RetrogeneDB ID: retro_hsap_4667

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: X:33059511..33059835(+)
• Located in intron of: ENSG00000198947

Retrocopy information

• Ensembl ID: ENSG00000226781
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TBCA
• Ensembl ID: ENSG00000171530
• Aliases: None
• Description: tubulin folding cofactor A [Source:HGNC Symbol;Acc:11579]

Sequence

>retro_hsap_4667
ATGGCCGATCCTCGCGTGAGACAGATCAAGATCAAGACCGGTGTGGTGAAGCGGTTGGTCAAATAAAAAGTGATGTATGA
AAAAGAGGCAAAACAACAAGAAGAAAAGATTGAAAAAATGAGAGCTGAAGATGGTGAAAATTATGACATCAAAAAGCAGG
CAGAGATCCTACAAGAATCCCGGATGATGATCCCAGATTGCCAGCGCAGGTTGGAAGCCGCATATTTGGATCTTCAACAG
ATATTAGAAAGTGAAAAAGACTTGGAAGAAGCTGAGGAATATAAAGAAGCACGTTTAGTACTGGATTCAGTGAAGTTAGA
AGCC

Alignment

ORF - retro_hsap_4667 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.22 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MADPRVRQIKIKTGVVKRLVKEKVMYEKEAKQQEEKIEKMRAEDGENYDIKKQAEILQESRMMIPDCQRR
          MADPRVRQIKIKTGVVKRLVK.KVMYEKEAKQQEEKIEKMRAEDGENYDIKKQAEILQESRMMIPDCQRR
Retrocopy MADPRVRQIKIKTGVVKRLVK*KVMYEKEAKQQEEKIEKMRAEDGENYDIKKQAEILQESRMMIPDCQRR

Parental  LEAAYLDLQRILENEKDLEEAEEYKEARLVLDSVKLEA
          LEAAYLDLQ.ILE.EKDLEEAEEYKEARLVLDSVKLEA
Retrocopy LEAAYLDLQQILESEKDLEEAEEYKEARLVLDSVKLEA

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	2.19 RPM	45.42 RPM
bodymap2_adrenal	3.52 RPM	52.65 RPM
bodymap2_brain	3.63 RPM	58.83 RPM
bodymap2_breast	4.67 RPM	51.83 RPM
bodymap2_colon	4.23 RPM	79.16 RPM
bodymap2_heart	0.30 RPM	30.98 RPM
bodymap2_kidney	1.28 RPM	94.78 RPM
bodymap2_liver	0.23 RPM	60.54 RPM
bodymap2_lung	0.11 RPM	49.42 RPM
bodymap2_lymph_node	0.38 RPM	48.99 RPM
bodymap2_ovary	5.74 RPM	75.41 RPM
bodymap2_prostate	0.16 RPM	80.92 RPM
bodymap2_skeletal_muscle	0.24 RPM	37.94 RPM
bodymap2_testis	5.67 RPM	72.26 RPM
bodymap2_thyroid	4.88 RPM	67.85 RPM
bodymap2_white_blood_cells	0.00 RPM	49.08 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_4667 was not detected

EST

No EST(s) were mapped for retro_hsap_4667 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_199304	835 libraries	184 libraries	304 libraries	353 libraries	153 libraries
TSS #2	TSS_199305	456 libraries	518 libraries	334 libraries	335 libraries	186 libraries

The graphical summary, for retro_hsap_4667 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_4667 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_4667 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000014223	4 retrocopies	retro_acar_11, retro_acar_130, retro_acar_142, retro_acar_195,
Callithrix jacchus	ENSCJAG00000019848	4 retrocopies	retro_cjac_114, retro_cjac_2160, retro_cjac_2173, retro_cjac_2974,
Cavia porcellus	ENSCPOG00000012187	1 retrocopy	retro_cpor_930,
Echinops telfairi	ENSETEG00000016572	1 retrocopy	retro_etel_93,
Homo sapiens	ENSG00000171530	3 retrocopies	retro_hsap_3065, retro_hsap_346, retro_hsap_4667 ,
Macaca mulatta	ENSMMUG00000011853	1 retrocopy	retro_mmul_229,
Mus musculus	ENSMUSG00000042043	3 retrocopies	retro_mmus_1486, retro_mmus_2839, retro_mmus_2970,
Otolemur garnettii	ENSOGAG00000010198	1 retrocopy	retro_ogar_3193,
Ochotona princeps	ENSOPRG00000002460	4 retrocopies	retro_opri_550, retro_opri_727, retro_opri_879, retro_opri_91,
Pongo abelii	ENSPPYG00000015579	2 retrocopies	retro_pabe_2540, retro_pabe_350,
Pan troglodytes	ENSPTRG00000017013	2 retrocopies	retro_ptro_2067, retro_ptro_274,
Rattus norvegicus	ENSRNOG00000048342	1 retrocopy	retro_rnor_140,
Sorex araneus	ENSSARG00000009943	1 retrocopy	retro_sara_699,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.30 RPM
CEU_NA11843	0.31 RPM
CEU_NA11930	0.07 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.14 RPM
CEU_NA12751	0.07 RPM
CEU_NA12760	0.09 RPM
CEU_NA12827	0.19 RPM
CEU_NA12872	0.11 RPM
CEU_NA12873	0.06 RPM
FIN_HG00183	0.19 RPM
FIN_HG00277	0.07 RPM
FIN_HG00315	0.03 RPM
FIN_HG00321	0.06 RPM
FIN_HG00328	0.02 RPM
FIN_HG00338	0.09 RPM
FIN_HG00349	0.17 RPM
FIN_HG00375	0.12 RPM
FIN_HG00377	0.08 RPM
FIN_HG00378	0.11 RPM
GBR_HG00099	0.20 RPM
GBR_HG00111	0.09 RPM
GBR_HG00114	0.11 RPM
GBR_HG00119	0.14 RPM
GBR_HG00131	0.06 RPM
GBR_HG00133	0.14 RPM
GBR_HG00134	0.11 RPM
GBR_HG00137	0.08 RPM
GBR_HG00142	0.11 RPM
GBR_HG00143	0.06 RPM
TSI_NA20512	0.14 RPM
TSI_NA20513	0.15 RPM
TSI_NA20518	0.28 RPM
TSI_NA20532	0.17 RPM
TSI_NA20538	0.14 RPM
TSI_NA20756	0.09 RPM
TSI_NA20765	0.04 RPM
TSI_NA20771	0.14 RPM
TSI_NA20786	0.05 RPM
TSI_NA20798	0.09 RPM
YRI_NA18870	0.20 RPM
YRI_NA18907	0.31 RPM
YRI_NA18916	0.06 RPM
YRI_NA19093	0.13 RPM
YRI_NA19099	0.16 RPM
YRI_NA19114	0.03 RPM
YRI_NA19118	0.21 RPM
YRI_NA19213	0.07 RPM
YRI_NA19214	0.05 RPM
YRI_NA19223	0.10 RPM

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Indel association:

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