Sequence
atgc intronic sequence ATGC exonic sequencegcaagtcgtctatgctttaaaactgcaagataaaagtttttatttttcataattttcatcttcctaaaagaatggattagttgagtggttacttccagttcatcatttaatccatttttgttttctcaagtttcaagatatttgtgttttgatgaaactacttgctcttcaaattttatagGTTCTTGGCTGGGCTCAAGCCATGCCTAAATTTGCTACTGATCTTGTGAAGTATGTTCAGACATTTCTTGAGAGGACATTTGAGAGATGTCGAACATCAT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G10380.1 |
intron # | 17 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G10380.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GLYMA10G35190.1 (Glycine max), 3'ss of exon 18
gcaagtcgtctatgctttaaaactgcaagataaaagtttttatttttcataattttcatcttcctaaaagaatggattagttgagtggttacttccagttcatcatttaatccatttttgttttctcaagtttcaagatatttgtgttttgatgaaactacttgctcttcaaattttatagGTTCTTGGCTGGGCTCAAGCCATGCCTAAATTTGCTACTGATCTTGTGAAGTATGTTCAGACATTTCTTGAGAGGACATTTGAGAGATGTCGAACATCAT
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-------------------------------------------------------------------------acattattttattgactatacttgattgatgctttg---catttc-atttgat--ggttagagaacatggatgtgttccctaacttttgtatctattttattcta--gGTGCTTGGCTGGGCACAAGCAATGCCCAAGTTCTCTAATGATCTGGTGAAGTATGTGCAAACTTTTCTGGAGAGGACTTATGAAAGATGCCGAACTGCAT
upper sequence: AT3G10380.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GLYMA20G32370.1 (Glycine max), 3'ss of exon 17
gcaagtcgtctatgctttaaaactgc----aagataaaagtttttatttttcataattttcatcttcctaaaagaatggattagttga--gtggttacttccagttcatcatttaat--ccatttttgttttctcaa--gtttcaagatatttgtgttttgatgaaactacttgctcttcaaattttatagGTTCTTGGCTGGGCTCAAGCCATGCCTAAATTTGCTACTGATCTTGTGAAGTATGTTCAGACATTTCTTGAGAGGACATTTGAGAGATGTCGAACATCAT
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gtaaattttaaattggataataatcttactaagatatgatgtttaactcttctatattaagcactagatgatatgatgcctggactaatagtttctgtgtttgggcaatattttattgactatacttgatggtttgatggttagagaacatggatgtgttccctgacttttgtatctattttattcta--gGTGCTTGGCTGGGCACGAGCAATGCCCAAGTTCTCTAATGATCTTGTGAAGTATGTGCAAACTTTTCTGGAGAGGACTTATGAAAGATGCCGGACTGCAT
upper sequence: AT3G10380.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: Vv13s0019g04770.t01 (Vitis vinifera), 3'ss of exon 15
gcaagtcgtctatgctttaaaactgcaagataaaagtttttatttttcataattt--tcatcttcctaaaagaatggattagttgagtggttacttccagtt---catcatttaatccatttttgttttctcaagtttca------agatatttgtgttttga---tgaaactacttgctcttcaaatttta---tagGTTCTTGGCTGGGCTCAAGCCATGCCTAAATTTGCTACTGATCTTGTGAAGTATGTTCAGACATTTCTTGAGAGGACATTTGAGAGATGTCGAACATCAT
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gtaaagtgaa-atttttgtcttccctattttgaaggggggtaattttcctaatatgatcaatttaatgaaaatgtggattgacatgtttatacagtgaagtttcacttcttttgctctgctctgtaaataaatagtttctcttatcagttatttttacagtaagcctacataaatttactgaatgtattttactctagGTGCTTGGTTGGGCTCAAGCAATGCCTAAATTTGCTGGTGACCTTGTGAAGTATGTGCAGACTTTCCTTGAACGAACCTATGAAAGATGTCGGACATCCTMapped 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|125232494|gb|EL246579.1|EL246579EST: TCTCCTTGCAAAAGAG GTTCTTGGCTGGGCTCAAGCCATGCCTAAATTTGCTACTGATCTTGTGAAG
genomic: TCTCCTTGCAAAAGAGgcaagtcgtc ... aattttatagGTTCTTGGCTGGGCTCAAGCCATGCCTAAATTTGCTACTGATCTTGTGAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caagtttcaagatatttgtgttttgatgaaactacttgctcttcaaattttatagGTTCTTGGCTGGGCTCAAGCCATGCCTAAATTTGCTACTGATCTTGTGAAGTATGTTCAGACATTTCTTGAGAGGACATTTGAGAGATGTCGAACATCAT
ttttgat putative branch site (score: 4)
tcttcaaattttata 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
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gcaagtcgtctatgctttaaaactgcaagataaaagtttttatttttcataattttcatcttcctaaaagaatggattagttgagtggttacttccagttcatcatttaatccatttttgttttctcaagtttcaagatatttgtgttttgatgaaactacttgctcttcaaattttatagGTTCTTGGCTGGGCTCAAGCCATGCCTAAATTTGCTACTGATCTTGTGAAGTATGTTCAGACATTTCTTGAGAGGACATTTGAGAGATGTCGAACATCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG