RetrogeneDB ID: retro_hsap_2487

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 20:48346127..48346379(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000231878
• 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_2487
ATGAGTTTATGTCTCAATCCCAGATCTTTCCTCAGTGGAGTAACAGGAAAGCCAAGGATGGTGAAACTTAAGCGGGGAAT
GGAGTACTAGGGCTACCTGGTATCTGTAGATGGCTACATGAACATGCAGCTTGCAAATACAGAAGAATACATAGATGGAG
CATTGTCTGGACATCTGGGTGAAGTTTTAATAAGGTGTAATAATGTCCTTTATATCAGAGGTGTGGAAGAAGAGGAAGAA
GATGGAGAAATG

Alignment

ORF - retro_hsap_2487 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.48 %
• Parental protein coverage: 97.67 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSLPLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHLGEVLIRCNNVL
          MSL.LNP..FL.G.TGKP.MVKLK.GMEY.GYLVSVDGYMNMQLANTEEYIDGALSGHLGEVLIRCNNVL
Retrocopy MSLCLNPRSFLSGVTGKPRMVKLKRGMEY*GYLVSVDGYMNMQLANTEEYIDGALSGHLGEVLIRCNNVL

Parental  YIRGVEEEEEDGEM
          YIRGVEEEEEDGEM
Retrocopy YIRGVEEEEEDGEM

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	0.00 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	0.00 RPM	37.28 RPM
bodymap2_prostate	0.00 RPM	21.08 RPM
bodymap2_skeletal_muscle	0.00 RPM	6.20 RPM
bodymap2_testis	0.00 RPM	33.63 RPM
bodymap2_thyroid	0.02 RPM	30.73 RPM
bodymap2_white_blood_cells	0.00 RPM	24.77 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_2487 was not detected

EST

No EST(s) were mapped for retro_hsap_2487 retrocopy.

TSS

No TSS is located nearby retro_hsap_2487 retrocopy 5' end.

Lab

• Experiment type: PCR amplification
• Forward primer: AATCTTGAACATAGTTTTCTCCTGAT (26 nt long)
• Reverse primer: TACCAGGTAGCCCTAGTAC (19 nt long)
• Anneling temperature: 51 °C
• (Expected) product size: 232
• Electrophoresis gel image:
• Additional comment: Red arrow indicates PCR product of retrogene in pooled cDNA from 16 human tissues (Clontech). Red number of lane indicates particular retrogene; L - GeneRuler 100 bp DNA Ladder (Thermo Fisher Scientific); N - No template control (water instead of cDNA)

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2487 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_1549

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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,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.00 RPM
CEU_NA11843	0.06 RPM
CEU_NA11930	0.03 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.00 RPM
CEU_NA12751	0.02 RPM
CEU_NA12760	0.00 RPM
CEU_NA12827	0.05 RPM
CEU_NA12872	0.11 RPM
CEU_NA12873	0.00 RPM
FIN_HG00183	0.03 RPM
FIN_HG00277	0.04 RPM
FIN_HG00315	0.03 RPM
FIN_HG00321	0.03 RPM
FIN_HG00328	0.00 RPM
FIN_HG00338	0.02 RPM
FIN_HG00349	0.03 RPM
FIN_HG00375	0.00 RPM
FIN_HG00377	0.08 RPM
FIN_HG00378	0.00 RPM
GBR_HG00099	0.03 RPM
GBR_HG00111	0.00 RPM
GBR_HG00114	0.00 RPM
GBR_HG00119	0.00 RPM
GBR_HG00131	0.03 RPM
GBR_HG00133	0.00 RPM
GBR_HG00134	0.00 RPM
GBR_HG00137	0.00 RPM
GBR_HG00142	0.00 RPM
GBR_HG00143	0.06 RPM
TSI_NA20512	0.03 RPM
TSI_NA20513	0.05 RPM
TSI_NA20518	0.06 RPM
TSI_NA20532	0.07 RPM
TSI_NA20538	0.00 RPM
TSI_NA20756	0.03 RPM
TSI_NA20765	0.02 RPM
TSI_NA20771	0.06 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.07 RPM
YRI_NA18907	0.03 RPM
YRI_NA18916	0.02 RPM
YRI_NA19093	0.00 RPM
YRI_NA19099	0.03 RPM
YRI_NA19114	0.00 RPM
YRI_NA19118	0.06 RPM
YRI_NA19213	0.00 RPM
YRI_NA19214	0.02 RPM
YRI_NA19223	0.00 RPM

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Indel association:

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