RetrogeneDB ID: retro_hsap_446

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 1:144612264..144612663(-)
• Located in intron of: ENSG00000225241

Retrocopy information

• Ensembl ID: ENSG00000203843
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PFN1
• Ensembl ID: ENSG00000108518
• Aliases: PFN1, ALS18
• Description: profilin 1 [Source:HGNC Symbol;Acc:8881]

Sequence

>retro_hsap_446
ATCTACAGCCTCGTGGCGGACGGGACCTGTTAGGACACTGCCATTGTGGGTAACAAGGACCCGCCTTCCATCTGGGCCGC
CGTCCCAGGGAAAACCTTCCTCAACATCACGCCAGCTGAGGTTGGTGTCCTGGTTGGCAAAGACTGGTCAAGCTTTGTCA
TGAATGGGCTGACACTGGGGGGCCAGAAATATACTGTGGTCCTGGACTCACTGCTGCAGGATGGGGAATTGACCACGGAT
CTTCGTATGAAGAGCATCGGTGGAGCCCCCACCTTCAACGTCATTGTCACCATGACTGCCAAGACGCTAGGCCTGCTGAT
GGGCAAAGAAGGTATCCATGGCAATTTCATCGACAAGTAATGTTATGAAATGGCCTCCCACCTTCAGCGTTCCCAGTAC

Alignment

ORF - retro_hsap_446 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.69 %
• Parental protein coverage: 95. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IDNLMADGTCQDAAIVGYKDSPSVWAAVPGKTFVNITPAEVGVLVGKDRSSFYVNGLTLGGQKCSVIRDS
          I..L.ADGTC.D.AIVG.KD.PS.WAAVPGKTF.NITPAEVGVLVGKD.SSF..NGLTLGGQK..V..DS
Retrocopy IYSLVADGTC*DTAIVGNKDPPSIWAAVPGKTFLNITPAEVGVLVGKDWSSFVMNGLTLGGQKYTVVLDS

Parental  LLQDGEFSMDLRTKSTGGAPTFNVTVTKTDKTLVLLMGKEGVHGGLINKKCYEMASHLRRSQY
          LLQDGE...DLR.KS.GGAPTFNV.VT.T.KTL.LLMGKEG.HG..I.K.CYEMASHL.RSQY
Retrocopy LLQDGELTTDLRMKSIGGAPTFNVIVTMTAKTLGLLMGKEGIHGNFIDK*CYEMASHLQRSQY

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	0.10 RPM	337.55 RPM
bodymap2_adrenal	0.23 RPM	548.44 RPM
bodymap2_brain	0.00 RPM	78.20 RPM
bodymap2_breast	0.02 RPM	232.32 RPM
bodymap2_colon	0.00 RPM	381.67 RPM
bodymap2_heart	0.06 RPM	82.54 RPM
bodymap2_kidney	0.31 RPM	230.30 RPM
bodymap2_liver	0.09 RPM	224.00 RPM
bodymap2_lung	0.05 RPM	363.01 RPM
bodymap2_lymph_node	0.15 RPM	391.06 RPM
bodymap2_ovary	0.19 RPM	213.76 RPM
bodymap2_prostate	0.02 RPM	385.65 RPM
bodymap2_skeletal_muscle	0.02 RPM	163.65 RPM
bodymap2_testis	0.09 RPM	200.07 RPM
bodymap2_thyroid	0.36 RPM	167.90 RPM
bodymap2_white_blood_cells	0.06 RPM	932.91 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_446 was not detected

EST

No EST(s) were mapped for retro_hsap_446 retrocopy.

TSS

No TSS is located nearby retro_hsap_446 retrocopy 5' end.

Lab

retro_hsap_446 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_446 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 51 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006193	2 retrocopies	retro_amel_1712, retro_amel_1781,
Bos taurus	ENSBTAG00000004915	1 retrocopy	retro_btau_141,
Callithrix jacchus	ENSCJAG00000011719	2 retrocopies	retro_cjac_1023, retro_cjac_1641,
Cavia porcellus	ENSCPOG00000013136	1 retrocopy	retro_cpor_1216,
Equus caballus	ENSECAG00000021116	3 retrocopies	retro_ecab_171, retro_ecab_28, retro_ecab_559,
Homo sapiens	ENSG00000108518	10 retrocopies	retro_hsap_214, retro_hsap_215, retro_hsap_221, retro_hsap_223, retro_hsap_224, retro_hsap_352, retro_hsap_446 , retro_hsap_447, retro_hsap_450, retro_hsap_451,
Gorilla gorilla	ENSGGOG00000022394	3 retrocopies	retro_ggor_285, retro_ggor_289, retro_ggor_366,
Macaca mulatta	ENSMMUG00000002772	5 retrocopies	retro_mmul_407, retro_mmul_527, retro_mmul_528, retro_mmul_574, retro_mmul_732,
Mus musculus	ENSMUSG00000018293	1 retrocopy	retro_mmus_1326,
Nomascus leucogenys	ENSNLEG00000017446	6 retrocopies	retro_nleu_16, retro_nleu_1870, retro_nleu_2425, retro_nleu_2429, retro_nleu_848, retro_nleu_886,
Otolemur garnettii	ENSOGAG00000031395	3 retrocopies	retro_ogar_1680, retro_ogar_2143, retro_ogar_3351,
Procavia capensis	ENSPCAG00000000291	1 retrocopy	retro_pcap_27,
Pelodiscus sinensis	ENSPSIG00000004124	1 retrocopy	retro_psin_8,
Pan troglodytes	ENSPTRG00000008616	5 retrocopies	retro_ptro_185, retro_ptro_196, retro_ptro_276, retro_ptro_332, retro_ptro_333,
Rattus norvegicus	ENSRNOG00000003975	1 retrocopy	retro_rnor_1623,
Sus scrofa	ENSSSCG00000017905	1 retrocopy	retro_sscr_275,
Ictidomys tridecemlineatus	ENSSTOG00000028950	1 retrocopy	retro_itri_129,
Tursiops truncatus	ENSTTRG00000001299	1 retrocopy	retro_ttru_14,
Vicugna pacos	ENSVPAG00000005327	3 retrocopies	retro_vpac_389, retro_vpac_395, retro_vpac_457,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.06 RPM
CEU_NA11843	0.11 RPM
CEU_NA11930	0.23 RPM
CEU_NA12004	0.15 RPM
CEU_NA12400	0.18 RPM
CEU_NA12751	0.27 RPM
CEU_NA12760	0.13 RPM
CEU_NA12827	0.05 RPM
CEU_NA12872	0.24 RPM
CEU_NA12873	0.35 RPM
FIN_HG00183	0.63 RPM
FIN_HG00277	0.33 RPM
FIN_HG00315	0.06 RPM
FIN_HG00321	0.33 RPM
FIN_HG00328	0.14 RPM
FIN_HG00338	0.11 RPM
FIN_HG00349	0.06 RPM
FIN_HG00375	0.15 RPM
FIN_HG00377	0.10 RPM
FIN_HG00378	0.23 RPM
GBR_HG00099	0.12 RPM
GBR_HG00111	0.26 RPM
GBR_HG00114	0.03 RPM
GBR_HG00119	0.60 RPM
GBR_HG00131	0.29 RPM
GBR_HG00133	0.07 RPM
GBR_HG00134	0.33 RPM
GBR_HG00137	0.25 RPM
GBR_HG00142	0.69 RPM
GBR_HG00143	0.13 RPM
TSI_NA20512	0.03 RPM
TSI_NA20513	0.58 RPM
TSI_NA20518	0.08 RPM
TSI_NA20532	0.71 RPM
TSI_NA20538	0.51 RPM
TSI_NA20756	0.09 RPM
TSI_NA20765	0.29 RPM
TSI_NA20771	0.14 RPM
TSI_NA20786	0.16 RPM
TSI_NA20798	0.19 RPM
YRI_NA18870	0.68 RPM
YRI_NA18907	0.14 RPM
YRI_NA18916	0.23 RPM
YRI_NA19093	0.10 RPM
YRI_NA19099	0.27 RPM
YRI_NA19114	0.03 RPM
YRI_NA19118	0.23 RPM
YRI_NA19213	0.17 RPM
YRI_NA19214	0.27 RPM
YRI_NA19223	0.44 RPM

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Indel association:

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