Identifying polyadenylation signals with biological embedding via self-attentive gated convolutional highway networks

2021 ◽  
Vol 103 ◽  
pp. 107133
Author(s):  
Yanbu Guo ◽  
Dongming Zhou ◽  
Weihua Li ◽  
Jinde Cao ◽  
Rencan Nie ◽  
...  
1993 ◽  
Vol 292 (2) ◽  
pp. 343-349 ◽  
Author(s):  
R Y Y Chan ◽  
H M Schulman ◽  
P Ponka

Ferrochelatase, which catalyses the last step in haem biosynthesis, i.e. the insertion of Fe(II) into protophorphyrin IX, is present in all cells, but is particularly abundant in erythroid cells during haemoglobinization. Using mouse ferrochelatase cDNA as a probe two ferrochelatase transcripts, having lengths of 2.9 kb and 2.2 kb, were found in extracts of mouse liver, kidney, brain, muscle and spleen, the 2.9 kb transcript being more abundant in the non-erythroid tissues and the 2.2 kb transcript more predominant in spleen. In mouse erythroleukemia cells the 2.9 kb ferrochelatase transcript is also more abundant; however, following induction of erythroid differentiation by dimethyl sulphoxide there is a preferential increase in the 2.2 kb transcript, which eventually predominates. With mouse reticulocytes, the purest immature erythroid cell population available, over 90% of the total ferrochelatase mRNA is present as the 2.2 kb transcript. Since there is probably only one mouse ferrochelatase gene, the occurrence of two ferrochelatase transcripts could arise from the use of two putative polyadenylation signals in the 3′ region of ferrochelatase DNA. This possibility was explored by using a 389 bp DNA fragment produced by PCR with synthetic oligoprimers having sequence similarity with a region between the polyadenylation sites. This fragment hybridized only to the 2.9 kb ferrochelatase transcript, indicating that the two transcripts differ at their 3′ ends and suggesting that the 2.2 kb transcript results from the utilization of the upstream polyadenylation signal. The preferential utilization of the upstream polyadenylation signal may be an erythroid-specific characteristic of ferrochelatase gene expression.


2007 ◽  
Vol 10 (1) ◽  
pp. 73-91 ◽  
Author(s):  
Genevieve Giuliano ◽  
Peter Gordon ◽  
Qisheng Pan ◽  
JiYoung Park ◽  
LanLan Wang

Genetics ◽  
1994 ◽  
Vol 138 (4) ◽  
pp. 1163-1170 ◽  
Author(s):  
E Wojcik ◽  
A M Murphy ◽  
H Fares ◽  
K Dang-Vu ◽  
S I Tsubota

Abstract A hybrid dysgenesis-induced mutation, enhancer of rudimentaryp1 (e(r)p1), is a recessive enhancer of a weak rudimentary mutant phenotype in Drosophila melanogaster. The e(r) gene was cloned using P element tagging and localized to region 8B on the X chromosome. It encodes a 1.0-kb and a 1.2-kb transcript. The 1.0-kb transcript is present in both adult males and females, while the 1.2-kb transcript is predominantly found in females. The difference in the lengths of the two e(r) transcripts is caused by two different polyadenylation sites spaced 228 bp apart. The amounts of both of these transcripts are drastically reduced in the e(r)p1 mutant. The P element in e(r)p1 is inserted in the 5'-untranslated leader region near the start of transcription. It may be producing its effect by suppressing transcription and/or by providing transcription termination and polyadenylation signals. The putative e(r) protein is 104 amino acids in length and bears no striking resemblance to protein sequences in GenBank or PIR. While its biochemical function is unknown at this time, sequence analysis indicates that the e(r) protein is highly conserved and, presumably, functionally very important. The amino acid sequences of the D. melanogaster and the Drosophila virilis proteins are 95% identical.


1974 ◽  
Vol 100 (1) ◽  
pp. 13-26
Author(s):  
Joseph M. Sussman ◽  
Ho-Kwan Wong ◽  
Roger Miller

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