Sequence
atgc intronic sequence ATGC exonic sequencegttaatttgctatatacaaattctgttctgttttttataaatgttcttgctcatttattgattgatctactgaatttggtgatactaattttatgttttgttttactaacttatatatacaaaaaagGTATCAAGAGGCTATTGAAGATATAACTAAAAGAATGGGTGCAGGAATGGCCAAGTTCATTTGCAAGGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G34650.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G34650.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os07g10130.1 (Oryza sativa), 3'ss of exon 4
gttaatttgctatatacaaattctgttctgttttttataaatgttcttgctcatttattgattgatctactgaatttggtgatactaattttatgttttgttttactaacttatatatacaaaaaagGTATCAAGAGGCTATTGAAGATATAACTAAAAGAATGGGTGCAGGAATGGCCAAGTTCATTTGCAAGGAG
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-----------------------ccctatgacattgattagtattttaattcaga-attatctagtcta-tgtaagtggtcccattcaagt-agaagaagcaatacatgtttac-tctgttatccagATACCAAGAGGCAATTGAAGAAATTACCAGGAGAATGGGTGCAGGAATGGCAAAGTTTATATGCAAGGAG
upper sequence: AT4G34650.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA11G11960.3 (Glycine max), 3'ss of exon 4
gttaatttgctatatacaaattctgttctgttttttataaatgttcttgctcatttattgattgatctactgaatttggtgatactaattttatgttttgttttactaacttatatatacaaaaaagGTATCAAGAGGCTATTGAAGATATAACTAAAAGAATGGGTGCAGGAATGGCCAAGTTCATTTGCAAGGAG
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------------------gattca---ctgcctttattagcttctctcatttatgtgtaattagagttgtggctgtgcattctataacaaacaaattaaatgttggtcaatggttt-tgca-----gCTACCAGGAAGCAATTGAGGACATTACCAAAAGAATGGGTGCTGGAATGGCCAAATTTATTTGCAAGGAG
upper sequence: AT4G34650.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA12G04220.3 (Glycine max), 3'ss of exon 4
gttaatttgctatatacaaattctgttctgttttttataaatgttcttgctcatttattgattgatctactgaatttggtgatactaattttatgttttgttttactaacttatatatacaaaaaagGTATCAAGAGGCTATTGAAGATATAACTAAAAGAATGGGTGCAGGAATGGCCAAGTTCATTTGCAAGGAG
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------------------gataattgactgcagattatcaataactatggtcctttgt-gtttg---tgatggctgtgcattctataacaaaaaattaaatgttggtcaatgatttttgca-----gCTACCAGGAAGCAATTGAGGACATTACCAAAAGAATGGGTGCTGGAATGGCCAAATTTATTTGCAAGGAG
upper sequence: AT4G34650.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv03s0038g00450.t01 (Vitis vinifera), 3'ss of exon 4
gttaatttgctatatacaaattctgttctgttttttataaatgttcttgctcatttattgattgatctactgaatttggtgatactaattttatgttttgttt-tactaacttatatatacaaaaaagGTATCAAGAGGCTATTGAAGATATAACTAAAAGAATGGGTGCAGGAATGGCCAAGTTCATTTGCAAGGAG
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-------------------------ttttgagttct-tgaatata--tacacatcttctatctgataaaaaaaaaatgtatacacatcttctacaaaccacttatgttatccaaaaaatttgttgcagTTATCAGGAGGCAATTGAAGACATCACCAAACGAATGGGGGCAGGAATGGCAAAATTTATTTGCAAAGAGMapped 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|86060546|gb|DR356303.1|DR356303EST: ATGGACCAATTTCACCATGTTTCTGCAGCTTTTCTGAAACTTGAAAAAGG GTATCAAGAGGCTATTGAAGATATAACTAAAAGAATGGGTGCAGGAATGGC
genomic: ATGGACCAATTTCACCATGTTTCTGCAGCTTTTCTGAAACTTGAAAAAGGgttaatttgc ... tacaaaaaagGTATCAAGAGGCTATTGAAGATATAACTAAAAGAATGGGTGCAGGAATGGC
EST:
gi|86047504|gb|DR343259.1|DR343259EST: ATGGACCAATTTCACCATGTTTCTGCAGCTTTTCTGAAACTTGAAAAAGG GTATCAAGAGGCTATTGAAGATATAACTAAAAGAATGGGTGCAGGAATGGC
genomic: ATGGACCAATTTCACCATGTTTCTGCAGCTTTTCTGAAACTTGAAAAAGGgttaatttgc ... tacaaaaaagGTATCAAGAGGCTATTGAAGATATAACTAAAAGAATGGGTGCAGGAATGGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatttggtgatactaattttatgttttgttttactaacttatatatacaaaaaagGTATCAAGAGGCTATTGAAGATATAACTAAAAGAATGGGTGCAGGAATGGCCAAGTTCATTTGCAAGGAG
tactaac putative branch site (score: 0)
taattttatgttttgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttaatttgctatatacaaattctgttctgttttttataaatgttcttgctcatttattgattgatctactgaatttggtgatactaattttatgttttgttttactaacttatatatacaaaaaagGTATCAAGAGGCTATTGAAGATATAACTAAAAGAATGGGTGCAGGAATGGCCAAGTTCATTTGCAAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG