RetrogeneDB ID: retro_hsap_4216

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 9:126521496..126521686(+)
• Located in intron of: ENSG00000119522

Retrocopy information

• Ensembl ID: ENSG00000229115
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: LSM5
• Ensembl ID: ENSG00000106355
• Aliases: LSM5, YER146W
• Description: LSM5 homolog, U6 small nuclear RNA associated (S. cerevisiae) [Source:HGNC Symbol;Acc:17162]

Sequence

>retro_hsap_4216
ATGGCGGCTAAGGCTACCACCTACTTGCCCAGCTGTTGCTGCTAGAGCTTGTAGACAAATGTATAGGCTCAAGAATTCAC
ATTGTGGTGAAGAGTCATTAAGAAATCGTGGGTACTCTTCTAGGAGTTGATGACTTTGTCAAGATGGACTAGAAGAGGTC
ACTGAGTTTGAAATCACACCAGAAGGAAGA

Alignment

ORF - retro_hsap_4216 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.79 %
• Parental protein coverage: 70.33 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAANATTNP-SQLLPLELVDKCIGSRIHIVMKSDKEIVGTLLGFDDFVNM-VLEDVTEFEITPEGR
          MAA.ATT....QLL.LELVDKCIGSRIHIV.KS..EIVGTLLG.DDFV.M..LE.VTEFEITPEGR
Retrocopy MAAKATTYL<AQLLLLELVDKCIGSRIHIVVKSH*EIVGTLLGVDDFVKM<GLEEVTEFEITPEGR

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	14.07 RPM
bodymap2_adrenal	0.00 RPM	30.58 RPM
bodymap2_brain	0.00 RPM	21.21 RPM
bodymap2_breast	0.00 RPM	22.96 RPM
bodymap2_colon	0.00 RPM	25.00 RPM
bodymap2_heart	0.00 RPM	19.24 RPM
bodymap2_kidney	0.00 RPM	24.63 RPM
bodymap2_liver	0.00 RPM	18.17 RPM
bodymap2_lung	0.00 RPM	14.28 RPM
bodymap2_lymph_node	0.00 RPM	24.56 RPM
bodymap2_ovary	0.00 RPM	24.79 RPM
bodymap2_prostate	0.00 RPM	25.32 RPM
bodymap2_skeletal_muscle	0.00 RPM	10.77 RPM
bodymap2_testis	0.00 RPM	25.77 RPM
bodymap2_thyroid	0.00 RPM	32.88 RPM
bodymap2_white_blood_cells	0.00 RPM	22.44 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_4216 was not detected

EST

No EST(s) were mapped for retro_hsap_4216 retrocopy.

TSS

No TSS is located nearby retro_hsap_4216 retrocopy 5' end.

Lab

retro_hsap_4216 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_4216 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2862
Gorilla gorilla	retro_ggor_2824
Pongo abelii	retro_pabe_3449

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009185	3 retrocopies	retro_cjac_1883, retro_cjac_2760, retro_cjac_3068,
Echinops telfairi	ENSETEG00000018068	8 retrocopies	retro_etel_1305, retro_etel_1502, retro_etel_1907, retro_etel_198, retro_etel_2054, retro_etel_2193, retro_etel_454, retro_etel_964,
Homo sapiens	ENSG00000106355	2 retrocopies	retro_hsap_3703, retro_hsap_4216 ,
Gorilla gorilla	ENSGGOG00000010325	2 retrocopies	retro_ggor_2504, retro_ggor_2824,
Microcebus murinus	ENSMICG00000005353	3 retrocopies	retro_mmur_1345, retro_mmur_69, retro_mmur_950,
Myotis lucifugus	ENSMLUG00000017028	1 retrocopy	retro_mluc_2439,
Oryctolagus cuniculus	ENSOCUG00000029043	5 retrocopies	retro_ocun_1284, retro_ocun_1452, retro_ocun_1513, retro_ocun_1556, retro_ocun_903,
Ochotona princeps	ENSOPRG00000002443	3 retrocopies	retro_opri_26, retro_opri_562, retro_opri_701,
Pongo abelii	ENSPPYG00000017661	1 retrocopy	retro_pabe_3449,
Rattus norvegicus	ENSRNOG00000042126	3 retrocopies	retro_rnor_1171, retro_rnor_567, retro_rnor_694,
Sus scrofa	ENSSSCG00000026064	1 retrocopy	retro_sscr_385,