982594..124988000.