RetrogeneDB ID: retro_hsap_2256

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 2:48860056..48860356(-)
• Located in intron of: ENSG00000242441

Retrocopy information

• Ensembl ID: ENSG00000239995
• 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_2256
ATTGACAGAAATGCCTCCGCAGAAGGCCCTGAGGGTGAGGGTACCGAAAGCACATTAATCACTTATGTTGATACTGTCAT
GAACCATCACTTGCAGGAAACAAACTTCAAAAAGAAGCCTACAAGAAGTACATCAAAGATTACATAAAATCAATCAAAGG
CCAACATGAAGAACAGAGACCTAAACAGTAAAACCTTTTATGACAGAAGCTGTAGAACAAACCAAGCACATCTTACTAAT
TTCAACAACTACCAGTTTTTTACCAGTAAAAACATGAATCCAGATGGCATAGTTGCTCTA

Alignment

ORF - retro_hsap_2256 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.92 %
• Parental protein coverage: 58.72 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  IGGNASAEGPEGEGTESTVITGVDIVMNHHLQETSF-TKEAYKKYIKDYMKSIKGKLEEQRPER-VKPFM
          I..NASAEGPEGEGTEST.IT.VD.VMNHHLQET.F..KEAYKKYIKDY.KSIKG..EEQRP...VKPFM
Retrocopy IDRNASAEGPEGEGTESTLITYVDTVMNHHLQETNF<QKEAYKKYIKDYIKSIKGQHEEQRPKQ<VKPFM

Parental  TGAAEQIKHI-LANFKNYQFFIGENMNPDGMVAL
          T.A.EQ.KHI.L.NF.NYQFF...NMNPDG.VAL
Retrocopy TEAVEQTKHI<LTNFNNYQFFTSKNMNPDGIVAL

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	3527.94 RPM
bodymap2_adrenal	0.00 RPM	4636.98 RPM
bodymap2_brain	0.00 RPM	876.21 RPM
bodymap2_breast	0.00 RPM	2853.61 RPM
bodymap2_colon	0.00 RPM	5094.86 RPM
bodymap2_heart	0.00 RPM	1727.64 RPM
bodymap2_kidney	0.00 RPM	2055.10 RPM
bodymap2_liver	0.00 RPM	1968.11 RPM
bodymap2_lung	0.00 RPM	4858.95 RPM
bodymap2_lymph_node	0.00 RPM	4774.03 RPM
bodymap2_ovary	0.00 RPM	5516.77 RPM
bodymap2_prostate	0.00 RPM	4414.84 RPM
bodymap2_skeletal_muscle	0.00 RPM	6949.31 RPM
bodymap2_testis	0.08 RPM	2986.84 RPM
bodymap2_thyroid	0.00 RPM	4592.00 RPM
bodymap2_white_blood_cells	0.00 RPM	4561.35 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_2256 was not detected

EST

No EST(s) were mapped for retro_hsap_2256 retrocopy.

TSS

No TSS is located nearby retro_hsap_2256 retrocopy 5' end.

Lab

retro_hsap_2256 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2256 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_1681

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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