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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTCGCTAAGTATAAGCTGGTGTTTCTGGGAGATCAATCCGTCGGCAAAACCAGTATCATTACTCGATTCATGTACGACAAATTCGACAACACTTACCAGgtaaatttccattgttcaaatctaggtattatctcgacgatgcacgacgtttgcttctattttgagggattatagtcgggaaaatcccagggtttgattg...

Basic information

species Arabidopsis thaliana
transcript AT2G44610.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G44610.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: LOC_Os07g31370.1 (Oryza sativa), 5'ss of exon 1
ACTCGCTAAGTATAAGCTGGTGTTTCTGGGAGATCAATCCGTCGGCAAAACCAGTATCATTACTCGATTCATGTACGACAAATTCGACAACACTTACCAGgtaaatttccattgttca--aatctaggtattatctcgacgatgcacgacg--tttgcttctattttga---gggattatagtcgg-gaaaatcccagggtttgattg
 ||||| ||||| ||||||||||| || || || || ||||||||||| ||||| ||||| || || |||||||||||||| ||||||||||| ||||||||   ||    || |  |    | | |   |   |||| |  |   ||  |  || |  |    | |||   |||   | |  ||| |      ||  ||        
GCTCGCCAAGTACAAGCTGGTGTTCCTCGGCGACCAGTCCGTCGGCAAGACCAGCATCATCACCCGCTTCATGTACGACAAGTTCGACAACACCTACCAGgtgcgttcttcttctctatcggtttcgccgtctgctcgcctctcttcggggggttggggttggatctgatcgggggccagatccggcggtggcgccctgg--------

upper sequence: AT2G44610.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GRMZM2G075719_T01 (Zea mays), 5'ss of exon 1
ACTCGCTAAGTATAAGCTGGTGTTTCTGGGAGATCAATCCGTCGGCAAAACCAGTATCATTACTCGATTCATGTACGACAAATTCGACAACACTTACCAGgta-aatttccattgttcaaatctaggtattatctcgacgatgcacgacgtttgcttctattttgagggattatagtcgggaaaatcc-cagggtttgattg
 ||||| ||||| ||||| || || ||||| || || ||||||||||| ||||| ||||| || || ||||||||||| || |||||||||||||||||||||  |   ||      |   ||        |||    |   ||  |  ||| |  | ||| ||   |  |    || |||    |     || |   ||  
GCTCGCCAAGTACAAGCTCGTCTTCCTGGGGGACCAGTCCGTCGGCAAGACCAGCATCATCACCCGCTTCATGTACGATAAGTTCGACAACACTTACCAGgtacgacggcccgcacgcctctccgatcccgatcgatccctcgcgtgctgttcgtgt-tatcttcccgcgtcggggttgggtttgtgggttggatccaatc-

upper sequence: AT2G44610.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GRMZM2G169694_T01 (Zea mays), 5'ss of exon 1
ACTCGCTAAGTATAAGCTGGTGTTTCTGGGAGATCAATCCGTCGGCAAAACCAGTATCATTACTCGATTCATGTACGACAAATTCGACAACACTTACCAGgtaaatttccattgttcaaatctaggtattatctcgacgatgcacga-cgtttgcttctattttgagggattatagtcgggaaaatcccagggtttgattg-
 ||||| ||||| ||||| || || ||||| || || ||||||||||| || || ||||| || || |||||||||||||| ||||| ||||| |||||||||      |      |   ||    | |     |||    |  ||| |  | || |    || | |  ||      || |       | ||  ||  | | 
GCTCGCCAAGTACAAGCTCGTCTTCCTGGGGGACCAGTCCGTCGGCAAGACGAGCATCATCACCCGCTTCATGTACGACAAGTTCGATAACACCTACCAGgtacgacggcccgcaccgcctccttctctggctccgatcccgatcgatccctcgcgtgctgttcgtgtcatctcccccgcgttgggggcggg--ttagtggg

upper sequence: AT2G44610.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GLYMA17G16200.1 (Glycine max), 5'ss of exon 1
ACTCGCTAAGTATAAGCTGGTGTTTCTGGGAGATCAATCCGTCGGCAAAACCAGTATCATTACTCGATTCATGTACGACAAATTCGACAACACTTACCAGgtaaatttccattgttcaaatctaggtattatctcgacgatgcacgacgtttgcttctat---tttgagggattatagtcgggaaaatcccagggtttgattg--
 ||||| ||||| |||||||||||  |||| ||||||||||| || |||||||| ||||| ||||| ||||||||||||||||||||||||||||| |||||     | | |  |||| ||| |     | | ||     | ||  || |||  |   |    ||  || ||| |  ||    |   |   | ||  | ||||  
TCTCGCAAAGTACAAGCTGGTGTTCTTGGGCGATCAATCCGTTGGGAAAACCAGCATCATCACTCGCTTCATGTACGACAAATTCGACAACACTTATCAGgt----cttcttctttcagatccaatctctctttcactatttcatcacattttttaaaaaaaattcaagagatcacggtttt-accgtggaatgggatcattgct

