RetrogeneDB ID: retro_hsap_4244

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 9:33019702..33020130(-)
• Located in intron of: ENSG00000137074

Retrocopy information

• Ensembl ID: ENSG00000225693
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: LAGE3
• Ensembl ID: ENSG00000196976
• Aliases: None
• Description: L antigen family, member 3 [Source:HGNC Symbol;Acc:26058]

Sequence

>retro_hsap_4244
ATGTGGGACGTGGATGCAGACGCAGGCGGAGGCGCCAACTGCGGGGATGGCTAGGGTGATCACAGCTGCCCCGGGGGCGC
GGACACCCCGGCAGCTCCGGCCAGCGGAGCTCCCCCACCGCACGTGTCAGGTCCTAGCAGAAACGCAGCGTCTGTGGCCA
AGGGCCAGGAATGCGGCCGCACATATTCACCCTCAGCGTGCCTTTCCCGACCCCCTTAGAGGTGGAAATTGCCCATGGGT
CCCTGGCTCCAGATGCCGAACCCCACCAAAGGGTGGTTGGGAAGGATCTCACAGTGAGCGGCAGGATCCTGGCCGTCCGC
TGGAAAGCTGAAGACTGTTGCCTGCTCCGAATTTCCCTTATCAACTTTCTCGACCATCTTTCTCTGGTGGTGCGGACCCT
GCAGCACTTTGGGCCCCCAGTTTCCCGC

Alignment

ORF - retro_hsap_4244 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.25 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MRDADADAGGGADGGDGRGGHSCRGGVDTAAAPAGGAPPAHAPGPGRDAASAARGSR-MRPHIFTLSVPF
          M.D.DADAGGGA..GDG.G.HSC.GG.DT.AAPA.GAPP.H..GP.R.AAS.A.G...MRPHIFTLSVPF
Retrocopy MWDVDADAGGGANCGDG*GDHSCPGGADTPAAPASGAPPPHVSGPSRNAASVAKGQE<MRPHIFTLSVPF

Parental  PTPLEAEIAHGSLAPDAEPHQRVVGKDLTVSGRILVVRWKAEDCRLLRISVINFLDQLSLVVRTMQRFGP
          PTPLE.EIAHGSLAPDAEPHQRVVGKDLTVSGRIL.VRWKAEDC.LLRIS.INFLD.LSLVVRT.Q.FGP
Retrocopy PTPLEVEIAHGSLAPDAEPHQRVVGKDLTVSGRILAVRWKAEDCCLLRISLINFLDHLSLVVRTLQHFGP

Parental  PVSR
          PVSR
Retrocopy PVSR

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	0.06 RPM	3.74 RPM
bodymap2_adrenal	0.08 RPM	5.61 RPM
bodymap2_brain	0.05 RPM	5.06 RPM
bodymap2_breast	0.04 RPM	4.28 RPM
bodymap2_colon	0.06 RPM	4.93 RPM
bodymap2_heart	0.00 RPM	3.90 RPM
bodymap2_kidney	0.14 RPM	3.83 RPM
bodymap2_liver	0.02 RPM	4.08 RPM
bodymap2_lung	0.12 RPM	4.15 RPM
bodymap2_lymph_node	0.15 RPM	7.20 RPM
bodymap2_ovary	0.27 RPM	9.29 RPM
bodymap2_prostate	0.31 RPM	9.04 RPM
bodymap2_skeletal_muscle	0.00 RPM	5.37 RPM
bodymap2_testis	0.40 RPM	5.47 RPM
bodymap2_thyroid	0.36 RPM	4.22 RPM
bodymap2_white_blood_cells	0.00 RPM	6.46 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_4244 was not detected

EST

1 EST(s) were mapped to retro_hsap_4244 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
BE855865	33019802	33019956	97.5	150	4	146

TSS

No TSS is located nearby retro_hsap_4244 retrocopy 5' end.

Lab

retro_hsap_4244 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_4244 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_3394

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000024143	1 retrocopy	retro_dnov_244,
Dipodomys ordii	ENSDORG00000009093	1 retrocopy	retro_dord_448,
Homo sapiens	ENSG00000196976	1 retrocopy	retro_hsap_4244 ,
Gorilla gorilla	ENSGGOG00000013507	1 retrocopy	retro_ggor_2845,
Macaca mulatta	ENSMMUG00000007739	1 retrocopy	retro_mmul_1145,
Mus musculus	ENSMUSG00000015289	2 retrocopies	retro_mmus_1411, retro_mmus_1665,
Nomascus leucogenys	ENSNLEG00000014285	1 retrocopy	retro_nleu_1373,
Ochotona princeps	ENSOPRG00000003778	2 retrocopies	retro_opri_196, retro_opri_549,
Pongo abelii	ENSPPYG00000020881	1 retrocopy	retro_pabe_3394,
Rattus norvegicus	ENSRNOG00000037249	1 retrocopy	retro_rnor_595,
Sus scrofa	ENSSSCG00000025528	1 retrocopy	retro_sscr_94,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.13 RPM
CEU_NA11843	0.26 RPM
CEU_NA11930	0.29 RPM
CEU_NA12004	0.23 RPM
CEU_NA12400	0.25 RPM
CEU_NA12751	0.36 RPM
CEU_NA12760	0.13 RPM
CEU_NA12827	0.24 RPM
CEU_NA12872	0.14 RPM
CEU_NA12873	0.22 RPM
FIN_HG00183	0.36 RPM
FIN_HG00277	0.26 RPM
FIN_HG00315	0.28 RPM
FIN_HG00321	0.66 RPM
FIN_HG00328	0.24 RPM
FIN_HG00338	0.06 RPM
FIN_HG00349	0.06 RPM
FIN_HG00375	0.42 RPM
FIN_HG00377	0.13 RPM
FIN_HG00378	0.08 RPM
GBR_HG00099	0.17 RPM
GBR_HG00111	0.28 RPM
GBR_HG00114	0.11 RPM
GBR_HG00119	0.22 RPM
GBR_HG00131	0.14 RPM
GBR_HG00133	0.10 RPM
GBR_HG00134	0.28 RPM
GBR_HG00137	0.27 RPM
GBR_HG00142	0.39 RPM
GBR_HG00143	0.06 RPM
TSI_NA20512	0.14 RPM
TSI_NA20513	0.41 RPM
TSI_NA20518	0.11 RPM
TSI_NA20532	0.48 RPM
TSI_NA20538	0.14 RPM
TSI_NA20756	0.12 RPM
TSI_NA20765	0.29 RPM
TSI_NA20771	0.06 RPM
TSI_NA20786	0.18 RPM
TSI_NA20798	0.28 RPM
YRI_NA18870	0.51 RPM
YRI_NA18907	0.21 RPM
YRI_NA18916	0.21 RPM
YRI_NA19093	0.08 RPM
YRI_NA19099	0.19 RPM
YRI_NA19114	0.21 RPM
YRI_NA19118	0.17 RPM
YRI_NA19213	0.26 RPM
YRI_NA19214	0.07 RPM
YRI_NA19223	0.32 RPM

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Indel association:

The presence of retro_hsap_4244 across human populations is associated with 1 indel. The percentage values indicate the frequencies of retro_hsap_4244 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.	9:33015516..33023800	99.18	99.43	99.48	100	100	100	100	100	100	99.46	100	100	100	100

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Indel #1, located at the genomic coordinates 9:33015516..33023800.