Sequence
atgc intronic sequence ATGC exonic sequencegtactgtttttactgttttacccttctcataatactgttttagtttacgttactttcataagtcataactactgttaagtgtacatgtttaagaaaaggattatatctaaagctgagattgttctactagtcagGTCAGTCCGGAGCTGTATGGTGACAACAGACCAAGATTGTTCACTTATTGGACG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G18460.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G18460.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA20G36380.1 (Glycine max), 3'ss of exon 4
gtactgtttttactgttttacccttctcataatactgttttagtttacgttactttcataagtcataactactgtta-agtgtacatgtttaagaaaaggattatatctaaagctgagattgttctactagtcagGTCAGTCCGGAGCTGTATGGTGACAACAGACCAAGATTGTTCACTTATTGGACG
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-------------------------------atac-acggcacattacattgcacactcaatgtgcgtgaaggaacagaaaattctaattttataaaatagtc---tctgaagctttgatcattctactagtcagGTCAGTCCGGAGCTCTATGGTGACAGCAGACCAAGATTGTTCACTTATTGGACG
upper sequence: AT5G18460.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA10G31140.1 (Glycine max), 3'ss of exon 4
gtactgtttttactgttttacccttctcataatactgttttagtttacgttactttcataagtcataactactgttaagtgtacatgtttaagaaaaggattatatctaaagctgagattgttctactagtcagGTCAGTCCGGAGCTGTATGGTGACAACAGACCAAGATTGTTCACTTATTGGACG
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------------------tacacggcacattacattgcaccgaatgtgcatgcgtgtaggaa-cataaatactaat-----------tttatcaaatag----tctctgaagctttgatcattctactagtcagGTTAGTCCGGAGCTCTATGGTGACAACAGACCCAGATTGTTCACTTATTGGACG
upper sequence: AT5G18460.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA03G41280.1 (Glycine max), 3'ss of exon 4
gtactgtttttactgttttacccttctcataatactgttttagtttacgttactttcataagtcataactactgttaagtgtacatgtttaagaaaaggattatatctaaagctgagattgttctactagtcagGTCAGTCCGGAGCTGTATGGTGACAACAGACCAAGATTGTTCACTTATTGGACG
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-----------------ctagatttacca-aataat-----agtatatatctctctcttaatct----------tttggtttatg-gtggaattaagaaatggtctctaaagctttgattgttctactagtcagGTCAGTCCGGAGCTTTATGGTGACAGCAGGCCCAGATTATTCACTTACTGGACG
upper sequence: AT5G18460.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA19G43900.1 (Glycine max), 3'ss of exon 6
------gtactgtt----tttactgtttt-acccttctcataatactgttttagtttacgt---tactttcataagtcataactactgttaagtgtacatgtttaagaaaaggattatatctaaagctgagattgttctactagtcagGTCAGTCCGGAGCTGTATGGTGACAACAGACCAAGATTGTTCACTTATTGGACG
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gtatatattctgtctaaattcaatgtggagaagctaagtttaattaccaaatagtgcatatatatatatatatatatctcttatatggtttttggtggattattaagaaatgt-tggtctctaaatctttgattgttctactagtcagGTCAGTCCGGAGCTTTATGGTGACAGCAGGCCCAGATTATTCACTTACTGGACG
upper sequence: AT5G18460.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv04s0043g00560.t01 (Vitis vinifera), 3'ss of exon 4
gtactgtttttactgttttacccttctcataatactgttttagtttacgttactttcataagtca--taactactgttaagtgtacatgtttaagaaaaggattatatctaaagctgagattgttc-tactagtcagGTCAGTCCGGAGCTGTATGGTGACAACAGACCAAGATTGTTCACTTATTGGACG
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gtacttttttccatttcctgtcctgccacacactcaatccaaagctcctcttttctaatgaatcaattaattattatttaataataaaataaatccacaagtgggattcttaaccgctgattctttatactagtcagGTCAGTCCGGAGCTTTATGGTGACAGCAGACCCAGATTATTCACTTATTGGACGMapped 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|116464715|gb|EG507307.1|EG507307EST: AGGTCCTGATCTCAATAGTATTGAAGCTGGCTGGCAGTCAG
genomic: AGGTCCTGATCTCAATAGTATTGAAGCTGGCT-G--G-CAGgtactgtttt ... tactagt
EST:
gi|116435455|gb|EG478047.1|EG478047EST: CTGGATCTTTCGTAGGTCCTGATCTCAATAGTATTGAAGCTGGCTGGCAGTCAG
genomic: CTGGATCTTTCGTAGGTCCTGATCTCAATAGTATTGAAGCTGGCT-G--G-CAGgtactgtttt ... tactagt
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtacatgtttaagaaaaggattatatctaaagctgagattgttctactagtcagGTCAGTCCGGAGCTGTATGGTGACAACAGACCAAGATTGTTCACTTATTGGACG
atctaaa putative branch site (score: 3)
ttgttct putative PPT
attatatctaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtactgtttttactgttttacccttctcataatactgttttagtttacgttactttcataagtcataactactgttaagtgtacatgtttaagaaaaggattatatctaaagctgagattgttctactagtcagGTCAGTCCGGAGCTGTATGGTGACAACAGACCAAGATTGTTCACTTATTGGACG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT