Sequence
atgc intronic sequence ATGC exonic sequencegtgggttcattcacttaacaaccatcatcatttcgttaccctgattaatttggtgggtataatgttcagGTTTTTACTTGGAACACTGATGCATGGGGATATGGTTCTGGAACCACTTCGTTATACCAGTCACATCCTTGGGTACTAGTTGTCCTTCCAACTGGAGAAA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G23640.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G23640.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os07g23880.1 (Oryza sativa), 3'ss of exon 2
------------------------gtgggttcattcacttaacaacca-tcatcatttcgttaccc-tgattaatttggtgggtataatgttca---gGTTTTTACTTGGAACACTGATGCATGGGGATATGGTTCTGGAACCACTTCGTTATACCAGTCACATCCTTGGGTACTAGTTGTCCTTCCAACTGGAGAAA
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gtacgttatctgcttgaagaaattgtttgtcatttcttgtaaattctagttcttagctgtttacaaacatttgatctcgtgt-tatgttttccactagGTTTTTACTTGGAACACAGATGCATGGGGTTTTGGGCCAGGAACCACTTCATTATATCAGTCACACCCTTGGGTTTTGGCTGTCCTCCCTGATGGAAAGG
upper sequence: AT3G23640.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os07g23944.1 (Oryza sativa), 3'ss of exon 2
gtgggttcattcacttaacaacca-tcatcatttcgttaccctgattaatttggt---gggtataatgttcagGTTTTTACTTGGAACACTGATGCATGGGGATATGGTTCTGGAACCACTTCGTTATACCAGTCACATCCTTGGGTACTAGTTGTCCTTCCAACTGGAGAAA
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gtatgtcatatttttgagaaattagtcattaaccttctgtttccataaatttgatctatgaaacattggttagGTTATTACTTGGAACACGGATGCATGGGATTATGGTCCAGGAACCACATCACTATATCAGTCACACCCTTGGGTACTGGCTGTTCTTCCTGATGGGAAGG
upper sequence: AT3G23640.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA04G14810.1 (Glycine max), 3'ss of exon 2
-------------gtgggttcattcacttaacaaccatcatcatttcgttaccctgat--taatttggtgggtataatgttcagGTTTTTACTTGGAACACTGATGCATGGGGATATGGTTCTGGAACCACTTCGTTATACCAGTCACATCCTTGGGTACTAGTTGTCCTTCCAACTGGAGAAA
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gtaagtcaatcttatggaatt-ttgtctttttaaaaagatttattt-attatctgggtgctgatcagttaaatttcatttgcagGTTTTCACATGGAACACAGATGCATGGGGTTATGGCCCTGGAACTACATCCTTGTACCAATCACATCCATGGGTGTTAGCAGTTCTTCCTAATGGCGAGG
upper sequence: AT3G23640.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv02s0033g01410.t01 (Vitis vinifera), 3'ss of exon 3
--------gtgggttcattcacttaacaaccatcatcatttcgttaccctgattaat--ttggtgggtataatgttcagGTTTTTACTTGGAACACTGATGCATGGGGATATGGTTCTGGAACCACTTCGTTATACCAGTCACATCCTTGGGTACTAGTTGTCCTTCCAACTGGAGAAA
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gtaagacagtttgtatagtttctcatcatgaagccttgttccagttctacaagtattgataaacttatattccatgtagGTTTTTACGTGGAACACAGATGCATGGGGTTATGGTTCTGGAACAACATCCTTGTACCAGTCACATCCTTGGGTTCTAGCTGTTCTTCCAAATGGGGAGG
upper sequence: AT3G23640.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv02s0087g00060.t01 (Vitis vinifera), 3'ss of exon 3
--------gtgggttcattcacttaacaaccatcatcatttcgttaccctgattaatt-tggtgggtataatgttcagGTTTTTACTTGGAACACTGATGCATGGGGATATGGTTCTGGAACCACTTCGTTATACCAGTCACATCCTTGGGTACTAGTTGTCCTTCCAACTGGAGAAA
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gtaagacagtttgtatagtttctcatcatgaagctttgtgtcagttctacaagcattgataacttatattccatgtagGTTTTTACGTGGAACATAGCTGCATGGGGTTTTGATTCTGGAACGACATCCTTGTACCAGTCACATCCTTGGGTTCTAGCTGTTCTTCCAAATGGGGAGGMapped 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|116479211|gb|EG521803.1|EG521803EST: TTTATGGGACGGGAGAAGTTAGTGGTCAGTTGGAGAGAACAGGCAAACGG GTTTTTACTTGGAACACTGATGCATGGGGATATGGTTCTGGAACCACTTCG
genomic: TTTATGGGACGGGAGAAGTTAGTGGTCAGTTGGAGAGAACAGGCAAACGGgtgggttcat ... taatgttcagGTTTTTACTTGGAACACTGATGCATGGGGATATGGTTCTGGAACCACTTCG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaacaaccatcatcatttcgttaccctgattaatttggtgggtataatgttcagGTTTTTACTTGGAACACTGATGCATGGGGATATGGTTCTGGAACCACTTCGTTATACCAGTCACATCCTTGGGTACTAGTTGTCCTTCCAACTGGAGAAA
gattaat putative branch site (score: 3)
tgattaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgggttcattcacttaacaaccatcatcatttcgttaccctgattaatttggtgggtataatgttcagGTTTTTACTTGGAACACTGATGCATGGGGATATGGTTCTGGAACCACTTCGTTATACCAGTCACATCCTTGGGTACTAGTTGTCCTTCCAACTGGAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA