RetrogeneDB ID: retro_hsap_2645

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 3:48202666..48202904(+)
• Located in intron of: ENSG00000164045

Retrocopy information

• Ensembl ID: ENSG00000235627
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SNRPF
• Ensembl ID: ENSG00000139343
• Aliases: None
• Description: small nuclear ribonucleoprotein polypeptide F [Source:HGNC Symbol;Acc:11162]

Sequence

>retro_hsap_2645
AGTTCACCTGTGAATCCCAAATCTTTCCCCAGTGGAACAACAGAAAGCCAGTGATGGCGAAACTCAAGTGGGGAACGAAG
TGTAAGGGGTATCTGTAGATGGTGATATAAACATGCAGCTTGCAAATACAGAATACAGAGATGGGGCGTTTTCTGTATAT
CTAGGTGAAGTTTCAATATGGTATAATAATGTCCTTTATATTAGAGGTGTTAAAGAGGAAGATGGGGAAATGAGAGAT

Alignment

ORF - retro_hsap_2645 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.67 %
• Parental protein coverage: 98.84 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SLPLNPKPFLNGLTG-KPVMVKLKW-GMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHLGEVLIRCNNV
          S.P.NPK.F..G.T..KPVM.KLKW.G.E..G..VSVDG..NMQLANTE.Y.DGA.S..LGEV.I..NNV
Retrocopy SSPVNPKSFPSGTTE<KPVMAKLKW<GNEV*G--VSVDGDINMQLANTE-YRDGAFSVYLGEVSIWYNNV

Parental  LYIRGVEEEEEDGEMRE
          LYIRGV...EEDGEMR.
Retrocopy LYIRGV--KEEDGEMRD

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	23.75 RPM
bodymap2_adrenal	0.00 RPM	43.40 RPM
bodymap2_brain	0.00 RPM	19.08 RPM
bodymap2_breast	0.00 RPM	19.40 RPM
bodymap2_colon	0.19 RPM	25.97 RPM
bodymap2_heart	0.00 RPM	9.60 RPM
bodymap2_kidney	0.00 RPM	20.25 RPM
bodymap2_liver	0.00 RPM	24.52 RPM
bodymap2_lung	0.00 RPM	19.87 RPM
bodymap2_lymph_node	0.00 RPM	24.76 RPM
bodymap2_ovary	0.04 RPM	37.28 RPM
bodymap2_prostate	0.00 RPM	21.08 RPM
bodymap2_skeletal_muscle	0.00 RPM	6.20 RPM
bodymap2_testis	0.04 RPM	33.63 RPM
bodymap2_thyroid	0.00 RPM	30.73 RPM
bodymap2_white_blood_cells	0.00 RPM	24.77 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_2645 was not detected

EST

No EST(s) were mapped for retro_hsap_2645 retrocopy.

TSS

No TSS is located nearby retro_hsap_2645 retrocopy 5' end.

Lab

retro_hsap_2645 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2645 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002166	3 retrocopies	retro_amel_1239, retro_amel_42, retro_amel_883,
Bos taurus	ENSBTAG00000016271	1 retrocopy	retro_btau_765,
Equus caballus	ENSECAG00000019817	1 retrocopy	retro_ecab_154,
Felis catus	ENSFCAG00000029966	4 retrocopies	retro_fcat_280, retro_fcat_66, retro_fcat_77, retro_fcat_861,
Homo sapiens	ENSG00000139343	3 retrocopies	retro_hsap_125, retro_hsap_2487, retro_hsap_2645 ,
Homo sapiens	ENSG00000164167	2 retrocopies	retro_hsap_1948, retro_hsap_2107,
Gorilla gorilla	ENSGGOG00000001127	2 retrocopies	retro_ggor_1549, retro_ggor_225,
Macaca mulatta	ENSMMUG00000009302	4 retrocopies	retro_mmul_1521, retro_mmul_361, retro_mmul_550, retro_mmul_893,
Mustela putorius furo	ENSMPUG00000007176	3 retrocopies	retro_mputfur_1309, retro_mputfur_377, retro_mputfur_941,
Mus musculus	ENSMUSG00000020018	4 retrocopies	retro_mmus_1060, retro_mmus_1197, retro_mmus_2537, retro_mmus_3210,
Nomascus leucogenys	ENSNLEG00000005835	3 retrocopies	retro_nleu_2259, retro_nleu_274, retro_nleu_651,
Pongo abelii	ENSPPYG00000004847	2 retrocopies	retro_pabe_381, retro_pabe_489,
Pteropus vampyrus	ENSPVAG00000009036	1 retrocopy	retro_pvam_1170,
Rattus norvegicus	ENSRNOG00000005556	4 retrocopies	retro_rnor_1822, retro_rnor_1849, retro_rnor_2926, retro_rnor_444,
Sus scrofa	ENSSSCG00000000895	1 retrocopy	retro_sscr_958,