RetrogeneDB ID: retro_hsap_2889

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 3:179367252..179367581(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000243977
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: H3F3A
• Ensembl ID: ENSG00000163041
• Aliases: H3F3A, H3.3A, H3F3
• Description: H3 histone, family 3A [Source:HGNC Symbol;Acc:4764]

Sequence

>retro_hsap_2889
CGCAAGAGTGCGCCCTCTACTGGACGGGTGAAGAAACCTCATCATTACAGACCTGGTACTGTGGCACTCGTGAAATTAGA
CGTTATCAGAAGTCCACTGAACTTCTGATTCGCAAACTTCCCTTCCAGTGTCTGGTGCGAGAAATTGCTCAGGACTTTAA
AACAGATATGCACTTCCAGAGTGCAGCTGTTGGTGCTTTGCAGGAGGCAAGTGAGGCCTACCTGGTTGGTCTTTTTGAAG
ACACCAACCTGTGTGCTATCCATGCCGAACATGTAACAATTATGCCAAAAGACATCCAGCTAACACACCACATACCTGAA
GAATGTGCT

Alignment

ORF - retro_hsap_2889 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.49 %
• Parental protein coverage: 80.88 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RKSAPSTGGVKKPHRYRPGTVAL-REIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQE
          RKSAPSTG.VKKPH.YRPGTVAL.REIRRYQKSTELLIRKLPFQ.LVREIAQDFKTD..FQSAA.GALQE
Retrocopy RKSAPSTGRVKKPHHYRPGTVAL<REIRRYQKSTELLIRKLPFQCLVREIAQDFKTDMHFQSAAVGALQE

Parental  ASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA
          ASEAYLVGLFEDTNLCAIHA..VTIMPKDIQL...I..E.A
Retrocopy ASEAYLVGLFEDTNLCAIHAEHVTIMPKDIQLTHHIPEECA

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	5.69 RPM
bodymap2_adrenal	0.00 RPM	17.77 RPM
bodymap2_brain	0.00 RPM	5.06 RPM
bodymap2_breast	0.00 RPM	7.20 RPM
bodymap2_colon	0.00 RPM	13.75 RPM
bodymap2_heart	0.00 RPM	5.80 RPM
bodymap2_kidney	0.00 RPM	11.81 RPM
bodymap2_liver	0.00 RPM	7.39 RPM
bodymap2_lung	0.00 RPM	24.77 RPM
bodymap2_lymph_node	0.00 RPM	25.95 RPM
bodymap2_ovary	0.00 RPM	10.68 RPM
bodymap2_prostate	0.00 RPM	16.49 RPM
bodymap2_skeletal_muscle	0.00 RPM	5.95 RPM
bodymap2_testis	0.00 RPM	10.39 RPM
bodymap2_thyroid	0.02 RPM	6.10 RPM
bodymap2_white_blood_cells	0.00 RPM	69.30 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_2889 was not detected

EST

No EST(s) were mapped for retro_hsap_2889 retrocopy.

TSS

No TSS is located nearby retro_hsap_2889 retrocopy 5' end.

Lab

retro_hsap_2889 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2889 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1954

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 75 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000024561	3 retrocopies	retro_btau_156, retro_btau_204, retro_btau_47,
Canis familiaris	ENSCAFG00000004916	2 retrocopies	retro_cfam_1117, retro_cfam_622,
Canis familiaris	ENSCAFG00000016119	4 retrocopies	retro_cfam_168, retro_cfam_1845, retro_cfam_650, retro_cfam_673,
Erinaceus europaeus	ENSEEUG00000013796	1 retrocopy	retro_eeur_2,
Felis catus	ENSFCAG00000003617	4 retrocopies	retro_fcat_1085, retro_fcat_1953, retro_fcat_592, retro_fcat_830,
Felis catus	ENSFCAG00000030424	5 retrocopies	retro_fcat_1251, retro_fcat_1532, retro_fcat_1533, retro_fcat_2011, retro_fcat_674,
Homo sapiens	ENSG00000132475	11 retrocopies	retro_hsap_1212, retro_hsap_1552, retro_hsap_2180, retro_hsap_24, retro_hsap_2971, retro_hsap_3231, retro_hsap_3294, retro_hsap_3299, retro_hsap_389, retro_hsap_4236, retro_hsap_911,
Homo sapiens	ENSG00000163041	5 retrocopies	retro_hsap_2825, retro_hsap_2889 , retro_hsap_3102, retro_hsap_3214, retro_hsap_4800,
Gadus morhua	ENSGMOG00000014306	1 retrocopy	retro_gmor_9,
Macaca mulatta	ENSMMUG00000031483	9 retrocopies	retro_mmul_108, retro_mmul_147, retro_mmul_201, retro_mmul_213, retro_mmul_215, retro_mmul_286, retro_mmul_337, retro_mmul_346, retro_mmul_7,
Nomascus leucogenys	ENSNLEG00000001577	2 retrocopies	retro_nleu_25, retro_nleu_35,
Otolemur garnettii	ENSOGAG00000024312	11 retrocopies	retro_ogar_1086, retro_ogar_1790, retro_ogar_1863, retro_ogar_2364, retro_ogar_2463, retro_ogar_2581, retro_ogar_2746, retro_ogar_3415, retro_ogar_478, retro_ogar_842, retro_ogar_955,
Otolemur garnettii	ENSOGAG00000025933	14 retrocopies	retro_ogar_1285, retro_ogar_1364, retro_ogar_1449, retro_ogar_1575, retro_ogar_1576, retro_ogar_2200, retro_ogar_2316, retro_ogar_2449, retro_ogar_2634, retro_ogar_3235, retro_ogar_42, retro_ogar_733, retro_ogar_937, retro_ogar_952,
Pongo abelii	ENSPPYG00000008636	1 retrocopy	retro_pabe_2662,
Pteropus vampyrus	ENSPVAG00000008459	2 retrocopies	retro_pvam_218, retro_pvam_52,

Population studies

Expression level across human populations :

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