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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTAATGCATGGAGCAGATCGAGATATTATCTGGCTTCAACGGGACTTCGGCATATATGTCTGCAATCTCTTTGACACAGGACAGgtttgattttgtttcagcgatgatcttctatttttttctatgacatttcctgtaaaacataggagatccagtatccataacatacaccttttgctttatg...

Basic information

species Arabidopsis thaliana
transcript AT5G35910.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G35910.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: LOC_Os10g30100.1 (Oryza sativa), 5'ss of exon 4
GTAATGCATGGAGCAGATCGAGATATTATCTGGCTTCAACGGGACTTCGGCATATATGTCTGCAATCTCTTTGACACAGGACAGgtttgattttgtttcagc--gatgatcttctatttttttctatgacatttcctgtaaaacataggagatccagtatccataacatacaccttttgctttatg-----------------
||||||||||| |||||||| ||||| || ||||||||||||||||| ||||||||||| ||||| || ||||||||||| ||||| |  |      | |||  |||       |  |  |||  || |||  || |||    || |   |||  | |   ||||   |    || ||     | |                 
GTAATGCATGGTGCAGATCGTGATATAATATGGCTTCAACGGGACTTTGGCATATATGTATGCAACCTTTTTGACACAGGCCAGgtatagtgcaacattagctggatagcggcatggtgctttgcattacagctc-tgttttgcaaatttgattaaatcatcatattgttattctgttaaccgaagcttgacattacaaacag

upper sequence: AT5G35910.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: LOC_Os03g06190.1 (Oryza sativa), 5'ss of exon 4
GTAATGCATGGAGCAGATCGAGATATTATCTGGCTTCAACGGGACTTCGGCATATATGTCTGCAATCTCTTTGACACAGGACAGgt---ttgattt-tgtttcagcgatgat-----cttctatttttttctatgacatttcctgtaaaacataggaga-tccagtatccat-aacatacacctttt---gctttatg-------------------------------------
||||||||||| || ||||| |||||||| ||||| |||||||| |||  ||||||||| |||||||| |||||||||||||||||   ||||||  |     |   ||  |     ||   | | |  |   |||     ||| |||   |        | || | ||| | || || | | ||||   |  ||||                                      
GTAATGCATGGGGCTGATCGTGATATTATGTGGCTCCAACGGGATTTCCACATATATGTTTGCAATCTTTTTGACACAGGACAGgtattttgattaataggctaataatactaaatactaaaactgtgattcttgattgcacctttaatttacctctttcttcattctccttcaaaatcctcattttcatgtcttataaactgaaccttggattttcctttctaactccaaacag

upper sequence: AT5G35910.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G118917_T02 (Zea mays), 5'ss of exon 4
GTAATGCATGGAGCAGATCGAGATATTATCTGGCTTCAACGGGACTTCGGCATATATGTCTGCAATCTCTTTGACACAGGACAGgtttg--------------attttgttt-cagcgatgat------cttctattt-ttttctatgacatttcctg-taaaacataggag--atccagtatccataacatacaccttttgctttatg---
||||||||||| |||| ||| ||||| || ||||||||||| |||||| |||||||||| ||||| || ||||||||||| ||||| ||              ||| ||||   ||   | |       ||||| ||| ||||   | ||||||  || | | || |||  |  |||    ||  |     ||     |     |||     
GTAATGCATGGTGCAGGTCGTGATATAATATGGCTTCAACGAGACTTCAGCATATATGTGTGCAACCTTTTTGACACAGGCCAGgtatggcacgcacagcatgattatgttcatagttcttacatttcacttctgtttcttttacttcacattttttggtcatacttagtcgccatcttaaattgaagctttatcttctccaacttaaatag

upper sequence: AT5G35910.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G000749_T01 (Zea mays), 5'ss of exon 4
GTAATGCATGGAGCAGATCGAGATATTATCTGGCTTCAACGGGACTTCGGCATATATGTCTGCAATCTCTTTGACACAGGACAGgtttgattttgtttcag-cgatgatcttctatttttttctatgacatttcctgtaaaacataggagatccagtatccataacatacaccttttgctttatg-----------------------------------
||||||||||| || ||||| ||||| || ||||| || |||||||||  ||| ||||| |||||||| ||||||||||||||||| ||  |   ||   | | || ||    |  || |   | || ||     | |      |     || |    |  | | | | |   || || || ||                                    
GTAATGCATGGTGCGGATCGTGATATAATGTGGCTCCAGCGGGACTTCCACATCTATGTGTGCAATCTTTTTGACACAGGACAGgtatgtgtaaattagggtcaataataccatgattctgattctgccacccaattttcttatttctttattcttcctggaaaccctcctatttatgtttaatagactgaagattgcttttctttctaacgataatcag

upper sequence: AT5G35910.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G039096_T01 (Zea mays), 5'ss of exon 5
GTAATGCATGGAGCAGATCGAGATATTATCTGGCTTCAACGGGACTTCGGCATATATGTCTGCAATCTCTTTGACACAGGACAGgtttgattttgtttcag-cgatgatcttctatttttttctatgacatttcctgtaaaacataggagatccagtatccataacatacaccttt-tgctttatg-----
||||||||||| || ||||| ||||| || ||||| || |||||||||  ||| ||||| |||||||| |||||||||||||| || ||  |   ||   | | || ||    |  || |   | || ||          ||  |      | |  ||| | |     | ||| |  |  || |||     
GTAATGCATGGTGCGGATCGTGATATAATGTGGCTCCAGCGGGACTTCCACATCTATGTGTGCAATCTTTTTGACACAGGACAAgtatgtgtaaattagggtcaataataccatgattctgattctgccaccc-------aattttcttatttctttattcttcctggaaaccctcctatttaatgtttaa

upper sequence: AT5G35910.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G145704_T02 (Zea mays), 5'ss of exon 4
GTAATGCATGGAGCAGATCGAGATATTATCTGGCTTCAACGGGACTTCGGCATATATGTCTGCAATCTCTTTGACACAGGACAGgtttgattttgtttcag-cgatgatcttctattttt--ttctatgac---atttcctgtaaaacataggagatccagtatccataacatacaccttttgctttatg-------------------------------
||||||||||| || ||||| ||||| || ||||| || |||||||||  ||| ||||| |||||||| |||||||||||||| || ||  |   ||   | | || ||    |  || |  ||||   ||   |||| ||        ||      |  | | || |   ||  |   |||  |  |                                 
GTAATGCATGGTGCGGATCGTGATATAATGTGGCTCCAGCGGGACTTCCACATCTATGTGTGCAATCTTTTTGACACAGGACAAgtatgtgtaaattagggtcaataataccatgattctgattctgccacccaattttcttatttctttattcttcctggaaaccctcctatttaatgtttaatagactgaagattgcttttctttctaacgataatcag

upper sequence: AT5G35910.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G452875_T01 (Zea mays), 5'ss of exon 4
GTAATGCATGGAGCAGATCGAGATATTATCTGGCTTCAACGGGACTTCGGCATATATGTCTGCAATCTCTTTGACACAGGACAGgtttgattttgtttcag-cgatgatcttctatttttttctatgacatttcctgtaaaacataggagatccagtatccataacatacaccttt-tgctttatg-----
||||||||||| || ||||| ||||| || ||||| || || ||||||  ||| ||||| |||||||| ||||||||||||||||| ||  |   ||   | | || ||    |  || |   | || ||          ||  |      | |  ||| | |     | ||| |  |  || |||     
GTAATGCATGGTGCGGATCGTGATATAATGTGGCTCCAGCGAGACTTCCACATCTATGTGTGCAATCTTTTTGACACAGGACAGgtatgtgtaaattagggtcaataataccatgattctgattctgccaccc-------aattttcttatttctttattcttcctggaaaccctcctatttaatgtttaa

upper sequence: AT5G35910.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA19G29260.1 (Glycine max), 5'ss of exon 4
GTAATGCATGGAGCAGATCGAGATATTATCTGGCTTCAACGGGACTTCGGCATATATGTCTGCAATCTCTTTGACACAGGACAGgtttgattttgtttcagcgatgatcttctattttt---ttctatgacatttcctgtaaaacataggagatccagtatccataacatacaccttttgctttatg
|| |||||||||||||||||||| ||| | ||||| |||||||| || ||||| ||||| |||||| | || || || || ||||||||  |||||       | ||| ||| || ||    ||   |  ||||   | | ||  | |  | ||    |||  |    ||| |  | || |   || 
GTCATGCATGGAGCAGATCGAGACATTGTGTGGCTGCAACGGGATTTTGGCATTTATGTTTGCAATATGTTCGATACTGGCCAGgtttg--tttgtaaagctcaggatgttcaatattggaattacttcccattagttatcaaggaaataaaattgtatattga-gttatataattgttaccacatt

upper sequence: AT5G35910.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv08s0056g01320.t01 (Vitis vinifera), 5'ss of exon 3
GTAATGCATGGAGCAGATCGAGATATTATCTGGCTTCAACGGGACTTCGGCATATATGTCTGCAATCTCTTTGACACAGGACAGgtttgattttgtttcagcgatgatcttctatttt-----tttctatga-catttcctgtaaaacataggagatccagtatccataacatacaccttttgctttatg
|| ||||| || |||||||| ||||| || |||||||||||||| || ||||||||  |||||||  | ||||| || |||||||||||  ||||   |||   |    ||  ||| |     ||| ||  | | |||  | |    ||| | |  |         || |  || |     || |     
GTTATGCACGGGGCAGATCGGGATATCATTTGGCTTCAACGGGATTTTGGCATATACATCTGCAACATGTTTGATACCGGACAGgtttg-ctttgaaacagtagtttatttggattctgggattttgtacaagccttttttctgcttcatggcattttagacgaaaattatttagaatgactggt-----

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|86064860|gb|DR360617.1|DR360617
EST:     TTCAACGGGACTTCGGCATATATGTCTGCAATCTCTTTGACACAGGACAG                         GCCTCCAGGGTTCTAAATTTGGAGAGAAATAGCCTGGAGTTTCTTTTGCAG
genomic: TTCAACGGGACTTCGGCATATATGTCTGCAATCTCTTTGACACAGGACAGgtttgatttt ... attttttcagGCCTCCAGGGTTCTAAATTTGGAGAGAAATAGCCTGGAGTTTCTTTTGCAG
EST: gi|116454660|gb|EG497252.1|EG497252
EST:     TTCAACGGGACTTCGGCATATATGTCTGCAATCTCTTTGACACAGGACAG                         GCCTCCAGGGTTCTAAATTTGGAGAGAAATAGCCTGGAGTTTCTTTTGCAG
genomic: TTCAACGGGACTTCGGCATATATGTCTGCAATCTCTTTGACACAGGACAGgtttgatttt ... attttttcagGCCTCCAGGGTTCTAAATTTGGAGAGAAATAGCCTGGAGTTTCTTTTGCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTAATGCATGGAGCAGATCGAGATATTATCTGGCTTCAACGGGACTTCGGCATATATGTCTGCAATCTCTTTGACACAGGACAGgtttgattttgtttcagcgatgatcttctatttttttctatgacatttcctgtaaaacataggagatccagtatccataacatacaccttttgctttatg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaacata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aacataca