Sequence
atgc intronic sequence ATGC exonic sequencegtaagtaagatttctagacataaaagcacaaacccaaaccacatttacttattactatctttccatggtctttagCCGCAGGAACTCCGGGTCTAGACTGGGCAACACGTGTTAAAATTGCTGCTGGTGCGGCTCGTGGACTAGCTTATCTCCATGAAGATT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G26150.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G26150.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os05g01040.1 (Oryza sativa), 3'ss of exon 2
-------------------------gtaagtaag-atttc-tagacataaaagcacaaacccaaaccacatttacttattactatctttccatggtctttagCCGCAGGAACTCCGGGTCTAGACTGGGCAACACGTGTTAAAATTGCTGCTGGTGCGGCTCGTGGACTAGCTTATCTCCATGAAGATT
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gtatggtttaacctcttgctacattgtacatggccatttcgttcttctgcaagtagaaactgaaac---atgtattga-----atcaacctgtaatcacagGACAGGGGAGGCCTGT-TCTAGATTGGTCGGCTAGGGTTAAAATTGCTGCAGGTGCTGCTCGTGGAATAGCGTATCTACATGAAGATT
upper sequence: AT1G26150.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM5G872442_T02 (Zea mays), 3'ss of exon 3
----------------gtaagtaagatt-tctagacataaaagcacaaacccaaaccacatttacttattactatctttcca---tggtctttagCCGCAGGAACT------CCGGGTCTAGACTGGGCAACACGTGTTAAAATTGCTGCTGGTGCGGCTCGTGGACTAGCTTATCTCCATGAAGATT
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gtcttgttacataggcagaactgcaattatttaggaacagaggta-gttctttgtccggactaaacaattaatgcatacccgcattgatttttcatcatagGACGTGGAGTACCAGTTTTGGAGTGGCCAGCTAGGGTTAAAATTGCGGCTGGTTCGGCTCGTGGAATAGCCTATCTTCACGAAGATT
upper sequence: AT1G26150.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G458548_T02 (Zea mays), 3'ss of exon 2
gtaagtaaga-----tttctagacat--aaaagcacaaacccaaaccacatttacttattact---atctttccatggtctttagCCGCAGGAACTCCGGGTCTAGACTGGGCAACACGTGTTAAAATTGCTGCTGGTGCGGCTCGTGGACTAGCTTATCTCCATGAAGATT
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gtatgttatagcctctttctaatcctttgcaagagtattcccatcttctgccagtacaaaaattgaactgaactgcaatctcagGACACGGAATGCCTGTGT-TAGAATGGTCCGCACGGGTTAAAATTGCTGCAGGTGCTGCTCGTGGAATTGCTTACCTACACGAAGATT
upper sequence: AT1G26150.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA02G14310.1 (Glycine max), 3'ss of exon 2
gtaagtaagatttctagacataaaagcacaaacccaaaccacatttacttatt--------actatct--ttccatggtctttagCCGCAGGAACTCCGGGTCTAGACTGGGCAACACGTGTTAAAATTGCTGCTGGTGCGGCTCGTGGACTAGCTTATCTCCATGAAGATT
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gtaaaactacatctgagtgataatag-attgtttcagtttattttgattgactttgattgtattaactgatattgtaatttgcagGGGAAGGCCAGCCTGTGCTAGAATGGGCAAACCGTGTTAAAATTGCAGCTGGTGCAGCCCGAGGACTAGCTTATCTCCATGAAGACT
upper sequence: AT1G26150.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA01G23180.1 (Glycine max), 3'ss of exon 2
gtaagtaagatttctagacataaaagcacaaacccaaaccacatttacttatt---actatctttcc-------atggtctttagCCGCAGGAACTCCGGGTCTAGACTGGGCAACACGTGTTAAAATTGCTGCTGGTGCGGCTCGTGGACTAGCTTATCTCCATGAAGATT
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gtaaa-actatatctgagtgataaaagattgtttcagttcattttgattgactttgattgtattaactgaaattataatttgcagGGGAAGGTCAGCCTGTATTAGAATGGGCTAACCGTGTGAAAATTGCAGCTGGTGCAGCCCGAGGACTAACTTATCTCCATGAAGACT
upper sequence: AT1G26150.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA16G19520.1 (Glycine max), 3'ss of exon 3
----------------------------------------------------------gtaagtaa--gatttctagacataaaagcacaaac-------ccaaaccacatttacttattactatctttccatgg-tctttagCCGCAGGAACTCCGGGTCTAGACTGGGCAACACGTGTTAAAATTGCTGCTGGTGCGGCTCGTGGACTAGCTTATCTCCATGAAGATT
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gtaaagctagttcagagggctagctgaatgattgtttcatgatattttgattaaatgtgtcagtgaatgtgttcaaaagagtgtattgctaacatttctctttgattaaatttaatctgtgctaactgaaagtgaatttgaagGGGAAGGTAGGCCAGTGCTGGACTGGACAAAACGTGTTAAAATTGCGGCTGGGGCAGCCAGAGGAATAGCTTATCTCCATGAAGACT
upper sequence: AT1G26150.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv01s0011g02460.t01 (Vitis vinifera), 3'ss of exon 2
gtaagtaag-atttctagacataaaagcacaaacc----caaaccacatttacttattactatctttccatggtctttagCCGCAGGAACTCCGGGTCTAGACTGGGCAACACGTGTTAAAATTGCTGCTGGTGCGGCTCGTGGACTAGCTTATCTCCATGAAGATT
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gtaaggctgtagtgataagcttccaagaatagtttgtggtaatggataactgattatgtgttgctccttgtaatttgtagGGGAAGGTAGGCCAGTTATGGACTGGGCAACACGTGTTAAGGTTGCTGCTGGTGCAGCTCGTGGAATAGCTTATCTTCATGAAGACTMapped 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|47832052|gb|CK121736.1|CK121736EST: GCTTATTTATGATTATGTCCCTAACAACAACCTTTACTTCCATCTTCACG CCGCAGGAACTCCGGGTCTAGACTGGGCAACACGTGTTAAAATTGCTGCTG
genomic: GCTTATTTATGATTATGTCCCTAACAACAACCTTTACTTCCATCTTCACGgtaagtaaga ... tggtctttagCCGCAGGAACTCCGGGTCTAGACTGGGCAACACGTGTTAAAATTGCTGCTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taaaagcacaaacccaaaccacatttacttattactatctttccatggtctttagCCGCAGGAACTCCGGGTCTAGACTGGGCAACACGTGTTAAAATTGCTGCTGGTGCGGCTCGTGGACTAGCTTATCTCCATGAAGATT
tctttccat CT-rich tract
atttacttattactat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtaagatttctagacataaaagcacaaacccaaaccacatttacttattactatctttccatggtctttagCCGCAGGAACTCCGGGTCTAGACTGGGCAACACGTGTTAAAATTGCTGCTGGTGCGGCTCGTGGACTAGCTTATCTCCATGAAGATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA