Sequence
atgc intronic sequence ATGC exonic sequencegtgtcaccattttacttgtctttcatcatttccttgtccgataacttccatctcttacagagctttctgattaaacaaacttctatccagATTTGCTACAATCTTCAGCCATGATTCTGATTCAATGCCACGTGTTTGGACTGGAAAGGAGGACATCAGAGCAATTACAAAAATGGCTCGTTCTGCG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G13870.2 |
intron # | 17 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G13870.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: LOC_Os01g39310.1 (Oryza sativa), 3'ss of exon 17
gtgtcaccattttacttgtctttcatcatttccttgtccgataacttccatctcttacagagctttctgattaaacaaacttctatccagATTTGCTACAATCTTCAGCCATGATTCTGATTCAATGCCACGTGTTTGGACTGGAAAGGAGGACATCAGAGCAATTACAAAAATGGCTCGTTCTGCG
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-------------gtgagctgcacaccaaatgttgattcaaatgatatgtgttttcagaga-----ctaattggatgaaaaac-atgaagGTTCTCAACACTATTCAGCCGTGATGCTGACTCAATGCCAAGAGTGTGGACCGGAAAGGAGGACATAAAGGCCATTACTAAAACTGCTCGTTCAGCT
upper sequence: AT3G13870.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GLYMA08G20610.1 (Glycine max), 3'ss of exon 17
gtgtcaccattttacttgtctttcatcatttccttgtccgataacttccatctcttacagagctttctgattaaacaaacttctatccagATTTGCTACAATCTTCAGCCATGATTCTGATTCAATGCCACGTGTTTGGACTGGAAAGGAGGACATCAGAGCAATTACAAAAATGGCTCGTTCTGCG
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gtgtgaatcttctgcaacttctaagttgactt-ttacctgttcgattgagttttacttagatgcacttaccttaac---tttgaaagcagGTTTACAATGTTGTTTAGCCATGATTCTGATTCAATGCCTCGTGTTTGGACGGGGAAAGAAGATATACGAGCCATCACCAAGACTGCTCGCTCTTCT
upper sequence: AT3G13870.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GLYMA07G01230.1 (Glycine max), 3'ss of exon 17
gtgtcaccatttt---acttgtctttcatcatttccttgtccgat-aacttccatctcttacagagctttctgattaaacaaacttctatccagATTTGCTACAATCTTCAGCCATGATTCTGATTCAATGCCACGTGTTTGGACTGGAAAGGAGGACATCAGAGCAATTACAAAAATGGCTCGTTCTGCG
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gtatgaatcttctgcaacttctaagttgacttttacctgttcgtttgagttttactttatatgcacttacct-------taactttgaatgcagGTTTACGATGTTGTTTAGCCATGATTCTGATTCAATGCCTCGTGTTTGGACGGGTAAAGAAGATATACGAGCCATCACCAAGACTGCTCGCTCTTCT
upper sequence: AT3G13870.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GLYMA15G02780.1 (Glycine max), 3'ss of exon 17
gtgtcaccattttacttgtctttcatcatttccttgtccgataacttccatctc-ttacagagctttctgattaaacaaacttctatccagATTTGCTACAATCTTCAGCCATGATTCTGATTCAATGCCACGTGTTTGGACTGGAAAGGAGGACATCAGAGCAATTACAAAAATGGCTCGTTCTGCG
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gtatga--aacttatgcaacatttaa-gttgacttgttagacttgttgagttttgctttagaggcacttatct---taaatttcaaagcagGTTTTTGACATTGTTTAGTCATGATTCTGATTCAATGCCTCGTATTTGGACGGGAAAAGAAGATGTTCGAGCAATCACCAAGTCTGCCCGCTCTTCG
upper sequence: AT3G13870.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GLYMA13G42650.1 (Glycine max), 3'ss of exon 18
gtgtcaccattttacttgtctttcatcatttccttgtccgataacttccatctcttacagagctttctgattaaacaaacttctatccagATTTGCTACAATCTTCAGCCATGATTCTGATTCAATGCCACGTGTTTGGACTGGAAAGGAGGACATCAGAGCAATTACAAAAATGGCTCGTTCTGCG
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-----------gtatgaaccttatacaacatgtaagtttacttgttgagttttactttagaggcacttatct---taaatttcaaagcagGTTTATGACATTGTTTAGTCATGATTCTGATTCAATGCCTCGTATTTGGACGGGAAAAGAAGATGTTCGAGCCATCACCAAGTCTGCCCGCTCTTCC
upper sequence: AT3G13870.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: Vv09s0002g02200.t01 (Vitis vinifera), 3'ss of exon 17
-------------------gtgtcaccattttacttgtctttcatcatttccttgtccgataact-----tccatctcttacagagctttctgattaa-acaaacttc----tatccagATTTGCTACAATCTTCAGCCATGATTCTGATTCAATGCCACGTGTTTGGACTGGAAAGGAGGACATCAGAGCAATTACAAAAATGGCTCGTTCTGCG
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gttgcaactgttacattatttgaaattcttttattttccctttttatttttagattacaagaaatcgggatctactgctttggactgtatcaaatggggatggattttactgcatgcagGTTTGCGACATTGTTTAGCCATGATTCTGACTCAATGCCACGTGTCTGGACTGGGAAAGAAGATATTCGTGCAATCACCAAAACTGCTCGTTCTTCTMapped 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|124927421|gb|EL005161.1|EL005161EST: AAGGAAGAGGCTGGAAGAGCGATGATGCGCATGAAGGATAG ATTTGCTACAATCTTCAGCCATGATTCTGATTCAATGCCA
genomic: AAGGAAGAGGCTGGAAGAGCGATGATGCGCATGAAGGATAGgtgtcaccat ... ttctatccagATTTGCTACAATCTTCAGCCATGATTCTGATTCAATGCCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtccgataacttccatctcttacagagctttctgattaaacaaacttctatccagATTTGCTACAATCTTCAGCCATGATTCTGATTCAATGCCACGTGTTTGGACTGGAAAGGAGGACATCAGAGCAATTACAAAAATGGCTCGTTCTGCG
ttctgat putative branch site (score: 3)
cttctatcc putative PPT
attaaacaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtcaccattttacttgtctttcatcatttccttgtccgataacttccatctcttacagagctttctgattaaacaaacttctatccagATTTGCTACAATCTTCAGCCATGATTCTGATTCAATGCCACGTGTTTGGACTGGAAAGGAGGACATCAGAGCAATTACAAAAATGGCTCGTTCTGCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA