FAM182B_1 listed as both coding and noncoding promoter in EPD hg38 most recent version.

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Benjamin Skubi

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Oct 30, 2025, 2:55:01 AM10/30/25
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Hello,

During an analysis, I noticed that the promoter name FAM182B_1 is listed in both the coding and noncoding BED files for hg38:


I'm not a FAM182B expert, so I apologize if this is deliberate. It was the only promoter name that I found repeated across the concatenation of these two files, and since it appears to be lncRNA, I thought I'd report it in case it was misannotated.

My best,
Ben Skubi
BME PhD Student (OHSU, Yardimci Lab and Adey Lab)
BME MS (U. Mich, Shea Lab)

Benjamin Skubi

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Oct 30, 2025, 3:06:04 AM10/30/25
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As a followup, I also noticed that in https://epd.expasy.org/ftp/epdnew/human/006/Hs_EPDnew_006_hg38.bed, TXNIP_1 and TXNIP_2 are identically positioned, which I suspect may be a data artifact.

chr1 145996568 145996628 TXNIP_1 900 - 145996568 145996579
chr1 145996568 145996628 TXNIP_2 900 - 145996568 145996579

My best,
Ben Skubi
BME PhD Student (OHSU, Yardimci Lab and Adey Lab)
BME MS (U. Mich, Shea Lab)
From: Benjamin Skubi
Sent: Wednesday, October 29, 2025 11:54 PM
To: ask...@googlegroups.com <ask...@googlegroups.com>
Subject: FAM182B_1 listed as both coding and noncoding promoter in EPD hg38 most recent version.
 

CCG EPFL

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Nov 13, 2025, 4:00:58 AM11/13/25
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Dear Ben, 

Thanks for bringing the issues with FAM182B_1 and TXNIP_2 to our attention. We really appreciate such feedback.
.
In both cases, these are clearly errors. We don't know exactly know why they happened in the first place and they were not detected by subsequent sanity checks.

FAM182B is a non-coding gene. Therefore the entry in the coding Section has no reason to be there.
TXNIP_1 and TXNIP_2  are indeed exact duplicates. TXNIP_2 should be ignored. 

We have posted warnings about the problematic entries  on our website, which are displayed by the entry viewers:


You can also find and access these warnings in text format on our ftp site:


I hope this answers your question. We are sorry for the inconvenience.

Philipp
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