Sequence
atgc intronic sequence ATGC exonic sequenceCTGAGCAATTATTCATCAATGGAAGGAGTGGTGTATTGTAGGCCTCATTTTGAGCAGCTTTTCAAGGAGTCTGGTAGTTTCAGCAAGAACTTTCAGTCACgtatgtaaaactcttttcttcaccttctggtccagcttttacatgtggtcactttaattttaatcttcaaactttttttttcctttcacag
Basic information
species | Arabidopsis thaliana |
transcript | AT2G39900.1 |
intron # | 3 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G39900.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA11G34830.1 (Glycine max), 5'ss of exon 4
CTGAGCAATTATTCATCAATGGAAGGAGTGGTGTATTGTAGGCCTCATTTTGAGCAGCTTTTCAAGGAGTCTGGTAGTTTCAGCAAGAACTTTCAGTCACgtatgtaaaactcttttcttcaccttctggtccagct-tttacatgtggtcactttaattttaatcttca--aact-----ttttttttcctttcacag
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CTGAGCAACTATTCCTCAATGGAAGGTGTTCTTTATTGTAAGCCTCACTTTGAGCAGCTCTTCAAGGAGAGTGGGTCCTTCAGCAAGAACTTCCAGTCACgtatgtgttcttccttttcttctttgagaatgaagctgtgtttgtgtggtt-tttgaatcatatgcctcattaattggccatatattcattttgaacag
upper sequence: AT2G39900.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA18G03490.1 (Glycine max), 5'ss of exon 4
-CTGAGCAATTATTCATCAATGGAAGGAGTGGTGTATTGTAGGCCTCATTTTGAGCAGCTTTTCAAGGAGTCTGGTAGTTTCAGCAAGAACTTTCAGTCACgtatgtaaaactcttttcttcaccttctggtccagct-tttacatgtggtcactttaattttaa---tcttcaaac--tttttttttcctttcacag-
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GCTGAGTAACTATTCCTCAATGGAAGGTGTTCTTTACTGTAAGCCTCACTATGAGCAGCTCTTCAAGGAGAGTGGCTCCTTCAGCAAGAACTTCCAGTCAcgtatgtg---ttctttttcttctttgaggatgaagttgtgtttgtgtggtt-tttgaatcatatgcctctttaattggccatattttcattttgaaca
upper sequence: AT2G39900.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv13s0019g03280.t01 (Vitis vinifera), 5'ss of exon 3
CTGAGCAATTATTCATCAATGGAAGGAGTGGTGTATTGTAGGCCTCATTTTGAGCAGCTTTTCAAGGAGTCTGGTAGTTTCAGCAAGAACTTTCAGTCACgtatgtaaaactcttttcttcac------cttctggtccagcttttacatgtggtcactttaatt--ttaatcttcaaactttttttttcctttcacag
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CTGAGCAATTATTCCTCAATGGAGGGTGTTCTTTACTGTAAGCCTCACTTTGAGCAGCTCTTTAAGGAGTCTGGAAATTTCAACAAGAATTTTCAGTCACgtgagtctt-cttgtttcaccagataagattctttgtttgatttctcaatggtttctattccattgtttaatgtgcaa--tatatttcattttcaacagMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|164212539|gb|ES092306.1|ES092306EST: GCAAGAACTTTCAGTCAC CTGCAAAGCCATTGACTGATAAGCCAACCCCGGAGCTG
genomic: GCAAGAACTTTCAGTCACgtatgtaaaa ... cctttcacagCTGCAAAGCCATTGACTGATAAGCCAACCCCGGAGCTG
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CTGAGCAATTATTCATCAATGGAAGGAGTGGTGTATTGTAGGCCTCATTTTGAGCAGCTTTTCAAGGAGTCTGGTAGTTTCAGCAAGAACTTTCAGTCACgtatgtaaaactcttttcttcaccttctggtccagcttttacatgtggtcactttaattttaatcttcaaactttttttttcctttcacag
- - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC