Sequence
atgc intronic sequence ATGC exonic sequencegtatgatacaagtgattgcgaaagagcctttattttcctattttctttgctttttgtttctggaaaaacaattatagctccaaatgtttcgcagaatattaggttgatgacgtggaaaatttgttttggtttcagGGAGTACCTGGTTGATTTAGTAGGAAAGCCAGGTCACTTATGGGAGCCTGATTCCTTGCTAAATGGTCCTTCATCTATCTCAATTTCTTCTCCTCTGCGG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G03730.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G03730.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA10G07610.1 (Glycine max), 3'ss of exon 5
gtatgatacaagtgattgcgaaagagcctttattttcctattttctttgctttttgtttctggaaaaacaattatagctccaaatgt-ttcgcag-aatattaggttgatgacgtggaaaatttgt--tttggtttcagGGAGTACCTGGTTGATTTAGTAGGAAAGCCAGGTCACTTATGGGAGCCTGATTCCTTGCTAAATGGTCCTTCATCTATCTCAATTTCTTCTCCTCTGCGG
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--------------------------------attggttaacttgtgagcattctgtttattg-----tcattttaaatatatgtttctttatagtaatattc--ctgacacctctcatctttcataatctaaatacagGGAGTATCTTGTTGATTTAATTGGAAAGCCAGGAAACTTATCCGAGCCTGATTCCTTGCTCAATGGTCCATCTTCCATCTCATTTTCTTCACCCTTGCGC
upper sequence: AT5G03730.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA13G21480.1 (Glycine max), 3'ss of exon 4
gtatgatacaagtgattgcgaaagagcctttattttcctattttctttgctttttgtttctggaaaaac-aattatagctccaaatgtttcgcagaatattaggttgatgacgtggaaaatttgttttggtttcagGGAGTACCTGGTTGATTTAGTAGGAAAGCCAGGTCACTTATGGGAGCCTGATTCCTTGCTAAATGGTCCTTCATCTATCTCAATTTCTTCTCCTCTGCGG
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--------------------------------attggttaacatgttaacattctgtttattgacattttaaatatatcttta--ttaatggtaatattcctgacacctctcatcttacat--aatctaaatacagGGAGTATCTTGTTGATTTAATTGGAAAGCCAGGAAACTTATCTGAGCCTGATTCCTTGCTCAATGGTCCATCTTCCATCTCATTTTCTTCACCCTTGCGC
upper sequence: AT5G03730.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv08s0007g03910.t01 (Vitis vinifera), 3'ss of exon 4
gtatgatacaagtgattgcgaaagagcctttattttcctattttctttgctttttgtttctggaaaaacaattatagctccaaatgtttcgcagaatattaggttgatgacgtggaaaatttgttttggtttcagGGAGTACCTGGTTGATTTAGTAGGAAAGCCAGGTCACTTATGGGAGCCTGATTCCTTGCTAAATGGTCCTTCATCTATCTCAATTTCTTCTCCTCTGCGG
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--------------------------------cttgtatcatatattgaattgcagtctctgtagcatgcctcatcattgaatatatta-gcaaactat-acaaacatctcagagtataattgtatta-ctgcagGGAGTTTCTAGTTGATTTGGTTGGCAAGCCAGGGTGCTTATGCGAGCCTGATTCTTTGCTCAATGGTCCAGCTTCCATCTCAATTTCTTCCCCATTGCGCMapped 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|116475867|gb|EG518459.1|EG518459EST: TGTAATAGAGACGATGCCGCTTCGTGCCTTGTCAGGTTTGGGCTTGATAG GGAGTACCTGGTTGATTTAGTAGGAAAGCCAGGTCACTTATGGGAGCCTGA
genomic: TGTAATAGAGACGATGCCGCTTCGTGCCTTGTCAGGTTTGGGCTTGATAGgtatgataca ... ttggtttcagGGAGTACCTGGTTGATTTAGTAGGAAAGCCAGGTCACTTATGGGAGCCTGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caaatgtttcgcagaatattaggttgatgacgtggaaaatttgttttggtttcagGGAGTACCTGGTTGATTTAGTAGGAAAGCCAGGTCACTTATGGGAGCCTGATTCCTTGCTAAATGGTCCTTCATCTATCTCAATTTCTTCTCCTCTGCGG
ggttgat putative branch site (score: 5)
tttgtttt putative PPT
aaaatttgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgatacaagtgattgcgaaagagcctttattttcctattttctttgctttttgtttctggaaaaacaattatagctccaaatgtttcgcagaatattaggttgatgacgtggaaaatttgttttggtttcagGGAGTACCTGGTTGATTTAGTAGGAAAGCCAGGTCACTTATGGGAGCCTGATTCCTTGCTAAATGGTCCTTCATCTATCTCAATTTCTTCTCCTCTGCGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC