Sequence
atgc intronic sequence ATGC exonic sequencegtagcaactgccatctcttctgccattcaattgtttactatttctttagatacgagtgtttttgactagtgagagtatcgagtatacttcagactgctggatatctcttcactcagttttaattgttgttttcagAATATGGTATATTACAAAATATCACACGTGGATGGTCGGATTACGCACCCTGAACAAAGAATTGCCAGCGATGTACCAAGATTCTCCTCAGAGTTGAGCG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G39850.3 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G39850.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA05G31270.1 (Glycine max), 3'ss of exon 2
gtagcaactgccatctcttctgccattcaattgtttactatttctttagatacgagtgtttttgactagtgagagtatcgagtatacttcagactgctggatatctcttcactcagttttaattgttgttttcagAATATGGTATATTACAAAATATCACACGTGGATGGTCGGATTACGCACCCTGAACAAAGAATTGCCAGCGATGTACCAAGATTCTCCTCAGAGTTGAGCG
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----------------------------------ttggtggttataggaagagtaatccgtgtgtcaacaaatgttataatgttctatttagtttttatgtcagctttctgtttatcatttacttttattt-cagAACATGGTGTATTACAAAATATCACATGTTGATGGTCGGATAACTAATCCGGAACAAAGAATTGCCAGTGATGTGCCAAGGTTCTGTTCAGAGTTGAGTG
upper sequence: AT4G39850.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA08G14480.1 (Glycine max), 3'ss of exon 1
gtagcaactgccatctcttctgccattcaattgtttactatttctttagatacgagtgtttttgactagtgagagtatcgagtatacttcagactgctggatatctcttcactcagttttaattgttgttttcagAATATGGTATATTACAAAATATCACACGTGGATGGTCGGATTACGCACCCTGAACAAAGAATTGCCAGCGATGTACCAAGATTCTCCTCAGAGTTGAGCG
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---------------------------------tttggtggttataggaagagtagtccatgtctc-aacaaatgtttaatgttctatttagtttttatgtcagatttctgtttatcatttacttttattt-cagAACATGGTGTATTACAAAATATCACATGTTGATGGTCGTATAACTAATCCGGAACAAAGAATTGCCAGTGATGTGCCAAGGTTCTGTTCAGAGTTGAGTG
upper sequence: AT4G39850.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA11G38160.1 (Glycine max), 3'ss of exon 4
gtagcaactgccatctcttctgccattcaattgtttactatttctttagatacgagtgtttttgactagtgagagtatcgagtatacttcagactgctggatatctcttcactcagttttaattgttgttttcagAATATGGTATATTACAAAATATCACACGTGGATGGTCGGATTACGCACCCTGAACAAAGAATTGCCAGCGATGTACCAAGATTCTCCTCAGAGTTGAGCG
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-----------------------------acaatgccctctctcatacgagaaaagc-caaaagact-gtataataaccctatgtagttc---ttgcaatggcttaatgtatatatctttcatt-ttgctttcagAACATGGTGTATTACAAAATATCGCATGTAGATGGTCGGATAACTAACCCAGAGCAAAGAATTGCCAGTGATGTGCCAAGGTTCTGTTCGGAGTTGAGTG
upper sequence: AT4G39850.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA18G02110.1 (Glycine max), 3'ss of exon 5
gtagcaactgccatctcttctgccattcaattgtttactatttctttagatacgagtgtttttgactagtgagagtatcgagtatacttcagactgctggatatctcttcactcagttttaattgttgttttcagAATATGGTATATTACAAAATATCACACGTGGATGGTCGGATTACGCACCCTGAACAAAGAATTGCCAGCGATGTACCAAGATTCTCCTCAGAGTTGAGCG
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---------------------------cactcagccactctcatatgaga----aaagcctaaagactgtattataaccctatgtagttc---ttgcaatggcttaatgtatatatctttcatt-ttgctttcagAACATGGTGTATTACAAAATATCGCATGTTGATGGTCGGATAACTAATCCAGAGCAAAGAATTGCCAGTGATGTGCCAAGGTTCTGTTCGGAGTTGAGTGMapped 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|116455491|gb|EG498083.1|EG498083EST: TGCGATTCAGAAAGATATTGACCAAGATTATCCATTCACACTATTTTGAG AATATGGTATATTACAAAATATCACACGTGGATGGTCGGATTACGCACCC
genomic: TGCGATTCAGAAAGATATTGACCAAGATTATCCATTCACACTATTTTGAGgtagcaactg ... ttgttttcagAATATGGTATATTACAAAATATCACACGTGGATGGTCGGATTACGCACCC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agtatacttcagactgctggatatctcttcactcagttttaattgttgttttcagAATATGGTATATTACAAAATATCACACGTGGATGGTCGGATTACGCACCCTGAACAAAGAATTGCCAGCGATGTACCAAGATTCTCCTCAGAGTTGAGCG
ttttaat putative branch site (score: 3)
ttgttttc putative PPT
ttttaattgttgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagcaactgccatctcttctgccattcaattgtttactatttctttagatacgagtgtttttgactagtgagagtatcgagtatacttcagactgctggatatctcttcactcagttttaattgttgttttcagAATATGGTATATTACAAAATATCACACGTGGATGGTCGGATTACGCACCCTGAACAAAGAATTGCCAGCGATGTACCAAGATTCTCCTCAGAGTTGAGCG
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