Sequence
atgc intronic sequence ATGC exonic sequence...ttccctttgaaacttatcttaaactttgatgttctctcttgggacctctttttatcgagaagccttaactgcactaagtatttcactttatttctcttagAGTGTGGAACTATGAGGAAGCAACTCTTCTCAATGGCTTTGACAATCATGATTTTCCTGACAAAGGAATTTCAAAGCTCTGCCTCATCAATGAACTTGAC
Basic information
species | Arabidopsis thaliana |
transcript | AT3G08850.1 |
intron # | 17 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G08850.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GLYMA09G41510.1 (Glycine max), 3'ss of exon 17
ttccctttgaaacttatcttaaactttgatgttctctcttgggacc--tctttttatcgagaagccttaactgc-actaagtatttcacttta---tttctcttagAGTGTGGAACTATGAGGAAGCAACTCTTCTCAATGGCTTTGACAATCATGATTTTCCTGACAAAGGAATTTCAAAGCTCTGCCTCATCAATGAACTTGAC
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------gcagaatatctttctggtcttgatgaatgtcattgctgttagtctttgtattgcccaatttggatttttgttggctaatgttctttggagttttccacagGATATGGAACCATGAGGAGGCAACACTACTGAACAGTTTTGATAATCATGATTTTCCTGACAAAGGAATTTCTAAGCTCTGCCTTGTAAATGAGCTTGAT
upper sequence: AT3G08850.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GLYMA18G44210.1 (Glycine max), 3'ss of exon 17
ttccctttgaaacttatcttaaactttgatgttctctcttgggacc--tctttttatcgagaagcctt-aactgcactaagtatttcacttta---tttctcttagAGTGTGGAACTATGAGGAAGCAACTCTTCTCAATGGCTTTGACAATCATGATTTTCCTGACAAAGGAATTTCAAAGCTCTGCCTCATCAATGAACTTGAC
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------tcaaaatatttttctggtcttgatgaatgttgttgctgttagtctttgtattgcccaatttggaattttgttagctaatgttctttggagttttccacagGATATGGAACCATGAGGAGGCTACACTGCTTAACAGTTTTGATAATCATGATTTTCCCGACAAAGGAATTTCTAAGCTCTGCCTTGTAAATGAGCTTGAT
upper sequence: AT3G08850.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: Vv08s0058g00890.t01 (Vitis vinifera), 3'ss of exon 17
ttccctttgaaacttatcttaaac-tttgatgttctctcttgggacctctt--tttatcgagaagccttaactgcac-taagtatttcactttatttctcttagAGTGTGGAACTATGAGGAAGCAACTCTTCTCAATGGCTTTGACAATCATGATTTTCCTGACAAAGGAATTTCAAAGCTCTGCCTCATCAATGAACTTGAC
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---ttatataagcctaaattaggtgtttgaatggctcacttatcatcatttcatttatcttttctgtttgcttatgcattaattcttcatttt-tgtttttcagGATTTGGAATTATGATGAAGCTACCCTTCTCAACAGCTTTGACAATCATAATTTTCCTGATAAAGGAATTTCTAAACTCTGCCTTGTGAACGAGCTTGATMapped 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|125074323|gb|EL138305.1|EL138305EST: CACCCATTCTCTCCTATTGTAGTTGCTGCAGACGAGAATGAACGGATCAG AGTGTGGAACTATGAGGAAGCAACTCTTC
genomic: CACCCATTCTCTCCTATTGTAGTTGCTGCAGACGAGAATGAACGGATCAGgtatgcgagt ... tttctcttagAGTGTGGAACTATGAGGAAGCAACTCTTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctctttttatcgagaagccttaactgcactaagtatttcactttatttctcttagAGTGTGGAACTATGAGGAAGCAACTCTTCTCAATGGCTTTGACAATCATGATTTTCCTGACAAAGGAATTTCAAAGCTCTGCCTCATCAATGAACTTGAC
ccttaac putative branch site (score: 3)
tttcactttatttctc putative PPT
tatttcactttattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttccctttgaaacttatcttaaactttgatgttctctcttgggacctctttttatcgagaagccttaactgcactaagtatttcactttatttctcttagAGTGTGGAACTATGAGGAAGCAACTCTTCTCAATGGCTTTGACAATCATGATTTTCCTGACAAAGGAATTTCAAAGCTCTGCCTCATCAATGAACTTGAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - ttgaaac
- - - - - - - - -cttaaac
- - - - - - - - - - - - - - - - tctctct