RetrogeneDB ID: retro_hsap_3130

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 4:185480334..185480937(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000249056
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GAR1
• Ensembl ID: ENSG00000109534
• Aliases: GAR1, NOLA1
• Description: GAR1 ribonucleoprotein homolog (yeast) [Source:HGNC Symbol;Acc:14264]

Sequence

>retro_hsap_3130
ATGTCTCTTCCGGGCGGAGGTCGTGGAGGCTTTGATCGAGGTGGTGGAGGTGGCGGTTTCAACCGCGGCAGCAGCAGCAA
CCGCTTCTGAGGTGCAGGCGGTGGAAATATCAGAGGTGGCGACAGGGGAGGATTTGGATGAGGGGGTGGCCACGGAGGCT
TTGACAAAGGCCAAGGCCAAGGACCTCCAGAACGTGCAGTCTTGTTAGGAGAGTTCCTGCATCCCTGTGAAGATGACATA
GTTTGTAAACGTACGGCAGATGAAAATAAGGTGTCTTATTTCAATGCTCCTGTTTACTTAGAAAACAAAGAACAAATTGG
AAAAGCGGATGAAATATTTGGACAACTTAGAGATTTTTATTTTTCCGTTAAAATGTCAGAAAACGAGAAGGCTTCATCCT
TTAAAAAACTCTGGAAGTTTTATATAGACCCATATGAGCTGCTGCCACTGCAGAGGTTTTTACCTCGGCCTCCAGGTGAG
AAAGGACCTCCAAGATGTGGTGGCAGGGGAGGCCGAGGAGGAAGAAGGGGAGGTGGCAGAGGCAGTGGCAGAAGCGGTGG
TTTTAGAGGTGGAAGAGGAGGTGGTGGTTTCAGAGGGAGAGGA

Alignment

ORF - retro_hsap_3130 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.5 %
• Parental protein coverage: 94.93 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSFRGGGRGGFNRGGGGGGFNRGGSSNHFRGGGGGGGGGNFRGGGRGGFGRGGGRGGFNKGQDQGPPERV
          MS..GGGRGGF.RGGGGGGFNRG.SSN.F.G.GGG....N.RGG.RGGFG.GGG.GGF.KGQ.QGPPER.
Retrocopy MSLPGGGRGGFDRGGGGGGFNRGSSSNRF*GAGGG----NIRGGDRGGFG*GGGHGGFDKGQGQGPPERA

Parental  VLLGEFLHPCEDDIVCKCTTDENKVPYFNAPVYLENKEQIGKVDEIFGQLRDFYFSVKLSENMKASSFKK
          VLLGEFLHPCEDDIVCK.T.DENKV.YFNAPVYLENKEQIGK.DEIFGQLRDFYFSVK.SEN.KASSFKK
Retrocopy VLLGEFLHPCEDDIVCKRTADENKVSYFNAPVYLENKEQIGKADEIFGQLRDFYFSVKMSENEKASSFKK

Parental  LQKFYIDPYKLLPLQRFLPRPPGEKGPPRGGGRGGRGGGRGGGGRGGGRGGGFRGGRGGGGGGFRG
          L.KFYIDPY.LLPLQRFLPRPPGEKGPPR.GGRGGR.GGR.GGGRG.GR.GGFRGGRGGGG...RG
Retrocopy LWKFYIDPYELLPLQRFLPRPPGEKGPPRCGGRGGR-GGRRGGGRGSGRSGGFRGGRGGGGFRGRG

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	23.24 RPM
bodymap2_adrenal	0.00 RPM	32.87 RPM
bodymap2_brain	0.00 RPM	17.98 RPM
bodymap2_breast	0.00 RPM	30.93 RPM
bodymap2_colon	0.00 RPM	23.84 RPM
bodymap2_heart	0.00 RPM	6.04 RPM
bodymap2_kidney	0.00 RPM	17.97 RPM
bodymap2_liver	0.00 RPM	6.65 RPM
bodymap2_lung	0.00 RPM	6.84 RPM
bodymap2_lymph_node	0.02 RPM	9.54 RPM
bodymap2_ovary	0.00 RPM	46.63 RPM
bodymap2_prostate	0.00 RPM	12.76 RPM
bodymap2_skeletal_muscle	0.00 RPM	6.80 RPM
bodymap2_testis	0.00 RPM	30.50 RPM
bodymap2_thyroid	0.00 RPM	27.12 RPM
bodymap2_white_blood_cells	0.00 RPM	11.93 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_3130 was not detected

EST

No EST(s) were mapped for retro_hsap_3130 retrocopy.

TSS

No TSS is located nearby retro_hsap_3130 retrocopy 5' end.

Lab

retro_hsap_3130 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3130 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_2144

---

Parental genes homology:

Parental genes homology involve 15 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004605	2 retrocopies	retro_amel_1932, retro_amel_682,
Homo sapiens	ENSG00000109534	1 retrocopy	retro_hsap_3130 ,
Gorilla gorilla	ENSGGOG00000008681	1 retrocopy	retro_ggor_2144,
Myotis lucifugus	ENSMLUG00000003776	1 retrocopy	retro_mluc_1866,
Macaca mulatta	ENSMMUG00000021225	1 retrocopy	retro_mmul_1992,
Mustela putorius furo	ENSMPUG00000008615	2 retrocopies	retro_mputfur_1491, retro_mputfur_689,
Mus musculus	ENSMUSG00000028010	1 retrocopy	retro_mmus_2012,
Nomascus leucogenys	ENSNLEG00000016578	1 retrocopy	retro_nleu_2251,
Oryctolagus cuniculus	ENSOCUG00000003901	1 retrocopy	retro_ocun_414,
Otolemur garnettii	ENSOGAG00000004693	1 retrocopy	retro_ogar_1017,
Ochotona princeps	ENSOPRG00000012089	1 retrocopy	retro_opri_1168,
Pongo abelii	ENSPPYG00000014996	1 retrocopy	retro_pabe_2586,
Pan troglodytes	ENSPTRG00000016364	1 retrocopy	retro_ptro_2119,
Tarsius syrichta	ENSTSYG00000013668	2 retrocopies	retro_tsyr_355, retro_tsyr_613,
Tursiops truncatus	ENSTTRG00000016318	1 retrocopy	retro_ttru_1539,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.00 RPM
CEU_NA11843	0.03 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	0.03 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	0.03 RPM
YRI_NA19118	0.00 RPM
YRI_NA19213	0.02 RPM
YRI_NA19214	0.00 RPM
YRI_NA19223	0.00 RPM

---

Indel association:

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