Sequence
atgc intronic sequence ATGC exonic sequenceTCCAGAGATATACAGCAATGACTTCACAACTACTTTACCAGCTGTGATAGACAAATGTATTCAGTCTGCACCAATTGACACACGAAGAGCTTTATATAAGgtttgaaacgccaaagactggtcagagttttaagataatttccaatccgcaatactgatgaatttgtgaaatcatttcag
Basic information
species | Arabidopsis thaliana |
transcript | AT1G13180.1 |
intron # | 6 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G13180.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G136662_T01 (Zea mays), 5'ss of exon 6
TCCAGAGATATACAGCAATGACTTCACAACTACTTTACCAGCTGTGATAGACAAATGTATTCAGTCTGCACCAATTGACACACGAAGAGCTTTATATAAGgtt------tgaaacgccaaagactggtcagagttttaagataatttcc---aat-ccgcaatactgatgaatttgtgaaatcatttcag
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TCCTGAGATTTACTCTGCCGATTTCTCCACTCCTTTGCCCGAGTTGATTGACAACTGTGTTCAGTCTGCACCAATTGACACAAGGAGAGCTCTGTACAAGgtgctttcatcaaactctgcatgtttatctaagatgggaagtgatgtttgtgaatgctgtgacatttatcagaat-tctactttttgcag
upper sequence: AT1G13180.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA08G13780.1 (Glycine max), 5'ss of exon 6
TCCAGAGATATACAGCAATGACTTCACAACTACTTTACCAGCTGTGATAGACAAATGTATTCAGTCTGCACCAATTGACACACGAAGAGCTTTATATAAGgtttgaaacgccaaagac-----tggtcagagt-tttaagataatttccaatccgcaat-actgatgaatttgtgaaatcatttcag-------------
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TCCTGAGATATATAGTAGTGACTTTACTACCCCTTTGCCAGTTGTAATAGACAAATGCATTCAGTCTGCGCCAATTGACACAAGGAGATCACTATACAAGgtgaagtactttacttacacgtgtattaataatctctaagagtgcttttaaattttagtgaaccgttacttctaatcataaaattagggatcttccaaac
upper sequence: AT1G13180.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA08G13810.1 (Glycine max), 5'ss of exon 6
TCCAGAGATATACAGCAATGACTTCACAACTACTTTACCAGCTGTGATAGACAAATGTATTCAGTCTGCACCAATTGACACACGAAGAGCTTTATATAAGgtttgaaacgccaaagactggtcagagttttaagataatttccaatccgcaatactgatgaatttgtga-aatcatttcag------------------------
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TCCCGAGATATATGGCAGTGACTTTACCACCCCTTTGCCAGTTGTAATAGACAAGTGTATTCAGTCTGCGCCAATTGACACAAGGAGATCATTATACAAGgt--gaagtacctttacatattgaggtgtatataaaaaatcccca---agagtgcttttaaattttagttaaccactttttatcataaaattagtgattttctta
upper sequence: AT1G13180.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA05G30630.1 (Glycine max), 5'ss of exon 6
TCCAGAGATATACAGCAATGACTTCACAACTACTTTACCAGCTGTGATAGACAAATGTATTCAGTCTGCACCAATTGACACACGAAGAGCTTTATATAAGgtttgaaacgccaaagactggtcagagttttaagataatttccaatccgcaatactgatgaattt--gtgaaatcatttcag-----------------------
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TCCTGAGATATATGGCAGTGACTTTACCACCCCTTTGCCAGTTGTAATAGACAAGTGCATTCAGTCTGCGCCAATTGACACAAGGAGATCATTATACAAGgt--gaagtaccttt-acttattaacgtgt--atataattaagctccaagagtgcttttaaattttagttaaccaatttttattataaaattagtgattttctta
upper sequence: AT1G13180.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: Vv01s0137g00280.t01 (Vitis vinifera), 5'ss of exon 6
TCCAGAGATATACAGCAATGACTTCACAACTACTTTACCAGCTGTGATAGACAAATGTATTCAGTCTGCACCAATTGACACACGAAGAGCTTTATATAAGgtttgaaacgccaaagactggtcagagttttaagataatttccaatccgcaatactgatgaatt-tgtgaaatcatttcag---------------------
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TCCTGAGATCTACAGCAGCGATTTTGCAACCCCTTTACCAGCTGTAATAGACAAGTGTATTCAGTCTGCACCAATTGACACAAGAAGGGCTTTGTATAAGg--taaagtacatagaccccaataaaaaacggtgaaaattttgtttcttcttgagatatgatccatgtgaaacaatgtagaattgcctatttgatgtttcaaMapped 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|125249718|gb|EL263803.1|EL263803EST: ACACGAAGAGCTTTATATAAG AATATAGTGTTGTCCGGAGGTTCAACTATGTTCAAAGATTTCGGAAGAAGG
genomic: ACACGAAGAGCTTTATATAAGgtttgaaacg ... atcatttcagAATATAGTGTTGTCCGGAGGTTCAACTATGTTCAAAGATTTCGGAAGAAGG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TCCAGAGATATACAGCAATGACTTCACAACTACTTTACCAGCTGTGATAGACAAATGTATTCAGTCTGCACCAATTGACACACGAAGAGCTTTATATAAGgtttgaaacgccaaagactggtcagagttttaagataatttccaatccgcaatactgatgaatttgtgaaatcatttcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT