Sequence
atgc intronic sequence ATGC exonic sequencegtaccactccttcccctctcctctcttcttcatcaatcaattttccattcgggatcttagaaccctaaatcctgcattgttttctaacgaatctccaatttatcctcgcagGACTCCAACAATCTCAAAGACGCTCTAAAGTTTTCTGCTCAAATGCTCAGCGAGCTTCGTACTTCCAAGCTTTCTCCTCATAAATACTATGAACTCT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G51310.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G51310.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA11G08390.1 (Glycine max), 3'ss of exon 1
-----------------------gtaccactccttcccctctcctctcttcttcatcaatcaattttccattcgggatcttagaaccctaaatcctgcattgttttctaacgaatctccaatttatcctcgcagGACTCCAACAATCTCAAAGACGCTCTAAAGTTTTCTGCTCAAATGCTCAGCGAGCTTCGTACTTCCAAGCTTTCTCCTCATAAATACTATGAACTCT
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gtaactcctcctccgttaaaccctaacctctctcttccttctattccacgcatccacgatcacactaatttttcagattc--gccttccaaattcctaattgattcggatccaatttcgatt----cgtcgcagGACTCGAACAATCTCAGGGATGCTTTGAAGTATTCGGCTCAGATGCTCTCCGAGCTCAGGACTTCCAAGCTTTCTCCTCACAAGTACTACGAACTAT
upper sequence: AT3G51310.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA01G36870.1 (Glycine max), 3'ss of exon 1
----------------------gtaccactccttcccctctcctctcttcttcatcaatcaattttccattcgggatcttagaacc-----ctaaatcctgcattgttttctaacgaatctccaatttatcctcgcagGACTCCAACAATCTCAAAGACGCTCTAAAGTTTTCTGCTCAAATGCTCAGCGAGCTTCGTACTTCCAAGCTTTCTCCTCATAAATACTATGAACTCT
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gtaactcctccgttaaaccctaatctctctctcttccttctattttctattccccgcagccacgatcactctaacttttcagattcgccttccaaattcctaattgattcggatccaatttcgatt----cgtcgcagGACTCGAACAATCTCAGGGACGCTTTGAAGTATTCGGCTCAGATGCTCTCCGAGCTCAGGACTTCCAAGCTTTCGCCTCACAAGTACTACGAACTAT
upper sequence: AT3G51310.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv04s0023g03870.t01 (Vitis vinifera), 3'ss of exon 1
gtaccactccttcccctctcctctcttcttcatcaatc--------------aattttcc----attcgggatcttagaaccct--------------aaatcctgcattgttttctaacgaatctccaatttatcctcgcagGACTCCAACAATCTCAAAGACGCTCTAAAGTTTTCTGCTCAAATGCTCAGCGAGCTTCGTACTTCCAAGCTTTCTCCTCATAAATACTATGAACTCT
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gtaacacgctctccttctctacctatgtttggtttgacggaagatagaggaaaatgttccccagattcgttccttttttccttttttccctttctgagaaacgcagcctaattttttcccttttttttttttttacttctcagGACTCGAACAATCTGAGGGACGCCCTCAAATACTCGGCTCAGATGCTTTCCGAGCTTCGTACTTCGAGGCTCTCCCCTCATAAATACTACGAACTATMapped 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|19874725|gb|AU235556.1|AU235556EST: CCGCAATCGCCGCCGTTAAGCAAAATGCTTTCTATATGCAGCGCGCTATC GACTCCAACAATCTCAAAGACGCTCTAAAGTTTTCTGCTCAAATGCTCAGC
genomic: CCGCAATCGCCGCCGTTAAGCAAAATGCTTTCTATATGCAGCGCGCTATCgtaccactcc ... atcctcgcagGACTCCAACAATCTCAAAGACGCTCTAAAGTTTTCTGCTCAAATGCTCAGC
EST:
gi|116404335|gb|EG446927.1|EG446927EST: CCGCAATCGCCGCCGTTAAGCAAAATGCTTTCTATATGCAGCGCGCTATC GACTCCAACAATCTCAAAGACGCTCTAAAGTTTTCTGCTCAAATGCTCAGC
genomic: CCGCAATCGCCGCCGTTAAGCAAAATGCTTTCTATATGCAGCGCGCTATCgtaccactcc ... atcctcgcagGACTCCAACAATCTCAAAGACGCTCTAAAGTTTTCTGCTCAAATGCTCAGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttagaaccctaaatcctgcattgttttctaacgaatctccaatttatcctcgcagGACTCCAACAATCTCAAAGACGCTCTAAAGTTTTCTGCTCAAATGCTCAGCGAGCTTCGTACTTCCAAGCTTTCTCCTCATAAATACTATGAACTCT
ttctaac putative branch site (score: 1)
tttatcctc putative PPT
aatttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaccactccttcccctctcctctcttcttcatcaatcaattttccattcgggatcttagaaccctaaatcctgcattgttttctaacgaatctccaatttatcctcgcagGACTCCAACAATCTCAAAGACGCTCTAAAGTTTTCTGCTCAAATGCTCAGCGAGCTTCGTACTTCCAAGCTTTCTCCTCATAAATACTATGAACTCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC