Repbase Reports |
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| 2024, Volume 24, Issue 12 |
| December 20, 2024 |
| Copyright © 2001-2024 - Genetic Information Research Institute, California |
| ISSN# 1534-830X |
| Page 9647 |
SINE2-21_Ilex |
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SINE2-21_Ilex, a consensus sequence for the holly genus. |
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Submitted: 03-Dec-2024 |
Accepted: 20-Dec-2024 |
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Key Words: SINE2/tRNA; SINE; Non-LTR Retrotransposon; Transposable Element; SINE2-21_Ilex |
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Source: Ilex |
Organism: Ilex |
Taxonomy: Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae; asterids; campanulids; Aquifoliales; Aquifoliaceae |
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Authors: Aguilera,P.M. and Grabiele,M. |
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Title: SINE retroposons from the yerba mate and related holly genomes. |
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Journal: Repbase Reports 24(12), 9647-9647 (2024) |
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Abstract: Analyzed genomes: Ilex paraguariensis YMM1 (NGDC:PRJCA032295), I. asprella (NCBI:GCA_023539305.1), I aquifolium (NCBI:GCA_951799425.1), I. latifolia (NGDC:GWHBIST00000000) and I. polyneura (NGDC:GWHBDNW00000000). Consensus of 52 total genomic copies; mean 85.0% identity to consensus. Additional features: tRNA-related region (1-73); A box (15-25); B box (59-69); tRNA-unrelated region (74-128). First 86 nt are almost identical to SINE2-20_Ilex (C/A and C/T divergences at positions 36 and 50, respectively). All SINE2-21_Ilex genomic elements share the core 128 nt region, however hold distinct tails composed by low complexity sequences (poly A) or SSRs (poly AT, poly TT/C), 7 to 52 nt long (mean 19.3 nt) and mean 90% AT-rich. TSDs, solely found at poly A and poly AT tail sequences, diverge also in length ranging from 8 to 24 nt (mean 15.3 nt) and are mean 68% AT-rich. SINE2-21_Ilex consensus sequence at Repbase does not include the tail for this element.
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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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