Sequence
atgc intronic sequence ATGC exonic sequencegtaagaaccctgtggggtgatatttaggtttacttattagttaatgcttaccctttttgtttcattgtcattttcagTGCCTGTTGGTGAAGGGATGGAAAGGATCGAGCTGGAGCTTTCCCCGCGGAAAAAAGAGCAAGGATGAAGAAGACCATGCTTGTGCCATACGTGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G13570.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G13570.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA02G08170.1 (Glycine max), 3'ss of exon 3
--------------gtaagaaccctgtggggtgatatttaggtttacttatta----gttaatgcttaccctttt---tgttt--cattgtcatttt-cagTGCCTGTTGGTGAAGGGATGGAAAGGATCGAGCTGGAGCTTTCCCCGCGGAAAAAAGAGCAAGGATGAAGAAGACCATGCTTGTGCCATACGTGAG
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atctctgaactgatataatagtattaagagattct-ttcagagctatttattgctatgttaagccatatttacttacatgcctgctgtggacactggacagTGCTTGCTAGTGAAGGGATGGAAAGGTTCAAGCTGGAGCTTCCCTCGTGGAAAAAAGAGCAAAGACGAAGAAGATCATGCATGTGCCATTAGAGAA
upper sequence: AT5G13570.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA16G27200.1 (Glycine max), 3'ss of exon 3
-------------------------gtaagaaccctgtggggtgatatttaggtttacttattagttaatgctta-ccctttttgtttcattgtcattttcagTGCCTGTTGGTGAAGGGATGGAAAGGATCGAGCTGGAGCTTTCCCCGCGGAAAAAAGAGCAAGGATGAAGAAGACCATGCTTGTGCCATACGTGAG
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aagatcctttcatatctgaactgatataatagtatcaagagattct-ttcagacttatttatt--tctatgttaagccctatttacttgcctgctgtggacagTGCTTGCTAGTGAAGGGATGGAAAGGTACAAGTTGGAGTTTCCCTCGTGGAAAAAAGAGCAAAGACGAAGAAGATCATGCATGTTCCATTAGAGAA
upper sequence: AT5G13570.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv13s0019g04310.t01 (Vitis vinifera), 3'ss of exon 3
----------------gtaagaaccctgtggggtgatatttaggtttacttattagttaatgcttaccct-ttttgtttcat------tgtcattttcagTGCCTGTTGGTGAAGGGATGGAAAGGATCGAGCTGGAGCTTTCCCCGCGGAAAAAAGAGCAAGGATGAAGAAGACCATGCTTGTGCCATACGTGAG
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acacataacagagttatctaatagtttgaagtaagtgattcagttctccttttaaaaatattgtcacactgttttgatacttgttttgtataattaacagTGCTTACTAGTGAAGGGATGGAAAGGAACAAGCTGGAGTTTTCCCCGTGGAAAAAAGAACAAAGATGAAGAAGACCACACGTGTGCCATTAGAGAAMapped 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|124913465|gb|EH987339.1|EH987339EST: GTCGAGTTCCAGTCACTGGGGCAATTATCCTGGATGAGACATATGAAAGG TGCCTGTTGGTGAAGGGATGGAAAGGATCGAGCTGGAGCTTT
genomic: GTCGAGTTCCAGTCACTGGGGCAATTATCCTGGATGAGACATATGAAAGGgtaagaaccc ... tcattttcagTGCCTGTTGGTGAAGGGATGGAAAGGATCGAGCTGGAGCTTT
EST:
gi|125306996|gb|EL321081.1|EL321081EST: GTCGAGTTCCAGTCACTGGGGCAATTATCCTGGATGAGACATATGAAAGG TGCCTGTTGGTGAAGGG
genomic: GTCGAGTTCCAGTCACTGGGGCAATTATCCTGGATGAGACATATGAAAGGgtaagaaccc ... tcattttcagTGCCTGTTGGTGAAGGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttaggtttacttattagttaatgcttaccctttttgtttcattgtcattttcagTGCCTGTTGGTGAAGGGATGGAAAGGATCGAGCTGGAGCTTTCCCCGCGGAAAAAAGAGCAAGGATGAAGAAGACCATGCTTGTGCCATACGTGAG
tgcttac putative branch site (score: 2)
tcattttc putative PPT
tttacttattagttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagaaccctgtggggtgatatttaggtttacttattagttaatgcttaccctttttgtttcattgtcattttcagTGCCTGTTGGTGAAGGGATGGAAAGGATCGAGCTGGAGCTTTCCCCGCGGAAAAAAGAGCAAGGATGAAGAAGACCATGCTTGTGCCATACGTGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG