Sequence
atgc intronic sequence ATGC exonic sequencegtttgtcattccatacttttggctttatttgtgttgcgaaatgagatacgcttgactttgaagatttacacacatctatccacttcatgatatataaactcaaatgcatattttgcttaacgatatctatttctttaccatgcagATTCCTCGATTTGCATTTGAAAAGTTTCCAGGATCTCAGCCATTGCTAACGACCCAGATGAAATCTGTTGGGGAATCTATGGCTCTCGGCCGTACATTCC
Basic information
species | Arabidopsis thaliana |
transcript | AT1G29900.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G29900.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os01g38970.1 (Oryza sativa), 3'ss of exon 1
gtttgtcattccatacttttggctttatttgtgttgcgaaatgagatacgcttgactttgaagatttacacacatctatccacttcatgatatataaactcaaatgcatattttgcttaacgatatctatttctttaccatgcagATTCCTCGATTTGCATTTGAAAAGTTTCCAGGATCTCAGCCATTGCTAACGACCCAGATGAAATCTGTTGGGGAATCTATGGCTCTCGGCCGTACATTCC
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------------------------------------------gacatgttcttcacattgttcatc-atacagaatttgtacctgtaagttaatgcagggctgttaaccttctttcctgac--ttaccatatatttacgatgcagATTCCACGGTTTGCATTTGAAAAGTTCCCTGGGTCTGAGCCAGTATTAACCACACAGATGAAGTCTGTTGGTGAGGCCATGGCTCTAGGACGGACCTTCC
upper sequence: AT1G29900.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA13G40380.1 (Glycine max), 3'ss of exon 2
gtttgtcattccatacttttggctttatttgtgttgcgaaatgagatacgcttgactttgaagatttacacacatctatccacttcatgatatataaactcaaatgcatattttgcttaacgatatctatttcttt-accatgcagATTCCTCGATTTGCATTTGAAAAGTTTCCAGGATCTCAGCCATTGCTAACGACCCAGATGAAATCTGTTGGGGAATCTATGGCTCTCGGCCGTACATTCC
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------------------------------------------taactaaact-aacatttctgatttttgt-tatggagcaaat-catgtgaattttgtcgcaatgc-tacttttctcattttttttttttttttttgtggtgcagATTCCACGGTTTGCTTTTGAGAAGTTTCCTGGTTCTCAGCCAATATTGACGACACAGATGAAATCTGTTGGTGAGTCAATGGCTGTAGGGCGAAACTTCC
upper sequence: AT1G29900.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv06s0004g03360.t01 (Vitis vinifera), 3'ss of exon 1
gtttgtcattccatacttttggctttatttgtgttgcgaaatgagatacgcttgactttgaagatttacacacatctatccacttcatgatatataaactcaaatgcatattttgcttaacgatatctattt-ctttaccatgcagATTCCTCGATTTGCATTTGAAAAGTTTCCAGGATCTCAGCCATTGCTAACGACCCAGATGAAATCTGTTGGGGAATCTATGGCTCTCGGCCGTACATTCC
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---------------------------------------------gccccccccccccccccccccccccctcttttaaatacatctaagtagatttttttatttacacatatttttcttccct-tctatttacatgatcatgcagATACCCCGGTTTGCATTTGAGAAATTCCCAGGTTCTCAACCAATATTGACGACCCAAATGAAATCTGTGGGTGAATCCATGGCTCTAGGCCGAACATTCCMapped 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|125239799|gb|EL253884.1|EL253884EST: GGAAAACACCGGCTAGCTTCGAGCCCTCCATCGATTATGTGGTGACTAAG ATTCCTCGATTTG
genomic: GGAAAACACCGGCTAGCTTCGAGCCCTCCATCGATTATGTGGTGACTAAGgtttgtcatt ... taccatgcagATTCCTCGATTTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatataaactcaaatgcatattttgcttaacgatatctatttctttaccatgcagATTCCTCGATTTGCATTTGAAAAGTTTCCAGGATCTCAGCCATTGCTAACGACCCAGATGAAATCTGTTGGGGAATCTATGGCTCTCGGCCGTACATTCC
gcttaac putative branch site (score: 3)
tctatttctttacc putative PPT
atatctatttcttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtcattccatacttttggctttatttgtgttgcgaaatgagatacgcttgactttgaagatttacacacatctatccacttcatgatatataaactcaaatgcatattttgcttaacgatatctatttctttaccatgcagATTCCTCGATTTGCATTTGAAAAGTTTCCAGGATCTCAGCCATTGCTAACGACCCAGATGAAATCTGTTGGGGAATCTATGGCTCTCGGCCGTACATTCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG