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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagccgtattgattttttttgtacagatattatctcgttaaatattgggaaatttcatatttttctctatctcctaaatcttcattgtgactttttcaattcagGTGCGTCTATTGTGATGTTCCACGGAGATTTACCTTACTCTTCCAAAGATATCATTAAGAAGCTGGAAATGTTGAATGAAGAGCACATAATTGGATGTGG

Basic information

species Arabidopsis thaliana
transcript AT1G31420.2
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G31420.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA09G34940.1 (Glycine max), 3'ss of exon 10
gtgagccgtattgattttt--tttgtacagatat-tatctcgttaaatattgggaaatttcatatttttctctatctcctaaatcttcattgtgactttttcaattcagGTGCGTCTATTGTGATGTTCCACGGAGATTTACCTTACTCTTCCAAAGATATCATTAAGAAGCTGGAAATGTTGAATGAAGAGCACATAATTGGATGTGG
||   |  |||   | | |   ||| | | | |  ||| |   | |   ||     | || | |||       |||    |||  |  | ||       |    |  |||||| || ||||||||||| ||||||||  |||| || ||||| ||||| ||||||||||| || || |  |||||||| || |||||||| ||    ||
gtttactctatctctctgtagcttgcatacagacctatttgagttatcttttttctactttacattgaaaa--atccttaaaaattagaatgcccaaaatgtcttgtagGTGCATCAATTGTGATGTTTCACGGAGACCTACCATATTCTTCAAAAGACATCATTAAGAAACTAGAGACTTTGAATGAGGAACACATAATAGGGATAGG

upper sequence: AT1G31420.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA01G35390.1 (Glycine max), 3'ss of exon 9
gtgagccgtattgattttttttgtacagatattatctcgttaaatattgggaaatttcatatttttctctatctcctaaatcttca----ttgtgactttttcaa-----ttcagGTGCGTCTATTGTGATGTTCCACGGAGATTTACCTTACTCTTCCAAAGATATCATTAAGAAGCTGGAAATGTTGAATGAAGAGCACATAATTGGATGTGG
        |  |  || | | | | ||| | | || | |    || ||| | ||| |  | | |   |     |   ||||| | |    |||  |       ||     |  |||||| || ||||||||||| || ||||| ||||| || ||||| ||||| ||||| ||||| || || |  |||||||| || |||||||| ||    ||
-----gttttctccttatctctctgcagctttcatatagacctat-ttgagtaatcttttttctactttacattgaaaaatccttaaaacttggaatgcccaaaatgtcttgtagGTGCATCAATTGTGATGTTTCATGGAGACTTACCATATTCTTCAAAAGACATCATCAAGAAACTAGAGACTTTGAATGAGGAACACATAATAGGGATAGG

upper sequence: AT1G31420.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv02s0087g00170.t01 (Vitis vinifera), 3'ss of exon 10
gtgagccgtattgattttttttgtacaga-tattatctcgttaaatattggg---aaattt--catatttttctctatct-----cctaaatcttcattgtgactttt-----------tcaattcagGTGCGTCTATTGTGATGTTCCACGGAGATTTACCTTACTCTTCCAAAGATATCATTAAGAAGCTGGAAATGTTGAATGAAGAGCACATAATTGGATGTGG
  | || ||  | ||   | || || |   || | |||   |   |||||||   | ||||   ||||  || ||  | |     |||| |  |  ||  |  || ||           | | ||||||||| || ||||| ||||| || |||||  | || |||||||| ||||||||||| || |||||||| |  |||||||| || ||||||||||| |  ||
--gtgctgttctcataactattctataacctactgtctgaatgtttattgggctaatatttattatatccttgtccttttgggatcctagaattcaatcatatctattgacaagttatataacttcagGTGCATCAATTGTTATGTTTCATGGAGACCTGCCATACTCTTCAAAAGATATCATCAAAAAGCTGGAGACATTGAATGAGGAACACATAATTGGTTCAGG

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|124946171|gb|EL022117.1|EL022117
EST:     AAGCCTTGCAAAGGATGTTGGTGGAG                         GTGCGTCTATTGTGATGTTCCACGGAGATTTACCTTACTCTTCCAAAGATA
genomic: AAGCCTTGCAAAGGATGTTGGTGGAGgtgagccgta ... ttcaattcagGTGCGTCTATTGTGATGTTCCACGGAGATTTACCTTACTCTTCCAAAGATA
EST: gi|124732498|gb|EH823900.1|EH823900
EST:     AAAGCTCGGTAAAGTCGAGATTAAAAGCCTTGCAAAGGATGTTGGTGGAG                         GTGCGTCTATTGTGATGTT
genomic: AAAGCTCGGTAAAGTCGAGATTAAAAGCCTTGCAAAGGATGTTGGTGGAGgtgagccgta ... ttcaattcagGTGCGTCTATTGTGATGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatttcatatttttctctatctcctaaatcttcattgtgactttttcaattcagGTGCGTCTATTGTGATGTTCCACGGAGATTTACCTTACTCTTCCAAAGATATCATTAAGAAGCTGGAAATGTTGAATGAAGAGCACATAATTGGATGTGG
                      tcctaaa  putative branch site (score: 2)
                                         ctttttc  putative PPT
       atatttttctctat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagccgtattgattttttttgtacagatattatctcgttaaatattgggaaatttcatatttttctctatctcctaaatcttcattgtgactttttcaattcagGTGCGTCTATTGTGATGTTCCACGGAGATTTACCTTACTCTTCCAAAGATATCATTAAGAAGCTGGAAATGTTGAATGAAGAGCACATAATTGGATGTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA