Sequence
atgc intronic sequence ATGC exonic sequenceCATATGAAAGATGGATGGGGACTGGCTACCGATGGAAAAGCGTTATTTGGAAGTGATGGCACTTCTACATTATATCGGATGGACCCTCAAACAATGAAAGgtttcttgcttatactgattaagtttttgtgcccttgagccacttacttaattatttacatagggagtagtatatttagcattttattgtgtctcttctctgcag
Basic information
species | Arabidopsis thaliana |
transcript | AT4G25720.2 |
intron # | 6 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G25720.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA09G24430.1 (Glycine max), 5'ss of exon 3
CATATGAAAGATGGATGGGGACTGGCTACCGATGGAAAAGCGTTATTTGGAAGTGATGGCACTTCTACATTATATCGGATGGACCCTCAAACAATGAAAGgtttcttgcttatactgattaagtttttgtgcccttgagccacttactta---------att-----atttacatagggagtagtatatttagcattttattgtgtctcttctctgcag----------------------------------------
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GCTATGAAAGATGGTTGGGGTCTGGCAACTGATGGAAAAGTCTTGTTTGGAAGTGATGGTAGTTCAACATTGTATCAAATTGATCCTCAAACATTTAAAGgtttgtctgtc-cattgaagttctattcctttcctttcaccatttatgtgcaaagccccattcctaaacctttttgggtcgtcctgctttcaa-acttgacaatgctttgtgtttgctttgaatttagatgaaacttaacactgctctcttttctgtag
upper sequence: AT4G25720.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA16G29760.2 (Glycine max), 5'ss of exon 6
CATATGAAAGATGGATGGGGACTGGCTACCGATGGAAAAGCGTTATTTGGAAGTGATGGCACTTCTACATTATATCGGATGGACCCTCAAACAATGAAAGgtttcttgcttatactgattaagtttttgtgcccttgagccacttactt----aattatttacatagggagtagtatatttagcattttattgtgtctcttctctgcag----------------------------------------------
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GATATGAAAGATGGTTGGGGTCTGGCAACTGATGGAACATTGTTGTTTGGAAGTGATGGCAGTTCAACATTGTATCAAATTGATCCTCAAACGTTTAAAGgtttgtctgtc-caatgaagttctattcctttcctttcaccatttatgtgcaaaacctcattcctaaacctttttgtgtccagctttcaaacttgacaatacttagtgtttgctttgcattttcatggaacttaacattgccctctttcctgtag
upper sequence: AT4G25720.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA09G24440.1 (Glycine max), 5'ss of exon 6
CATATGAAAGATGGATGGGGACTGGCTACCGATGGAAAAGCGTTATTTGGAAGTGATGGCACTTCTACATTATATCGGATGGACCCTCAAACAATGAAAGgttt------------------------cttgcttatactgattaagtttttgtgccctt---gagccacttac-ttaattatttaca-tagggagtagtatatttagc--attttattgtgtctcttctctgcag--------------------------------
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GATATGAAAGAGGGTTGGGGTCTGGCAACTGATGGAAAAGTCTTGTTTGGAAGTGATGGCAGTTCAACATTGTATCAATTTGAGCCTCAACCATTTAAAGgtttgtctgtccaatgaagttccacacttttcctttcactttttatgtgcaaacccctttcccaaatcatttgtgtccacttttcaaacttgaaaatactctgtttagtttatctctgtttgtcttgcattttcatggaatttacattgccctattggctgtacgtag
upper sequence: AT4G25720.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA09G24450.1 (Glycine max), 5'ss of exon 6
CATATGAAAGATGGATGGGGACTGGCTACCGATGGAAAAGCGTTATTTGGAAGTGATGGCACTTCTACATTATATCGGATG---------GACCCTCAAACAATGAAAGgtttcttgctta--tactgattaagtt---tttgtgcccttgagccacttacttaattatttacataggg--agtagtata-tttagcattttattgtgtctcttctctgcag-------------------------------------------
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---------GATGGTTGGGGTCTGGCAACTGATGGAAAAGTCTTGTTTGGAAGTGATGGCAGTTCAACATTGTATCAAATGATTCAAACTGATCCTCAGACATTTAAAGgtttgccaattgcctgtcaatgaagttccattcctttcctttcaccattttttcccaaacttttttgggtccagttttctaacttgacaatactttgtttagttaatgtgtatgccttgcattttagtggaatttacattgccctattttctgtag
upper sequence: AT4G25720.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: Vv16s0050g01140.t01 (Vitis vinifera), 5'ss of exon 6
CATATGAAAGATGGATGGGGACTGGCTACCGATGGAAAAGCGTTATTTGGAAGTGATGGCACTTCTACATTATATCGGATGGACCCTCAAACAATGAAAGgtttcttgcttatactgattaagtttttgtgcccttgagccacttacttaattatttacatagggagtagtatatttagcattttattgtgtctcttctc-tgcag-
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CATATGCGGGATGGTTGGGGACTGGCAACTAATGGGGAAGTTTTGTTTGGAAGTGATGGAACTTCGACACTGTATCAGATTGATCCTCAATCAATGAAAGgtctttt--ttatac-----aaattctttcagttccagtacttttttctaacaatttatttttgaggtagaggctacaattttttctctttccttttgggatggaggMapped 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|125274816|gb|EL288901.1|EL288901EST: AAGTGATGGCACTTCTACATTATATCGGATGGACCCTCAAACAATGAAAG TTACTGATAAGCATATAGTCAGATATAATGGCCGTGAGGTACG
genomic: AAGTGATGGCACTTCTACATTATATCGGATGGACCCTCAAACAATGAAAGgtttcttgct ... ttctctgcagTTACTGATAAGCATATAGTCAGATATAATGGCCGTGAGGTACG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CATATGAAAGATGGATGGGGACTGGCTACCGATGGAAAAGCGTTATTTGGAAGTGATGGCACTTCTACATTATATCGGATGGACCCTCAAACAATGAAAGgtttcttgcttatactgattaagtttttgtgcccttgagccacttacttaattatttacatagggagtagtatatttagcattttattgtgtctcttctctgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA