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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaaacattttgaataatcagtttcatgttttgcatccaagataccactttttttttttttttgttaaaatcatattggctttgtttacattttccagGTTTTATGTAGCGGAAGTACTTCTTGCAATGGAATATCTTCATATGCTTGGCATCATATACCGCGATCTAAAGCCAGAGAATGTTCTTGTTAGAGATGAT

Basic information

species Arabidopsis thaliana
transcript AT4G26610.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G26610.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os09g08420.1 (Oryza sativa), 3'ss of exon 2
gtaaaaacattttgaataatcagtttcatgttttgcatccaagataccactttttttttttttttgttaaaatcatattggc-tttgttta------cattttccagGTTTTATGTAGCGGAAGTACTTCTTGCAATGGAATATCTTCATATGCTTGGCATCATATACCGCGATCTAAAGCCAGAGAATGTTCTTGTTAGAGATGAT
         | |    |  |   | |  | |  || |   |   ||| |    ||  |    | |   | | |||| |||   |||| ||         |||| |||||||||||| || || || ||||||||  | ||||| || |||||||||||||||||||| || || || |||||||| ||||||||||| ||||| |||
------gtgtctgccctggttt-tctggtatcatggagtgatagtactaaaccttgctcaagtctaagagagtcatgttgatgtttggttgattaattcttttgcagGTTTTATGTGGCTGAGGTGCTTCTTGCTCTAGAATACCTGCATATGCTTGGCATCATATATCGGGACCTTAAGCCAGAAAATGTTCTTGTGAGAGAAGAT

upper sequence: AT4G26610.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os08g38320.2 (Oryza sativa), 3'ss of exon 2
-gtaaaaacattttgaataatcagtt--tcatgttttgcatccaagataccactttttttttttttttgttaaaatcatattggctttgtttacattttccagGTTTTATGTAGCGGAAGTACTTCTTGCAATGGAATATCTTCATATGCTTGGCATCATATACCGCGATCTAAAGCCAGAGAATGTTCTTGTTAGAGATGAT
  | ||    | ||   |||    ||  |  | ||| || ||    |   || |   |   | || |  || |||   | ||||   | | |   | || |||||| ||||| || || || ||||||||| | ||||| || ||||||||||| || |||||||| ||||| || ||||| ||||| |||||  | || |||
gatcaattgttgtttgctaactcattaattctttttggcgtcttgaaaggca-tggatgactcttctcattgaaac--ttttggtgatctcttggtatttcagGTTCTATGTGGCAGAGGTTCTTCTTGCATTAGAATACCTGCATATGCTTGGGATTATATACCGTGATCTGAAACCAGAAAATGTCCTTGTCCGGGAGGAT

upper sequence: AT4G26610.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os09g30150.3 (Oryza sativa), 3'ss of exon 2
gtaaaaacattttgaataatcagtttcatgttttgcatccaagataccactttttttt----tttttttgttaaaatcatattggctttgtttacattt--tccagGTTTTATGTAGCGGAAGTACTTCTTGCAATGGAATATCTTCATATGCTTGGCATCATATACCGCGATCTAAAGCCAGAGAATGTTCTTGTTAGAGATGAT
         |||   || |    || |    |     | ||| |||  |   ||| |       |||   ||||| |  || |   | | || |  |||  | |||||| |||||||| || || || || ||  |||| || || ||||||||||| ||||||||||| ||||| |||||||| ||||| || ||| | || || 
------ctgtttgttatcagtctttgccaaatcaatcttcaatataaaaaagtttatgcaagcatttagcttaaactggtactcaatctcttgatgtttctttcagGTTCTATGTAGCAGAGGTTCTCCTAGCGTTGGAGTACCTGCATATGCTTGGTATCATATACCGTGATCTGAAGCCAGAAAATGTCCTAGTTCGGGAGGAC

upper sequence: AT4G26610.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: AC217842.3_FGT001 (Zea mays), 3'ss of exon 1
gtaaaaacattttgaataatcagtt-tcatgttttgcatccaagataccacttt-------ttttttttttttgttaaaatcatattggctttgtttacattttccagGTTTTATGTAGCGGAAGTACTTCTTGCAATGGAATATCTTCATATGCTTGGCATCATATACCGCGATCTAAAGCCAGAGAATGTTCTTGTTAGAGATGAT
      | |||| | || ||  | |  | || ||  |||   |  | | |||          ||  |    |   | || | || ||| | |     | | | | ||||||||||||||| || || ||||||||  ||||||| || || |||||||| ||||||||||| ||  |||||||||||||||||||||| || || |||
------atatttagcatgataggctgccctgattgtcatgtcatttgcaactgcaagaagccttaatcaaatctatgaacttatgttgacatcaa--aaaatatgcagGTTTTATGTAGCAGAGGTGCTTCTTGCTCTGGAATACCTGCACATGCTTGGTATCATATACCGTGACTTAAAGCCAGAGAATGTTCTTGTGAGGGAAGAT

upper sequence: AT4G26610.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G026065_T01 (Zea mays), 3'ss of exon 2
gtaaaaacattttgaataatcagtttcatg---ttttgcatccaagataccactttttttttttttttgttaa-aatcatattggctttgtttacattttccagGTTTTATGTAGCGGAAGTACTTCTTGCAATGGAATATCTTCATATGCTTGGCATCATATACCGCGATCTAAAGCCAGAGAATGTTCTTGTTAGAGATGAT
 |    || | || |  ||  || ||  ||   || |   ||     ||  ||   |||   || ||||  |   || || |      |   |  || || |||||| ||||| || || ||||| |||||| ||||||| || ||||||||||| || |||||||| ||||| || ||||| ||||| || ||| | || |||
tttctgacctatttataaactagatttgtgctattatctgtcttcattaaaacgactttaaattatttggcattgattatctaa----taccttgatgtttcagGTTCTATGTGGCAGAGGTACTCCTTGCATTGGAATACCTGCATATGCTTGGGATTATATACCGTGATCTTAAACCAGAAAATGTCCTCGTTCGGGAAGAT

upper sequence: AT4G26610.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G464985_T01 (Zea mays), 3'ss of exon 2
--------gtaaaaacattttgaataatcagtttcatgttttgcatccaagataccactttttttttttttttgttaaaatcatattggctttgtttacattttccagGTTTTATGTAGCGGAAGTACTTCTTGCAATGGAATATCTTCATATGCTTGGCATCATATACCGCGATCTAAAGCCAGAGAATGTTCTTGTTAGAGATGAT
         |      ||||| |   ||  ||   || || ||  | ||  | |    |||    || |||          |  | ||| | | || |  |||  |||||| || ||||| || || || |||||| ||||||| || ||||||||||| || |||||||| ||||| || ||||| ||||| || ||| | || |||
tggatactcttgtgctatttttatagatttgtgctattttctgtcttcattaaaatgatttcaacttattt------ggcgctgactgggtatcttgatgttt--cagGTTCTACGTAGCTGAGGTGCTCCTTGCATTGGAATACCTGCATATGCTTGGGATTATATACCGTGATCTCAAACCAGAAAATGTCCTCGTTCGGGAAGAT

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|124737737|gb|EH829139.1|EH829139
EST:     ACCCTTCGACAAAGACAGCCCGGGAAGCGATTTTCAGAACAAGCAGCAAA                         GTTTTATGTAGCGGAAGT
genomic: ACCCTTCGACAAAGACAGCCCGGGAAGCGATTTTCAGAACAAGCAGCAAAgtaaaaacat ... cattttccagGTTTTATGTAGCGGAAGT
EST: gi|125116385|gb|EL165947.1|EL165947
EST:     AGAACAAGCAGCAAA                         GTTTTATGTAGCGGAAGTACTTCTTGCAATGGAATATCTTCATATGCTTGG
genomic: AGAACAAGCAGCAAAgtaaaaacat ... cattttccagGTTTTATGTAGCGGAAGTACTTCTTGCAATGGAATATCTTCATATGCTTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accactttttttttttttttgttaaaatcatattggctttgtttacattttccagGTTTTATGTAGCGGAAGTACTTCTTGCAATGGAATATCTTCATATGCTTGGCATCATATACCGCGATCTAAAGCCAGAGAATGTTCTTGTTAGAGATGAT
                                             cattttcc  CT-rich tract
     tttttttttttttttg  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaaacattttgaataatcagtttcatgttttgcatccaagataccactttttttttttttttgttaaaatcatattggctttgtttacattttccagGTTTTATGTAGCGGAAGTACTTCTTGCAATGGAATATCTTCATATGCTTGGCATCATATACCGCGATCTAAAGCCAGAGAATGTTCTTGTTAGAGATGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG