Sequence
atgc intronic sequence ATGC exonic sequence...tgtttagttagaagtatacaaatatggatgtgtaacagagtagctagtatttaaaagaacttcatctacaatttctctctctgatatgagctctcatcagATCCGTGAAGCTGATATTTCTCGGCTCTCCTTTGCTGTTGAGCTTGCGGAAGAATTTTATGGAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G38840.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G38840.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os03g58240.1 (Oryza sativa), 3'ss of exon 6
tgtttagttagaagtatacaaatatggatgtgtaacagagtagctagtatttaaaagaacttcatctacaatttctctctctgatatgagctctcatcagATCCGTGAAGCTGATATTTCTCGGCTCTCCTTTGCTGTTGAGCTTGCGGAAGAATTTTATGGAAG
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--gtaatctatctctctactcatatacacgcataa---actcacttgtctgtttgtg---tgtgcttagacttttact---tgttatg---tcattgcagGTGCGTGAAGCTGATATATCTAGGCTCTCATTTGCTGTTGAGATTGCAGAAGAATTCTATGGAAG
upper sequence: AT2G38840.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os07g08400.1 (Oryza sativa), 3'ss of exon 6
tgtttagttagaagtatacaaatatggatgtgtaacagagtagctagtatttaaaagaacttcatctacaatttctctctctgatatgagctctcatcagATCCGTGAAGCTGATATTTCTCGGCTCTCCTTTGCTGTTGAGCTTGCGGAAGAATTTTATGGAAG
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-------------gtgtgtttctctggct-catgacatgctcacctccattc-------tctcatttgatagctattaacttgacttatcttgatcatagATTCGTGAAGCTGATATATCTAGACTCTCATTTGCTGTTGAAATTGCTGAAGAATTCTATGGAAG
upper sequence: AT2G38840.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA02G16130.1 (Glycine max), 3'ss of exon 8
--tgtttagttagaagtatacaaatatggatgtgtaacagagtagctagtatttaaaagaacttcatctacaatttctctctctgatatgagctct---cat-cagATCCGTGAAGCTGATATTTCTCGGCTCTCCTTTGCTGTTGAGCTTGCGGAAGAATTTTATGGAAG
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tttacttggtaaagactgaataatcttgaactcttcaatcagca-----tatttcattttatttgttttataggttaga-ctgaaatgttatctttgtgcattcagATACGTGAAGCTGACATCTCTCGACTCTCTTTTGCGGTTGAGCTTGCTGAAGAATTTTATGGGAG
upper sequence: AT2G38840.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA10G03660.1 (Glycine max), 3'ss of exon 8
-------------------------------------------------------------------------tgtttagttagaa--------gtatacaaatatggatgtgtaacagagtagctag--tatttaaaagaacttcatctacaatttctctctctgatatgagctct----catcagATCCGTGAAGCTGATATTTCTCGGCTCTCCTTTGCTGTTGAGCTTGCGGAAGAATTTTATGGAAG
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gttctctcacttaacaactagcttttaaggcagggtttcccaagtggttgaatgattatcagaattttacttatatctagtttcaatttacttggtaaagacttaataatcttgaacccttcaaccagcatatttcattttatttgttttataggttaga-ctgaaatgttatctttgtgtattcagATACGTGAGGCTGACATCTCTCGACTCTCTTTTGCGGTTGAGCTTGCTGAAGAATTTTATGGGAG
upper sequence: AT2G38840.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv07s0141g00110.t01 (Vitis vinifera), 3'ss of exon 6
----tgtttagttagaagtatacaaatatggatgtgtaacaga-gtagcta-gtatttaaaagaacttcatctacaatttctctctctgatatgagctctcatcagATCCGTGAAGCTGATATTTCTCGGCTCTCCTTTGCTGTTGAGCTTGCGGAAGAATTTTATGGAAG
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ctcacatttggt--gggttctttttattttaatttttaatttttgtgtgtgtgtgtgttcttggatattaatattaatatgcttgtctggt-tgggtgtt---cagATTCGTGAAGCCGACATTTCTCGATTATCATTTGCTGTTGAGCTTGCTGAAGAATTCTATGGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agtatttaaaagaacttcatctacaatttctctctctgatatgagctctcatcagATCCGTGAAGCTGATATTTCTCGGCTCTCCTTTGCTGTTGAGCTTGCGGAAGAATTTTATGGAAG
ctctgat putative branch site (score: 4)
ctctcatc putative PPT
ttaaaagaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtttagttagaagtatacaaatatggatgtgtaacagagtagctagtatttaaaagaacttcatctacaatttctctctctgatatgagctctcatcagATCCGTGAAGCTGATATTTCTCGGCTCTCCTTTGCTGTTGAGCTTGCGGAAGAATTTTATGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
tgtttag
- - - - - - - -atacaaa
- - - - - - - - - - - - - - - - -aacagag
- - - - - - - - - - - - - - - - - - - - - - - - - - aaaagaa