RetrogeneDB ID: retro_hsap_2971

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 4:113486143..113486551(+)
• Located in intron of: ENSG00000138658

Retrocopy information

• Ensembl ID: ENSG00000250966
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: H3F3B
• Ensembl ID: ENSG00000132475
• Aliases: H3F3B, H3.3B
• Description: H3 histone, family 3B (H3.3B) [Source:HGNC Symbol;Acc:4765]

Sequence

>retro_hsap_2971
ATGGCTCGTACAAGGCAGACTGCCCACAAATCAACCGGTGGTAAACCACCCAGGAAGCAACTGGCTACAAAAGCCGCTCG
CAAGAGTGTGCCCTCTACTGGAGGGGTGAAGAAACCTCATCGTTACAGGCCTGGTACTGTGGCGCTCCGTGAAATTAGAT
GTTATCAGAAGTCCACTGAACTTCTGATTCGCTAACTTCCCTTCCAGCGTCTGGTGCGAGAAATTGCTCAGGACTTTAAA
ACAGATCTGCACTTCCAGAGCGCAGCTATCGGTGCTTTGCAGGAGGCAAGTGAGGCCTATCTGGTTGGCCTTTTTGAAGA
CACCAACCTGTGTGCTATCCATGCCAAACGTGTAACAATTATGCCAAAAGACATCCAGCTAGCATGCCACATACGTTGAG
AATGTGCT

Alignment

ORF - retro_hsap_2971 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.91 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQR
          MART.QTA.KSTGGK.PRKQLATKAARKS.PSTGGVKKPHRYRPGTVALREIR.YQKSTELLIR.LPFQR
Retrocopy MARTRQTAHKSTGGKPPRKQLATKAARKSVPSTGGVKKPHRYRPGTVALREIRCYQKSTELLIR*LPFQR

Parental  LVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA
          LVREIAQDFKTDL.FQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLA..IR.E.A
Retrocopy LVREIAQDFKTDLHFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLACHIR*ECA

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	0.02 RPM	358.42 RPM
bodymap2_adrenal	0.06 RPM	566.78 RPM
bodymap2_brain	0.00 RPM	541.14 RPM
bodymap2_breast	0.00 RPM	323.45 RPM
bodymap2_colon	0.04 RPM	361.41 RPM
bodymap2_heart	0.06 RPM	91.05 RPM
bodymap2_kidney	0.15 RPM	326.19 RPM
bodymap2_liver	0.06 RPM	114.76 RPM
bodymap2_lung	0.21 RPM	619.46 RPM
bodymap2_lymph_node	0.05 RPM	265.57 RPM
bodymap2_ovary	0.02 RPM	1184.97 RPM
bodymap2_prostate	0.17 RPM	568.46 RPM
bodymap2_skeletal_muscle	0.07 RPM	113.47 RPM
bodymap2_testis	0.06 RPM	496.18 RPM
bodymap2_thyroid	0.04 RPM	1081.08 RPM
bodymap2_white_blood_cells	0.39 RPM	627.57 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_2971 was not detected

EST

No EST(s) were mapped for retro_hsap_2971 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_138985	234 libraries	415 libraries	964 libraries	168 libraries	48 libraries

The graphical summary, for retro_hsap_2971 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_hsap_2971 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2971 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2009

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012702	10 retrocopies	retro_cjac_145, retro_cjac_198, retro_cjac_201, retro_cjac_224, retro_cjac_235, retro_cjac_238, retro_cjac_307, retro_cjac_334, retro_cjac_366, retro_cjac_68,
Dasypus novemcinctus	ENSDNOG00000024843	2 retrocopies	retro_dnov_1624, retro_dnov_775,
Equus caballus	ENSECAG00000006904	1 retrocopy	retro_ecab_916,
Equus caballus	ENSECAG00000016948	1 retrocopy	retro_ecab_266,
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,
Latimeria chalumnae	ENSLACG00000004118	1 retrocopy	retro_lcha_104,
Loxodonta africana	ENSLAFG00000008083	3 retrocopies	retro_lafr_837, retro_lafr_959, retro_lafr_99,
Microcebus murinus	ENSMICG00000002139	2 retrocopies	retro_mmur_36, retro_mmur_371,
Mustela putorius furo	ENSMPUG00000004555	4 retrocopies	retro_mputfur_389, retro_mputfur_82, retro_mputfur_99, retro_mputfur_990,
Pongo abelii	ENSPPYG00000008636	1 retrocopy	retro_pabe_2662,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.09 RPM
CEU_NA11843	0.03 RPM
CEU_NA11930	0.07 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.00 RPM
CEU_NA12751	0.02 RPM
CEU_NA12760	0.04 RPM
CEU_NA12827	0.05 RPM
CEU_NA12872	0.03 RPM
CEU_NA12873	0.00 RPM
FIN_HG00183	0.08 RPM
FIN_HG00277	0.11 RPM
FIN_HG00315	0.06 RPM
FIN_HG00321	0.06 RPM
FIN_HG00328	0.02 RPM
FIN_HG00338	0.02 RPM
FIN_HG00349	0.03 RPM
FIN_HG00375	0.05 RPM
FIN_HG00377	0.03 RPM
FIN_HG00378	0.00 RPM
GBR_HG00099	0.09 RPM
GBR_HG00111	0.00 RPM
GBR_HG00114	0.08 RPM
GBR_HG00119	0.00 RPM
GBR_HG00131	0.03 RPM
GBR_HG00133	0.05 RPM
GBR_HG00134	0.00 RPM
GBR_HG00137	0.03 RPM
GBR_HG00142	0.11 RPM
GBR_HG00143	0.10 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.05 RPM
TSI_NA20518	0.03 RPM
TSI_NA20532	0.14 RPM
TSI_NA20538	0.05 RPM
TSI_NA20756	0.00 RPM
TSI_NA20765	0.04 RPM
TSI_NA20771	0.00 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.03 RPM
YRI_NA18870	0.07 RPM
YRI_NA18907	0.07 RPM
YRI_NA18916	0.04 RPM
YRI_NA19093	0.03 RPM
YRI_NA19099	0.08 RPM
YRI_NA19114	0.03 RPM
YRI_NA19118	0.04 RPM
YRI_NA19213	0.00 RPM
YRI_NA19214	0.00 RPM
YRI_NA19223	0.00 RPM

---

Indel association:

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