upper sequence: AT2G44610.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GLYMA05G05860.1 (Glycine max), 5'ss of exon 1
ACTCGCTAAGTATAAGCTGGTGTTTCTGGGAGATCAATCCGTCGGCAAAACCAGTATCATTACTCGATTCATGTACGACAAATTCGACAACACTTACCAGgtaaatttccattgttcaaatctaggtattatctcgacgatgcacgacgtttgcttc--tatttt-gagggattatagtcgggaaaatcccagggtttgattg-
 ||||| ||||| |||||||||||  |||| ||||| ||||| || |||||||| ||||| ||||| ||||||||||||||||||||||||||||| |||||     | | |  |||| ||| |       | ||     | ||   | ||| | |   ||||||  |   |||  ||     |   |   |  ||  ||| | 
TCTCGCAAAGTACAAGCTGGTGTTCTTGGGTGATCAGTCCGTTGGGAAAACCAGCATCATCACTCGCTTCATGTACGACAAATTCGACAACACTTATCAGgt----cttcttctttcagatccaatctcactttcactatttcattgcatttccattattattttcaaaacattcaagagatcacggttttatcgtgggatggg

upper sequence: AT2G44610.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GLYMA11G04330.1 (Glycine max), 5'ss of exon 1
ACTCGCTAAGTATAAGCTGGTGTTTCTGGGAGATCAATCCGTCGGCAAAACCAGTATCATTACTCGATTCATGTACGACAAATTCGACAACACTTACCAGgtaaatttc--cattgttcaaatctaggtattatctcgacgatgcacgacgtttgcttctattttgagggattatagtcggga--aaatcccagggtttgattg
  | || ||||| ||||| || ||  |||| || |||||||| ||||||||||| ||||| ||||| ||||||||||| |||||||| ||||| || ||||||  ||||  | |    | || |     ||    ||    |  | |  ||    || |||  ||      |||| |     |  |  ||  |    || |   
TTTAGCCAAGTACAAGCTCGTCTTCTTGGGTGACCAATCCGTGGGCAAAACCAGCATCATCACTCGCTTCATGTACGATAAATTCGATAACACCTATCAGgtacgtttctccctaaccctaaccctcagatccaatcctaaac-cgcatcgagaactcctaagttagctctttatggctaaaaccacttcgtaaaccttca---

upper sequence: AT2G44610.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GLYMA01G41100.1 (Glycine max), 5'ss of exon 1
ACTCGCTAAGTATAAGCTGGTGTTTCTGGGAGATCAATCCGTCGGCAAAACCAGTATCATTACTCGATTCATGTACGACAAATTCGACAACACTTACCAGgtaaatttccattgttcaaatctaggtattatctcgacgatgcac----gacgtttgcttctattttgagggattatagtcgggaaaatcccagggtttgattg-
  | || ||||| ||||| || || ||||| || |||||||| ||||||||||| ||||| ||||| |||||||| || |||||||| ||||| || |||||   |  | |    | |     || |   ||| | |   ||||      ||  |    |    | | |  |  || | ||    |  ||  |    || | |  
TTTAGCCAAGTACAAGCTCGTCTTCCTGGGTGACCAATCCGTGGGCAAAACCAGCATCATCACTCGCTTCATGTATGATAAATTCGATAACACCTATCAGgtttgtccctaaccctaaccctcagatccaatc-caaaactgcatcgaaaactataaagttagctcttaaaggctaaaatc----acttcttaaaccttcactct

upper sequence: AT2G44610.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GLYMA01G41090.1 (Glycine max), 5'ss of exon 1
ACTCGCTAAGTATAAGCTGGTGTTTCTGGGAGATCAATCCGTCGGCAAAACCAGTATCATTACTCGATTCATGTACGACAAATTCGACAACACTTACCAGgtaaatttccattgttcaaatctaggtattatctcgacgatgcacgacgtttgcttctattttgagggattatagtcgggaaaatcccagggtt--tgattg---
 || || ||||| |||||||||||  |||| ||||| || || || ||||| || ||||| ||||| |||||||| |||||||| ||||||||||| |||||    |   ||     |  || ||  | | | |  | | | ||    |||| |||  ||     || | || | |   || ||   | |   |  | |      
TCTTGCAAAGTACAAGCTGGTGTTCTTGGGTGATCAGTCTGTGGGAAAAACTAGCATCATCACTCGCTTCATGTATGACAAATTTGACAACACTTATCAGgtctgatcagatccactatctc-agccacttttt--aagtttcaatgtgtttcctttgatc--agggaaataaaatgacgacaaatgctgcactgctaaccatta

upper sequence: AT2G44610.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: Vv15s0021g00640.t01 (Vitis vinifera), 5'ss of exon 1
ACTCGCTAAGTATAAGCTGGTGTTTCTGGGAGATCAATCCGTCGGCAAAACCAGTATCATTACTCGATTCATGTACGACAAATTCGACAACACTTACCAGgt-aaatttccattgttcaaatctaggtatta--tctcgacgatgcacgacgtttgcttctattttgaggg-attatagtcgggaaaatcccagggtttgattg-
 ||||| ||||| ||||| || ||  ||||||| ||||||||||| || || || ||||| |||||||||||||||||||||||||||||||| || ||||| |||| |  || | ||   | |   |||    | ||  | ||       ||| | || | |||||     | | | |  | |||  |    |     |||   
TCTCGCCAAGTACAAGCTCGTCTTCTTGGGAGACCAATCCGTCGGAAAGACTAGCATCATCACTCGATTCATGTACGACAAATTCGACAACACCTATCAGgtcaaatctttatggatctgct-tgtttatcgattttcagcaattt----tgttggtttgtgttttggttttagttttggtgcgaatttgtttgatcccgatcct

upper sequence: AT2G44610.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: PP1S456_9V6.1 (Physcomitrella patens), 5'ss of exon 2
ACTCGCTAAGTATAAGCTGGTGTTTCTGGGAGATCAATCCGTCGGCAAAACCAGTATCATTACTCGATTCATGTACGACAAATTCGACAACACTTACCAGgtaaatt-----tccattgttcaaatctaggtattatctcgacgatgcacgacgtttgcttctattttgagggattatagtcgggaaaatcccagggtttg--attg---------------------------------------------------------------------
                                            | ||||| ||||| || || ||||| ||||| ||||| ||||||||||| |||||||| ||||     |  ||   |    |||  ||   |     ||  |||   | | |   |    |||   ||| |  |      |  ||||    ||   |  |||                                                                      
--------------------------------------------GAAAAACAAGTATTATCACGCGATTTATGTATGACAAGTTCGACAACACGTACCAGgtgaattaatttttaataactttcttctctgtgcaaatgtaactttgctgcaagctctgtatggtttcatgggctagtttctcagcgaatctagaggagagtcattagcggttttgagtccttcatgcatcatacttgttcttaatgctctgtttgtacttcattcgtttcggcag

upper sequence: AT2G44610.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: PP1S288_43V6.1 (Physcomitrella patens), 5'ss of exon 1
ACTCGCTAAGTATAAGCTGGTGTTTCTGGGAGATCAATCCGTCGGCAAAACCAGTATCATTACTCGATTCATGTACGACAAATTCGACAACACTTACCAGgtaaatttccattgttcaaatctaggtattatctcgacgatgcac---gacgtttgctt--ctattttgagggattatagtcgggaaaatcccagggtttgattg
 ||  | ||||| ||| |||| ||||| || |||||   ||||||||| || || |||||||||||||||||||| ||||| || ||| | || ||||||||||     ||      |           | |||||      | |   |  | | |||   || | ||  |   ||      |||   ||   |  |||      
GCTTTCGAAGTACAAGTTGGTCTTTCTTGGTGATCAGAGCGTCGGCAAGACTAGCATCATTACTCGATTCATGTATGACAAGTTTGACCAGACGTACCAGgtaatgaatcacaacaaattctctctctctctctcgctcgctcgctcggttgctcgctctcctgtctttcgttgttccttgtgggtggattgaaaagttc-----

upper sequence: AT2G44610.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: PP1S39_147V6.2 (Physcomitrella patens), 5'ss of exon 2
ACTCGCTAAGTATAAGCTGGTGTTTC-TGGGAGATCAATCCGTCGGCA------AAACCAGTATCATTACTCGAT-----TCATGTACGACAAATTCGACAACACTTACCAGgtaaatttccattgttcaaatctaggtattatctcgacgatgcacgacgtttgcttctattttgagggattatagtcgggaaaatcccagg---gtttgattg----------------------------
       |||||| | |  | | ||| ||   ||  |||  | |  ||      |    ||  || || |    |     || || |  | |||||        || ||        ||| |  |     |||      ||  ||| || | |      | |||  || | | | |   ||   |   | || |  | | |||   ||   ||||                            
GTAAAACAAGTATCATCACGCGATTCATGTATGACAAATTTGACAACACGTACCAGgttagcttctttccctcctagtcttcttgcataa-aaattgtgtgctgctgacatttctggtttgccgtacatcaataactccatactctggatggtttcattctttttgttttttctagtaagaacctgtcctggcaggttcaaggttggtgctattgatgagttttcccttgataactttggcag

upper sequence: AT2G44610.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: PP1S2_143V6.1 (Physcomitrella patens), 5'ss of exon 3
ACTCGCTAAGTATAAGCTGGTGTTTCTGGGAGATCAATCCGTCGGCAAAACCAGTATCATTACTCGATTCATGTACGACAAATTCGACAACACTTACCAGgtaaatttccattgttcaaatctaggtattatctcgacgatgcacgacgtttgcttctattttgagggattatagtcgggaaaatcccagggtttgattg
                                            ||||||| ||||| || || ||||||||||| || ||||| |||||||||||||||||    |||  || || |  |            |     |  |   |||| |  || |     |     |||   |   | | || | | |  ||    |
--------------------------------------------GCAAAACAAGTATTATCACGCGATTCATGTATGATAAATTTGACAACACTTACCAGgttggcttctctttttgattttcttccccaggatacgtcacactgtacgtgtaattatccgacgttcttttaacattttggagatactatgcattctgag

Mapped 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|124735129|gb|EH826531.1|EH826531
EST:     TTCATGTACGACAAATTCGACAACACTTACCAG                         GCCACAATTGGTATTGATTTTCTATCAAAGACAATGTACCTTGAAGATCGA
genomic: TTCATGTACGACAAATTCGACAACACTTACCAGgtaaatttcc ... taatcatcagGCCACAATTGGTATTGATTTTCTATCAAAGACAATGTACCTTGAAGATCGA
EST: gi|125036385|gb|EL108654.1|EL108654
EST:     AAATTCGACAACACTTACCAG                         GCCACAATTGGTTATTGATTTTCTATCAAAGACAATGTACCTTGAAGATCG
genomic: AAATTCGACAACACTTACCAGgtaaatttcc ... taatcatcagGCCACAATTGG-TATTGATTTTCTATCAAAGACAATGTACCTTGAAGATCG
EST: gi|116467570|gb|EG510162.1|EG510162
EST:     CCAGTATCATTACTCGATTCATGTACGACAAATTCGACAACACTTACCAG                         GCCACAATTGGTATTGATTTTCTATCAAAGACAATGTACCTTGAAGATCGA
genomic: CCAGTATCATTACTCGATTCATGTACGACAAATTCGACAACACTTACCAGgtaaatttcc ... taatcatcagGCCACAATTGGTATTGATTTTCTATCAAAGACAATGTACCTTGAAGATCGA
EST: gi|125052321|gb|EL124149.1|EL124149
EST:     ATTCATGTACGACAAATTCGACAACACTTACCAG                         GCCACAATTGGTATTGATTTTCTATCAAAGACAATGTACCTTGAAGATCGA
genomic: ATTCATGTACGACAAATTCGACAACACTTACCAGgtaaatttcc ... taatcatcagGCCACAATTGGTATTGATTTTCTATCAAAGACAATGTACCTTGAAGATCGA
EST: gi|164149879|gb|ES044049.1|ES044049
EST:     TCGATTCATGTACGACAAATTCGACAACACTTACCAG                         GCCACAATTGGTATTGATTTTCTATCAAAGACAATGTACCTTGAAGATCGA
genomic: TCGATTCATGTACGACAAATTCGACAACACTTACCAGgtaaatttcc ... taatcatcagGCCACAATTGGTATTGATTTTCTATCAAAGACAATGTACCTTGAAGATCGA
EST: gi|124816599|gb|EH901465.1|EH901465
EST:     ATGTACGACAAATTCGACAACACTTACCAG                         GCCACAATTGGTATTGATTTTCTATCAAAGACAATGTACCTTGAAGATCGA
genomic: ATGTACGACAAATTCGACAACACTTACCAGgtaaatttcc ... taatcatcagGCCACAATTGGTATTGATTTTCTATCAAAGACAATGTACCTTGAAGATCGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTCGCTAAGTATAAGCTGGTGTTTCTGGGAGATCAATCCGTCGGCAAAACCAGTATCATTACTCGATTCATGTACGACAAATTCGACAACACTTACCAGgtaaatttccattgttcaaatctaggtattatctcgacgatgcacgacgtttgcttctattttgagggattatagtcgggaaaatcccagggtttgattg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gggaaaat