Sequence
atgc intronic sequence ATGC exonic sequencegtgagttccatattcattttactctcttttcctttttttcagttcgaaaactgagtgtatataactctttgtggttcttctcttgtggcagGGAACTTGTGATGAAGTTGTTGACTGTTCTCATGGAAAACAACTATGGGAACTCTCTAAAGAGAAATATGAACCGCTTTGGCTCGAAGGCGGTAACCACT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G14390.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G14390.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os12g18860.1 (Oryza sativa), 3'ss of exon 4
-------gtgagttccatattcatttta--ctctcttttcctttttttcagttcgaaaactgagtgtat-ataactctttgtggttcttctcttgtggcagGGAACTTGTGATGAAGTTGTTGACTGTTCTCATGGAAAACAACTATGGGAACTCTCTAAAGAGAAATATGAACCGCTTTGGCTCGAAGGCGGTAACCACT
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ctgataggccagtatcaagtttacttgaaattgtgcattgcataatcctgcatgtatgcctgaatattttattagtcta-atctctttcctccctctgcagGGAACTGCTGATGAAGTAGTTGATTGGTCTCATGGTAAGCAACTATGGGAGCTTTGCAAAGAGAAATATGAGCCTTTATGGCTCAAGGGAGGGAAGCACT
upper sequence: AT5G14390.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA19G07360.1 (Glycine max), 3'ss of exon 4
---gtgagttccatattcattttactctcttt-tcctttttttcagttcgaaaactgagtgtatataactct--ttgtggttcttc--tcttgtg--gcagGGAACTTGTGATGAAGTTGTTGACTGTTCTCATGGAAAACAACTATGGGAACTCTCTAAAGAGAAATATGAACCGCTTTGGCTCGAAGGCGGTAACCACT
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ttaagaaactgtgt-ctcaatgtactatatctgtaaatgtctacataatgaagaatctgttaaaaaccttatgattgaagttccttaatgttatcatgtagGGGACTTCAGATGAAGTTGTAGATTGCTCCCACGGAAAACAACTGTGGGAACTGTGTAAAGAGAAATATGAGCCACTATGGCTCAAAGGAGGTAACCATT
upper sequence: AT5G14390.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA05G24080.1 (Glycine max), 3'ss of exon 4
gtgagttccatat---tcattttactctcttttcctttttttcagt--tcgaaaactgagtgtatataac-tctttgtggttcttc--tcttgtg--gcagGGAACTTGTGATGAAGTTGTTGACTGTTCTCATGGAAAACAACTATGGGAACTCTCTAAAGAGAAATATGAACCGCTTTGGCTCGAAGGCGGTAACCACT
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-gaaatttcatgtgtcacaatgtagtttatctgcaaatgtttacataatgaagaatctggtaaaaaccttatgattgaagttccttaatgttatcatgtagGGAACTTCAGATGAAGTTGTAGATTGCTCCCACGGAAAACAACTGTGGGAACTGTGTAAAGAGAAGTATGAGCCACTATGGCTCAAAGGAGGAAACCACT
upper sequence: AT5G14390.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA16G07280.1 (Glycine max), 3'ss of exon 4
------gtgagt--tccatattcattttactctcttttcctttttttcagttcgaaaactgagtgtatataactctttgtggttcttc-tcttgtggcagGGAACTTGTGATGAAGTTGTTGACTGTTCTCATGGAAAACAACTATGGGAACTCTCTAAAGAGAAATATGAACCGCTTTGGCTCGAAGGCGGTAACCACT
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caatgcataattagtccaaataaatacatagtgacatatctttttaaaattttacaatattgttgcaaatcctccaaataaatacatagtcattgtgtagGGTACTTCAGATGAAGTTGTAGATTGCTCCCATGGCAAGCAACTCTGGGAACTGTGTAAAGAGAAGTACGAACCACTGTGGCTCAAAGGAGGAAACCATTMapped 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|124915792|gb|EH989666.1|EH989666EST: TACCTCTTGTGAATTGCCCGGTTCTCGTCATTCAC GGAACTTGTGATGAGGTTGTTGACTGTTCTCATGGAAAACAACTATGGGAA
genomic: TACCTCTTGTGAATTGCCCGGTTCTCGTCATTCACgtgagttcca ... cttgtggcagGGAACTTGTGATGAAGTTGTTGACTGTTCTCATGGAAAACAACTATGGGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttcagttcgaaaactgagtgtatataactctttgtggttcttctcttgtggcagGGAACTTGTGATGAAGTTGTTGACTGTTCTCATGGAAAACAACTATGGGAACTCTCTAAAGAGAAATATGAACCGCTTTGGCTCGAAGGCGGTAACCACT
atataac putative branch site (score: 3)
ttcttctcttgt putative PPT
tgtatataa TA-rich tract
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagttccatattcattttactctcttttcctttttttcagttcgaaaactgagtgtatataactctttgtggttcttctcttgtggcagGGAACTTGTGATGAAGTTGTTGACTGTTCTCATGGAAAACAACTATGGGAACTCTCTAAAGAGAAATATGAACCGCTTTGGCTCGAAGGCGGTAACCACT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA