RetrogeneDB ID: retro_hsap_3676

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 6:144521586..144522102(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000217027
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TPT1
• Ensembl ID: ENSG00000133112
• Aliases: TPT1, HRF, TCTP, p02, p23
• Description: tumor protein, translationally-controlled 1 [Source:HGNC Symbol;Acc:12022]

Sequence

>retro_hsap_3676
ATGATTATCTACCGCGACCTCATCAGCCACGATGAGATGTTTTCCGACATCTACAAGATCTGGGAGATCATGGACGGGCT
GTACCTGGAGGTGGAGGGGAAGATGGTCAGTAGGATAGAAGGTAACATTGATGACTCGCTCATTGGTGGTAATACCTCCG
CTGAATGACCCTAGGGCGAAGGTACAGAAAGCACAGTAATCACTGGTGTTGATATTGTCATGAACCATCACCTGCAGGAA
ACAAGTTTCACAAAAGAAGCCTACAAGAAGTATATCAAAGATTACATGAAATCAATCAAAGCCAAACTTGAAGAACAGAG
ACCAGAAACAGTAAAACCTTTTATGACAGGGGCTGCAAAACAAATCAAGGACATCCTTGCTAATTTCAAAAACTACCAGT
TCTTTAATTGTGAAAACATGAATCCAGATGGCATGGTTGCTCTATTGGACTACCGTGAAGATGGTGTGACCCCATATATG
ATTTTCTTTAAGGATGATTTAGAAATGGAAAAATGT

Alignment

ORF - retro_hsap_3676 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.86 %
• Parental protein coverage: 91.49 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MIIYRDLISHDEMFSDIYKIREIADGLCLEVEGKMVSRTEGNIDDSLIGGNASAEGPEGEGTESTVITGV
          MIIYRDLISHDEMFSDIYKI.EI.DGL.LEVEGKMVSR.EGNIDDSLIGGN.SAE.P.GEGTESTVITGV
Retrocopy MIIYRDLISHDEMFSDIYKIWEIMDGLYLEVEGKMVSRIEGNIDDSLIGGNTSAE*P*GEGTESTVITGV

Parental  DIVMNHHLQETSFTKEAYKKYIKDYMKSIKGKLEEQRPERVKPFMTGAAEQIKHILANFKNYQFFIGENM
          DIVMNHHLQETSFTKEAYKKYIKDYMKSIK.KLEEQRPE.VKPFMTGAA.QIK.ILANFKNYQFF..ENM
Retrocopy DIVMNHHLQETSFTKEAYKKYIKDYMKSIKAKLEEQRPETVKPFMTGAAKQIKDILANFKNYQFFNCENM

Parental  NPDGMVALLDYREDGVTPYMIFFKDGLEMEKC
          NPDGMVALLDYREDGVTPYMIFFKD.LEMEKC
Retrocopy NPDGMVALLDYREDGVTPYMIFFKDDLEMEKC

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	0.48 RPM	3527.94 RPM
bodymap2_adrenal	0.45 RPM	4636.98 RPM
bodymap2_brain	0.07 RPM	876.21 RPM
bodymap2_breast	0.53 RPM	2853.61 RPM
bodymap2_colon	0.79 RPM	5094.86 RPM
bodymap2_heart	0.04 RPM	1727.64 RPM
bodymap2_kidney	0.15 RPM	2055.10 RPM
bodymap2_liver	0.02 RPM	1968.11 RPM
bodymap2_lung	0.11 RPM	4858.95 RPM
bodymap2_lymph_node	0.37 RPM	4774.03 RPM
bodymap2_ovary	0.67 RPM	5516.77 RPM
bodymap2_prostate	0.50 RPM	4414.84 RPM
bodymap2_skeletal_muscle	0.22 RPM	6949.31 RPM
bodymap2_testis	0.08 RPM	2986.84 RPM
bodymap2_thyroid	0.47 RPM	4592.00 RPM
bodymap2_white_blood_cells	0.26 RPM	4561.35 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_3676 was not detected

EST

No EST(s) were mapped for retro_hsap_3676 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_160180	453 libraries	696 libraries	641 libraries	35 libraries	4 libraries

The graphical summary, for retro_hsap_3676 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_3676 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3676 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 116 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000006531	2 retrocopies	retro_acar_156, retro_acar_58,
Ailuropoda melanoleuca	ENSAMEG00000013022	8 retrocopies	retro_amel_1153, retro_amel_1521, retro_amel_1593, retro_amel_1804, retro_amel_1878, retro_amel_472, retro_amel_569, retro_amel_969,
Canis familiaris	ENSCAFG00000004533	10 retrocopies	retro_cfam_1110, retro_cfam_1328, retro_cfam_1476, retro_cfam_1508, retro_cfam_1846, retro_cfam_254, retro_cfam_341, retro_cfam_483, retro_cfam_661, retro_cfam_777,
Dasypus novemcinctus	ENSDNOG00000000653	22 retrocopies	retro_dnov_1071, retro_dnov_1202, retro_dnov_1349, retro_dnov_1705, retro_dnov_2082, retro_dnov_2283, retro_dnov_2305, retro_dnov_237, retro_dnov_2412, retro_dnov_2531, retro_dnov_2687, retro_dnov_276, retro_dnov_342, retro_dnov_397, retro_dnov_417, retro_dnov_453, retro_dnov_71, retro_dnov_847, retro_dnov_870, retro_dnov_909, retro_dnov_934, retro_dnov_981,
Equus caballus	ENSECAG00000018348	3 retrocopies	retro_ecab_337, retro_ecab_686, retro_ecab_727,
Felis catus	ENSFCAG00000002107	8 retrocopies	retro_fcat_1366, retro_fcat_1544, retro_fcat_1996, retro_fcat_443, retro_fcat_553, retro_fcat_645, retro_fcat_735, retro_fcat_992,
Homo sapiens	ENSG00000133112	13 retrocopies	retro_hsap_1083, retro_hsap_2234, retro_hsap_2256, retro_hsap_2382, retro_hsap_2503, retro_hsap_3156, retro_hsap_3676 , retro_hsap_3828, retro_hsap_3946, retro_hsap_4307, retro_hsap_4701, retro_hsap_4786, retro_hsap_678,
Gorilla gorilla	ENSGGOG00000001684	12 retrocopies	retro_ggor_1561, retro_ggor_1681, retro_ggor_1807, retro_ggor_2045, retro_ggor_2484, retro_ggor_2628, retro_ggor_2652, retro_ggor_2877, retro_ggor_2878, retro_ggor_2980, retro_ggor_584, retro_ggor_855,
Latimeria chalumnae	ENSLACG00000004306	2 retrocopies	retro_lcha_24, retro_lcha_34,
Microcebus murinus	ENSMICG00000002027	9 retrocopies	retro_mmur_102, retro_mmur_1060, retro_mmur_1163, retro_mmur_1627, retro_mmur_248, retro_mmur_318, retro_mmur_490, retro_mmur_641, retro_mmur_967,
Macaca mulatta	ENSMMUG00000022979	2 retrocopies	retro_mmul_158, retro_mmul_85,
Monodelphis domestica	ENSMODG00000014940	2 retrocopies	retro_mdom_128, retro_mdom_9,
Mustela putorius furo	ENSMPUG00000001640	10 retrocopies	retro_mputfur_1043, retro_mputfur_30, retro_mputfur_364, retro_mputfur_565, retro_mputfur_574, retro_mputfur_582, retro_mputfur_677, retro_mputfur_870, retro_mputfur_960, retro_mputfur_967,
Pongo abelii	ENSPPYG00000005335	5 retrocopies	retro_pabe_1958, retro_pabe_2626, retro_pabe_2809, retro_pabe_83, retro_pabe_900,
Sarcophilus harrisii	ENSSHAG00000001545	1 retrocopy	retro_shar_227,
Ictidomys tridecemlineatus	ENSSTOG00000006931	7 retrocopies	retro_itri_1192, retro_itri_146, retro_itri_266, retro_itri_325, retro_itri_612, retro_itri_700, retro_itri_999,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.11 RPM
CEU_NA11843	0.20 RPM
CEU_NA11930	0.39 RPM
CEU_NA12004	0.08 RPM
CEU_NA12400	0.07 RPM
CEU_NA12751	0.19 RPM
CEU_NA12760	0.22 RPM
CEU_NA12827	0.09 RPM
CEU_NA12872	0.08 RPM
CEU_NA12873	0.10 RPM
FIN_HG00183	0.16 RPM
FIN_HG00277	0.26 RPM
FIN_HG00315	0.06 RPM
FIN_HG00321	0.00 RPM
FIN_HG00328	0.19 RPM
FIN_HG00338	0.13 RPM
FIN_HG00349	0.37 RPM
FIN_HG00375	0.22 RPM
FIN_HG00377	0.15 RPM
FIN_HG00378	0.11 RPM
GBR_HG00099	0.17 RPM
GBR_HG00111	0.04 RPM
GBR_HG00114	0.11 RPM
GBR_HG00119	0.07 RPM
GBR_HG00131	0.06 RPM
GBR_HG00133	0.12 RPM
GBR_HG00134	0.00 RPM
GBR_HG00137	0.14 RPM
GBR_HG00142	0.14 RPM
GBR_HG00143	0.10 RPM
TSI_NA20512	0.14 RPM
TSI_NA20513	0.00 RPM
TSI_NA20518	0.28 RPM
TSI_NA20532	0.07 RPM
TSI_NA20538	0.32 RPM
TSI_NA20756	0.15 RPM
TSI_NA20765	0.08 RPM
TSI_NA20771	0.23 RPM
TSI_NA20786	0.08 RPM
TSI_NA20798	0.06 RPM
YRI_NA18870	0.07 RPM
YRI_NA18907	0.03 RPM
YRI_NA18916	0.06 RPM
YRI_NA19093	0.10 RPM
YRI_NA19099	0.08 RPM
YRI_NA19114	0.13 RPM
YRI_NA19118	0.02 RPM
YRI_NA19213	0.14 RPM
YRI_NA19214	0.10 RPM
YRI_NA19223	0.08 RPM

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Indel association:

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