Repbase Reports |
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| 2023, Volume 23, Issue 4 |
| April 27, 2023 |
| Copyright © 2001-2023 - Genetic Information Research Institute, California |
| ISSN# 1534-830X |
| Page 2677 |
SINE2-10a_Atr |
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SINE2-10a_Atr, a novel SINE retroposon from the Amborella trichopoda genome. |
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Submitted: 08-Apr-2023 |
Accepted: 27-Apr-2023 |
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Key Words: SINE2/tRNA; SINE; Non-LTR Retrotransposon; Transposable Element; SINE2-10a_Atr |
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Source: Amborella trichopoda |
Organism: Amborella trichopoda |
Taxonomy: Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; basal Magnoliophyta; Amborellales; Amborellaceae; Amborella |
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Authors: Grabiele,M. and Aguilera,P.M. |
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Title: SINE retroposons from the Amborella genome. |
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Journal: Repbase Reports 23(4), 2677-2677 (2023) |
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Abstract: De novo TE library from GCA_000471905.1. Consensus of 30 seqs; mean 82.69% identity to consensus. Additional features: tRNA related region (1-71; 113-185); A box (14-25; 126-137); B box (57-67; 171-181); LINE-related region (72-112; 186-218); poly A tail (219-227). SINE2-10a_Atr is heterodimeric and exist copies with visible TSDs; forward region is related to SINE2-6_Atr (87% of length, up to the poly T stretch of the second tandem repetion) and second one to SINE2-3_Atr (full length); copies of SINE2-10a_Atr with three forward tandem repetitions of the SINE2-6_Atr related region and visible poly A tail also occur (444 nt mean) but without detectable TSDs; at the scaffold 109 there is a copy of SINE2-10a_Atr with poly A tail and visible TSDs (CAATAGGTCCTGGAG/CAATAGGTCTTGGAG) that carries a copy of the U6 spliceosomal RNA gene ENSRNA049453437 (100 nt; flanked by and terminated in a poly T stretch) just after the poly T stretch that commonly separate the different SINE related regions. 20 consensus seqs belonging to SINE2-1_Atr to SINE2-11_Atr share the L1 lineage origin (L1-5_Atr and related seqs of Repbase).
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Derived: [1] (Consensus) |
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Download Sequence - Format: IG, EMBL, FASTA |
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References: |
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