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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAGAGCTTGCTGAGGATGGTTACTCTGGTGTTGAGGTTCGCGTCACTCCTATGCGTACTGAGATCATCATTAGAGCCACTCGTACTCAAAACGTTCTCGgtatgttggtgcattttcgttaaccttgctctgattcgacctttttttgtttctatgatatcaatttgatgattctctgtttggtttag

Basic information

species Arabidopsis thaliana
transcript AT5G35530.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G35530.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G093902_T02 (Zea mays), 5'ss of exon 2
AGAGAGCTTGCTGAGGATGGTTACTCTGGTGTTGAGGTTCGCGTCACTCCTATGCGTACTGAGATCATCATTAGAGCCACTCGTACTCAAAACGTTCTCGgtatgttggtgcattttcgttaaccttgctctgattcgacctttttttgtttctatgatatcaat-ttgatgattctctgtttggtttag
 | ||||| || |||||||| ||||| || || ||||| |||||||| || ||||| || |||||||||||  | ||||| || ||||| ||||||||||||||||    ||  ||     | ||  |  | |||   | || |   |  |||  | |    | | ||  |   ||||  | | | ||||
CGCGAGCTCGCGGAGGATGGCTACTCCGGCGTCGAGGTCCGCGTCACCCCCATGCGCACCGAGATCATCATCCGTGCCACCCGCACTCAGAACGTTCTCGgtatgt----gcgcttctacaagccccgtcccgatcacagctgtgaatacttcggttactgaactgtttttttctctcgatctcgcttag

upper sequence: AT5G35530.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv11s0016g01380.t01 (Vitis vinifera), 5'ss of exon 2
AGAGAGCTTGCTGAGGATGGTTACTCTGGTGTTGAGGTTCGCGTCACTCCTATGCGTACTGAGATCATCATTAGAGCCACTCGTACTCAAAACGTTCTCGgtatgttggtgcattttcgttaaccttg--ctctgattcgacctttttttgtttctatgatatcaatttgatgattctctgtttggtttag
|||||||| || |||||||| ||||||||||| |||||| | || || || ||||| ||||| |||||||| ||||||||||||||||| |||||||| |||   |   ||   |||  |||  ||||   ||   ||  |  ||| || |||| | |||      |||  || || |  | ||   ||||
AGAGAGCTGGCCGAGGATGGCTACTCTGGTGTCGAGGTTAGGGTTACGCCAATGCGCACTGAAATCATCATCAGAGCCACTCGTACTCAGAACGTTCTTGgtgattcaatg-gctttgattattcttgagttcgcgtttcagatttgttggttt-tctgactctccttttttgctttttggctt---ttag

upper sequence: AT5G35530.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: PP1S127_74V6.1 (Physcomitrella patens), 5'ss of exon 2
AGAGAGCTTGCTGAGGATGGTTACTCTGGTGTTGAGGTTCGCGTCACTCCTATGCGTACTGAGATCATCATTAGAGCCACTCGTACTCAAAACGTTCTCGgtatgttggtgcattttcgttaaccttgctctgattcgacctttttttgtttctatgatatcaatttgatgattctctgtttggtttag----------------------------------------------------
 |||||||||||||||| || || || || || ||||| |||||||| |||||||| ||||||||||||||  | || || |||||||| || ||  | |||  ||   |     | |  | || ||   |    | || ||  |   || | |  |||   |||| |    || ||| |||||                                                         
CGAGAGCTTGCTGAGGACGGCTATTCCGGAGTGGAGGTGCGCGTCACGCCTATGCGAACTGAGATCATCATCCGCGCAACCCGTACTCAGAATGTATTGGgtgagtctct-tggctgcactgacattatgcgctatggatctggt--agtctttgagat---aattagggttttttctctttggccggaggtgaatttgcgggggtagtcggattgaagtagggtgactgctccctggtag

upper sequence: AT5G35530.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: PP1S136_175V6.1 (Physcomitrella patens), 5'ss of exon 2
AGAGAGCTTGCTGAGGATGGTTACTCTGGTGTTGAGGTTCGCGTCACTCCTATGCGTACTGAGATCATCATTAGAGCCACTCGTACTCAAAACGTTCTCGgtatgt-tggtgcattttcgttaaccttgctctgattcgacctttttttgtttctatgatatcaat-ttgatgattctctgtttggtttag---------------------------------------------
 | ||||| ||||| |||||||||||||| || ||||| || ||||| || |||||||| |||||||||||  | || || ||||| || |||||| | |||  || | | || | |  |      |||| |   || |    |  | |||||    |  || ||  || | ||  | |   |||||   |                                             
CGCGAGCTCGCTGAAGATGGTTACTCTGGCGTGGAGGTGCGTGTCACCCCCATGCGTACCGAGATCATCATCCGCGCTACCCGTACCCAGAACGTTTTGGgtgggtctcgagcctctctgggttttttgcac-atttggttactgctgtgtttaagagtcattaaaattaacgaagcgcgagttggtgacgtatagggtttggaggattgaggtagggtgagtgtgttgttggcag

upper sequence: AT5G35530.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: PP1S454_3V6.1 (Physcomitrella patens), 5'ss of exon 2
AGAGAGCTTGCTGAGGATGGTTACTCTGGTGTTGAGGTTCGCGTCACTCCTATGCGTACTGAGATCATCATTAGAGCCACTCGTACTCAAAACGTTCTCGgtatgttggtgcattttcg----ttaaccttgctctgattcgacctttttttgtttctatgatatcaatttgatgattctctgtttggtttag----------------------------------------------------------------------
 | ||||||||||| ||||| |||||||| || || || ||||||||||| |||||||| |||||||||||  | |||||||| || || |||||  | |||| |||| | | || | |    |||   | |    ||||     ||||| ||    |    | | | |  || |    | |||||  |||                                                                        
CGGGAGCTTGCTGAAGATGGGTACTCTGGCGTGGAAGTGCGCGTCACTCCCATGCGTACCGAGATCATCATCCGTGCCACTCGCACCCAGAACGTGTTGGgtacgttgat-cgttctggcggcttagagtgggagagatttagggtttttgtgcgggtggagtttgagtaggaagcgaatgtgtttttttttttttttttttttttttttaaattattctttaacttggtcttgaggattgactgttcgatcttgtgatgcag

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|152037822|gb|BP799088.2|BP799088
EST:     TATGCGTACTGAGATCATCATTAGAGCCACTCGTACTCAAAACGTTCTCG                         GTGAGAAGGGAAGGAGGATTGGGGAATTGACATCTCTTGTACAAAAGAGAT
genomic: TATGCGTACTGAGATCATCATTAGAGCCACTCGTACTCAAAACGTTCTCGgtatgttggt ... tttggtttagGTGAGAAGGGAAGGAGGATTAGGGAATTGACATCTCTTGTACAAAAGAGAT
EST: gi|164230556|gb|ES068879.1|ES068879
EST:     AGATCATCATTAGAGCCACTCGTACTCAAAACGTTCTCG                         GTGAGAAGGGAAGGAGGATTAGGGAATTGACATCTCTTGTACAAAAGA
genomic: AGATCATCATTAGAGCCACTCGTACTCAAAACGTTCTCGgtatgttggt ... tttggtttagGTGAGAAGGGAAGGAGGATTAGGGAATTGACATCTCTTGTACAAAAGA
EST: gi|124833427|gb|EH917866.1|EH917866
EST:     TATGCGTACTGAGATCATCATTAGAGCCACTCGTACTCAAAACGTTCTCG                         GTGAGAAGGGAAGGAG
genomic: TATGCGTACTGAGATCATCATTAGAGCCACTCGTACTCAAAACGTTCTCGgtatgttggt ... tttggtttagGTGAGAAGGGAAGGAG
EST: gi|125075171|gb|EL138839.1|EL138839
EST:     CTCAAAACGTTCTCG                         GTGAGAAGGGAAGGAGGATTAGGGAATTGACATCTCTTGTACAAAAGAGAT
genomic: CTCAAAACGTTCTCGgtatgttggt ... tttggtttagGTGAGAAGGGAAGGAGGATTAGGGAATTGACATCTCTTGTACAAAAGAGAT
EST: gi|47831884|gb|CK121568.1|CK121568
EST:     TATGCGTACTGAGATCATCATTAGAGCCACTCGTACTCAAAACGTTCTCG                         GTGAGAAGGGAAGGAGGATTAGGGAATTGACATCTCTTGTACAAAAGAGAT
genomic: TATGCGTACTGAGATCATCATTAGAGCCACTCGTACTCAAAACGTTCTCGgtatgttggt ... tttggtttagGTGAGAAGGGAAGGAGGATTAGGGAATTGACATCTCTTGTACAAAAGAGAT
EST: gi|47831852|gb|CK121536.1|CK121536
EST:     TATGCGTACTGAGATCATCATTAGAGCCACTCGTACTCAAAACGTTCTCG                         GTGAGAAGGGAAGGAGGATTAGGGAATTGACATCTCTTGTACAAAAGAGAT
genomic: TATGCGTACTGAGATCATCATTAGAGCCACTCGTACTCAAAACGTTCTCGgtatgttggt ... tttggtttagGTGAGAAGGGAAGGAGGATTAGGGAATTGACATCTCTTGTACAAAAGAGAT
EST: gi|47831894|gb|CK121578.1|CK121578
EST:     TATGCGTACTGAGATCATCATTAGAGCCACTCGTACTCAAAACGTTCTCG                         GTGAGAAGGGAAGGAGGATTAGGGAATTGACATCTCTTGTACAAAAGAGAT
genomic: TATGCGTACTGAGATCATCATTAGAGCCACTCGTACTCAAAACGTTCTCGgtatgttggt ... tttggtttagGTGAGAAGGGAAGGAGGATTAGGGAATTGACATCTCTTGTACAAAAGAGAT
EST: gi|164138702|gb|ES082990.1|ES082990
EST:     TATGCGTACTGAGATCATCATTAGAGCCACTCGTACTCAAAACGTTCTCG                         GTGAGAAGGGAAGGAGGATTAGGGAATTGACATCTC
genomic: TATGCGTACTGAGATCATCATTAGAGCCACTCGTACTCAAAACGTTCTCGgtatgttggt ... tttggtttagGTGAGAAGGGAAGGAGGATTAGGGAATTGACATCTC
EST: gi|164052011|gb|ES205553.1|ES205553
EST:     AGCCACTCGTACTCAAAACGTTCTCG                         GTGAGAAGGGAAGGAGGATTAGGGAATTGACATCTCTTGTACAAAAGAGA
genomic: AGCCACTCGTACTCAAAACGTTCTCGgtatgttggt ... tttggtttagGTGAGAAGGGAAGGAGGATTAGGGAATTGACATCTCTTGTACAAAAGAGA
EST: gi|124994958|gb|EL067227.1|EL067227
EST:     ATGCGTACTGAGATCATCATTAGAGCCACTCGTACTCAAAACGTTCTCG                         GTGAGAAGGGAAGGAGGATTAGGGAATTGACATCTCTTGTACAAAAGAGAT
genomic: ATGCGTACTGAGATCATCATTAGAGCCACTCGTACTCAAAACGTTCTCGgtatgttggt ... tttggtttagGTGAGAAGGGAAGGAGGATTAGGGAATTGACATCTCTTGTACAAAAGAGAT
EST: gi|124903417|gb|EH977497.1|EH977497
EST:     CGTACTGAGATCATCATTAGAGCCACTCGTACTCAAAACGTTCTCG                         GTGAGAAGGGAAGGAGGATTAGGGAATTGACATCTCTTGTACAAAAGAGAT
genomic: CGTACTGAGATCATCATTAGAGCCACTCGTACTCAAAACGTTCTCGgtatgttggt ... tttggtttagGTGAGAAGGGAAGGAGGATTAGGGAATTGACATCTCTTGTACAAAAGAGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAGAGCTTGCTGAGGATGGTTACTCTGGTGTTGAGGTTCGCGTCACTCCTATGCGTACTGAGATCATCATTAGAGCCACTCGTACTCAAAACGTTCTCGgtatgttggtgcattttcgttaaccttgctctgattcgacctttttttgtttctatgatatcaatttgatgattctctgtttggtttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA