Sequence
atgc intronic sequence ATGC exonic sequencegtacgtatctcaacattctttttctacaacttttctgctcttttgtttctaatggtggactctgtttactctctcctctagGCTGTGAGCAGAGAGATACGCAAGATTCTGACAGAGCGGGCTTCTAACTTTGACATTGCTCTTGATGATGTCTCCATCACGACTCTGACATTCGGCAAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G03860.3 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G03860.3 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os03g60000.1 (Oryza sativa), 3'ss of exon 3
--------------------------------------------------------gtacgtatctcaacattctttttctacaactttt---ctgctcttttgtttctaatggtggactctgt---ttactctctcctcta-----gGCTGTGAGCAGAGAGATACGCAAGATTCTGACAGAGCGGGCTTCTAACTTTGACATTGCTCTTGATGATGTCTCCATCACGACTCTGACATTCGGCAAAG
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gtactgtcatcatatctatctgtgtttaaatatctaatatgtttccatggtatgctatgctagtttaagagctaatatagtaggatatttagtttaagagttaatatagtaggatatatgctaataattactcctttatccaacacagGCTGTGAGCAGGGAGATTAGGAAGATCCTGACAGAGAGGGCTAGCAACTTCAACATTGCTCTGGATGATGTGTCCATCACAAGTCTCAGCTTTGGAAAAG
upper sequence: AT1G03860.3 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os03g62490.1 (Oryza sativa), 3'ss of exon 3
----------------------------------------------------------------gtacgtatctcaacattctttttctacaacttttctgctcttttgtttctaatggtg---gactctgtttactctctcctcta-----gGCTGTGAGCAGAGAGATACGCAAGATTCTGACAGAGCGGGCTTCTAACTTTGACATTGCTCTTGATGATGTCTCCATCACGACTCTGACATTCGGCAAAG
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gtactgtcttatcatatctatctgtgtttaaatatctaatatgtttccatggtatgctatgctagtttaagagctaatatagtagtatgatatttagtttaagagctaatatagtaggatatatggtaataattattcctttatccaacacagGCTGTGAGCAGGGAGATTAGGAAGATCCTGACAGAGAGGGCTAGCAACTTCAACATTGCTCTGGATGATGTGTCCATCACAAGTCTCAGCTTTGGAAAAG
upper sequence: AT1G03860.3 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G352289_T01 (Zea mays), 3'ss of exon 2
gtacgtatctcaacattctttttctacaacttttctgctcttttgtttctaatggtggactctgttt-actctctcctctagGCTGTGAGCAGAGAGATACGCAAGATTCTGACAGAGCGGGCTTCTAACTTTGACATTGCTCTTGATGATGTCTCCATCACGACTCTGACATTCGGCAAAG
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gtacgattgaacgtatgaagttgctagtaactacttaatagc--aattct----gtttactcttttccgccaccaatttcagGCTGTGAGTAGGGAGATTAGGAAGATACTGACCGAGAGGGCTAGATTCTCCAACATTGCTCTTGATGATGTCTCCATCACAAGCCTAAGCTTCGGGAGGGMapped 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|86032647|gb|DR328400.1|DR328400EST: AAGCAGTGGTAGCTCAGTACAATGCAAGCCAGCTCATTACCCAGAGAGAA GCTGTGAGCAGAGAGATACGCAAGATTCTGACAGAGCGGGCTTCTAACTTT
genomic: AAGCAGTGGTAGCTCAGTACAATGCAAGCCAGCTCATTACCCAGAGAGAAgtacgtatct ... tctcctctagGCTGTGAGCAGAGAGATACGCAAGATTCTGACAGAGCGGGCTTCTAACTTT
EST:
gi|125261305|gb|EL275390.1|EL275390EST: CAATGCAAGCCAGCTCATTACCCAGAGAGAA GCTGTGAGCAGAGAGATACGCAAGA
genomic: CAATGCAAGCCAGCTCATTACCCAGAGAGAAgtacgtatct ... tctcctctagGCTGTGAGCAGAGAGATACGCAAGA
EST:
gi|116435505|gb|EG478097.1|EG478097EST: TACAATGCAAGCCAGCTCATTACCCAGAGAGAA GCTGTGAGCAGAGAGATACGCAAGATTCTGACAGAGCGGGCTTCTAACTTT
genomic: TACAATGCAAGCCAGCTCATTACCCAGAGAGAAgtacgtatct ... tctcctctagGCTGTGAGCAGAGAGATACGCAAGATTCTGACAGAGCGGGCTTCTAACTTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caacttttctgctcttttgtttctaatggtggactctgtttactctctcctctagGCTGTGAGCAGAGAGATACGCAAGATTCTGACAGAGCGGGCTTCTAACTTTGACATTGCTCTTGATGATGTCTCCATCACGACTCTGACATTCGGCAAAG
ttctaat putative branch site (score: 2)
ctctgtttactctctc putative PPT
ttttgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacgtatctcaacattctttttctacaacttttctgctcttttgtttctaatggtggactctgtttactctctcctctagGCTGTGAGCAGAGAGATACGCAAGATTCTGACAGAGCGGGCTTCTAACTTTGACATTGCTCTTGATGATGTCTCCATCACGACTCTGACATTCGGCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG