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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAGAGCTAGCAGAGGATGGTTACTCTGGTGTTGAGGTTAGGGTTACTCCAATGAGGACTGAGATTATCATCAGAGCTACTCGTACTCAGAATGTTCTTGgtatgtttgtttgatcatttcttctctctttcgattttgaatgtgtttcgagatctgatatcgaaaatgttgggttttag

Basic information

species Arabidopsis thaliana
transcript AT2G31610.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G31610.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA09G28440.1 (Glycine max), 5'ss of exon 2
AGAGAGCTAGCAGAGGATGGTTACTCTGGTGTTGAGGTTAGGGTTACTCCAATGAGGACTGAGATTATCATCAGAGCTACTCGTACTCAGAATGTTCTTGgtatgtttgtttg---atcatttcttctctctttcgattttgaatgt--gtttcgagatctgatatcgaaaatgttgggttttag------------
 | ||| | || ||||| |||||||| || || |||||||||||||| || ||| | || ||||||||||||||||| ||  | || ||    ||||| |||  ||||||||    | | || | |     ||  |   | |||| |   ||   | ||  | |     || |||   |||||              
CGTGAGTTGGCGGAGGACGGTTACTCCGGCGTGGAGGTTAGGGTTACGCCGATGCGCACCGAGATTATCATCAGAGCCACCAGAACCCAAGCCGTTCTCGgtgcgtttgtttctgtaaccttccgttaaatttgtgggatcgaattttcattcataaattagttccatgaattgtgttgttttgattgtatatatag

upper sequence: AT2G31610.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv11s0016g01380.t01 (Vitis vinifera), 5'ss of exon 2
AGAGAGCTAGCAGAGGATGGTTACTCTGGTGTTGAGGTTAGGGTTACTCCAATGAGGACTGAGATTATCATCAGAGCTACTCGTACTCAGAATGTTCTTGgtatgtttgt----ttgatcatttctt--ctctctttcgattttgaatgtgtttcgagatctgatatcgaaaatgttgggttttag
|||||||| || |||||||| ||||||||||| |||||||||||||| |||||| | ||||| || ||||||||||| |||||||||||||| |||||||||   |   |    ||||| |||  |    || | ||  |  ||   ||  ||||    |||  | |      | |||| ||||||
AGAGAGCTGGCCGAGGATGGCTACTCTGGTGTCGAGGTTAGGGTTACGCCAATGCGCACTGAAATCATCATCAGAGCCACTCGTACTCAGAACGTTCTTGgtgattcaatggctttgattattcttgagttcgcgtttcagatttgttggttttctgactctccttttttgctttttggcttttag

upper sequence: AT2G31610.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: EDP07493 (Chlamydomonas reinhardtii), 5'ss of exon 2
AGAGAGCTAGCAGAGGATGGTTACTCTGGTGTTGAGGTTAGGGTTACTCCAATGAGGACTGAGATTATCATCAGAGCTACTCGTACTCAGAATGTTCTTGgtatgtttgtttgatcatttcttctctct---ttcgattttgaatgtgtttcgagat-ctgatatcgaaaatgttgggttttag-----------------
 | ||||| || |||||||| ||||| ||||| |||||  | || || || ||| | ||||||||||||||| | |||||||| |||||||| || || |||  |       || ||   ||          |  |  | |          || | | |   ||    |   | || | | |                   
CGCGAGCTGGCCGAGGATGGCTACTCCGGTGTGGAGGTCCGCGTGACCCCCATGCGCACTGAGATTATCATCCGCGCTACTCGCACTCAGAACGTGCTGGgtgagcgcaga-gagcaggcctcggagggagatggggctcttggcagccgccgcggtgcctgtacatcactcgctgagctatgtgcagcgctttgtgactg

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|164040443|gb|ES146024.1|ES146024
EST:     TGAGGACTGAGATTATCTATTCAGAGCTACTCGTACTCAGAATGTTCTTG                         GTGAGAAGGGGAGGAGAATTAGGGA
genomic: TGAGGACTGAGATTATC-A-TCAGAGCTACTCGTACTCAGAATGTTCTTGgtatgtttgt ... tgggttttagGTGAGAAGGGGAGGAGAATTAGGGA
EST: gi|125147817|gb|EL181839.1|EL181839
EST:     AATGAGGACTGAGATTATCATCAGAGCTACTCGTACTCAGAATGTTCTTG                         GTGAGAAGGGGAGGAGAA
genomic: AATGAGGACTGAGATTATCATCAGAGCTACTCGTACTCAGAATGTTCTTGgtatgtttgt ... tgggttttagGTGAGAAGGGGAGGAGAA
EST: gi|163992665|gb|ES132302.1|ES132302
EST:     AATGAGGACTGAGATTATCATCAGAGCTACTCGTACTCAGAATGTTCTTG                         GTGAGAAGGGGAGGAGAATT-GGGAATTGACATCTCT
genomic: AATGAGGACTGAGATTATCATCAGAGCTACTCGTACTCAGAATGTTCTTGgtatgtttgt ... tgggttttagGTGAGAAGGGGAGGAGAATTAGGGAATTGACATCTCT
EST: gi|116442865|gb|EG485457.1|EG485457
EST:     AATGAGGACTGAGATTATCATCAGAGCTACTCGTACTCAGAATGTTCTTG                         GTGAGAAGGGGAGGAGAATTAGGGAATTGACATCTCTTGTCCAGAAGAGAT
genomic: AATGAGGACTGAGATTATCATCAGAGCTACTCGTACTCAGAATGTTCTTGgtatgtttgt ... tgggttttagGTGAGAAGGGGAGGAGAATTAGGGAATTGACATCTCTTGTCCAGAAGAGAT
EST: gi|164227744|gb|EL998396.1|EL998396
EST:     GAATGTTCTTG                         GTGAGAAGGGGAGGAGAATTAGGGAATTGACATCTCTTGTCCAGAAGAGAT
genomic: GAATGTTCTTGgtatgtttgt ... tgggttttagGTGAGAAGGGGAGGAGAATTAGGGAATTGACATCTCTTGTCCAGAAGAGAT
EST: gi|152035868|gb|BP863417.2|BP863417
EST:     AATGAGGACTGAGATTATCATCAGAGCTACTCGTACTCAGAATGTTCTTG                         GTGAGAAGGGGAGGAGAATTAGGGAATTGACATCTCTTGTCCAGAAGAGAT
genomic: AATGAGGACTGAGATTATCATCAGAGCTACTCGTACTCAGAATGTTCTTGgtatgtttgt ... tgggttttagGTGAGAAGGGGAGGAGAATTAGGGAATTGACATCTCTTGTCCAGAAGAGAT
EST: gi|124928807|gb|EL006416.1|EL006416
EST:     ATTATCATCAGAGCTACTCGTACTCAGAATGTTCTTG                         GTGAGAAGGGGAGGAGAATTAGGGAATTGACATCTCTTGTCCAGAAGAGAT
genomic: ATTATCATCAGAGCTACTCGTACTCAGAATGTTCTTGgtatgtttgt ... tgggttttagGTGAGAAGGGGAGGAGAATTAGGGAATTGACATCTCTTGTCCAGAAGAGAT
EST: gi|164131112|gb|ES086084.1|ES086084
EST:     GAATGTTCTTG                         GTGAGAAGGGGAGGAGAATTAGGGAATTGACATCTCTTGTCCAGAAGAGAT
genomic: GAATGTTCTTGgtatgtttgt ... tgggttttagGTGAGAAGGGGAGGAGAATTAGGGAATTGACATCTCTTGTCCAGAAGAGAT
EST: gi|164104852|gb|ES018115.1|ES018115
EST:     GAATGTTCTTG                         GTGAGAAGGGGGAGGAGAATTAGGGAATTGACATCTCTTGTCCAGAAGAGA
genomic: GAATGTTCTTGgtatgtttgt ... tgggttttagGTGAGAA-GGGGAGGAGAATTAGGGAATTGACATCTCTTGTCCAGAAGAGA
EST: gi|163974585|gb|EL989888.1|EL989888
EST:     AATGAGGACTGAGATTATCATCAGAGCTACTCGTACTCAGAATGTTCTTG                         GTGAGGGAGGGGAGGAGAA
genomic: AATGAGGACTGAGATTATCATCAGAGCTACTCGTACTCAGAATGTTCTTGgtatgtttgt ... tgggttttagGTGAGA-AGGGGAGGAGAA
EST: gi|164057613|gb|ES172900.1|ES172900
EST:     AATGAGGACTGAGATTATCATCAGAGCTACTCGTACTCAGAATGTTCTTG                         GTGAGGAGGGGAGGAGAA
genomic: AATGAGGACTGAGATTATCATCAGAGCTACTCGTACTCAGAATGTTCTTGgtatgtttgt ... tgggttttagGTGAGAAGGGGAGGAGAA
EST: gi|163983190|gb|ES114370.1|ES114370
EST:     GAGGACTGAGATTATCATCAGAGCTACTCGTACTCAGAATGTTCTTG                         GTGAGAAGGGGAGGAGAATTAGGGAATTGACATCTCTTGTCCAGAAGAG
genomic: GAGGACTGAGATTATCATCAGAGCTACTCGTACTCAGAATGTTCTTGgtatgtttgt ... tgggttttagGTGAGAAGGGGAGGAGAATTAGGGAATTGACATCTCTTGTCCAGAAGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAGAGCTAGCAGAGGATGGTTACTCTGGTGTTGAGGTTAGGGTTACTCCAATGAGGACTGAGATTATCATCAGAGCTACTCGTACTCAGAATGTTCTTGgtatgtttgtttgatcatttcttctctctttcgattttgaatgtgtttcgagatctgatatcgaaaatgttgggttttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT