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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttcaaataatctttgcgttgacttgtgttgatagacatgtttgtggaacttaatgttatcatctattttattcttgttgattggtgattggaaaacagGACTAGATGGAGAGGCAGGAGGTAAGTCAAAACAAAGCAGAAGTGAGAAGAAGAGTCGCAAAGCCATGCTCAAGCTTGGCATGAAACCCATCACTGGTGT

Basic information

species Arabidopsis thaliana
transcript AT3G12390.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G12390.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G465333_T01 (Zea mays), 3'ss of exon 2
ttttcaaataatctttgcgttgact-tgtgttgatagacatgtt-tgtggaacttaatgttatcatctattttattcttgttgattggtgattggaaaacagGACTAGATGGAGAGGCAGGAGGTAAGTCAAAACAAAGCAGAAGTGAGAAGAAGAGTCGCAAAGCCATGCTCAAGCTTGGCATGAAACCCATCACTGGTGT
 |  |    |  |||||  ||  || | ||||  ||    || | |||| |||  | ||    | | ||| | |    | ||| |      ||      |||||| ||| || || ||  | || |||||||| |||||||| |||||||||||||| |||||||||||||| |||||||||||||| ||||||||||||||
-taacctgcaccctttgaatttgctgtctgtttttatctctggtgtgtgaaaca-attgcagacctgtatctgacaagtattggtgtcattttcatcttcagGACAAGAAGGGGATGCCAGCGGCAAGTCAAAGCAAAGCAGGAGTGAGAAGAAGAGCCGCAAAGCCATGCTGAAGCTTGGCATGAAGCCCATCACTGGTGT

upper sequence: AT3G12390.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G000923_T01 (Zea mays), 3'ss of exon 2
ttttcaaataatctttgcgttgact-tgtgttgatagacatg-tttgtggaacttaatgttatcatctattttattcttgttgattggtgattggaaaacagGACTAGATGGAGAGGCAGGAGGTAAGTCAAAACAAAGCAGAAGTGAGAAGAAGAGTCGCAAAGCCATGCTCAAGCTTGGCATGAAACCCATCACTGGTGT------
   ||   |   |||||  ||  || | ||||  ||    || | |||| |||  |||   | || ||      |  ||||    |  | ||       |  ||| ||| || || ||  | || |||||||| |||||||| |||||||||||||| ||||| |||||||| |||||||||||||| ||||||||||||||      
---tcctgtgcgctttgaatttgctgtctgtttttatctctggtatgtgaaac--aattacaacacctgacaagtatttgtctcattttcatcttt---cgcgacaagAAGGGGATGCCAGTGGCAAGTCAAAGCAAAGCAGGAGTGAGAAGAAGAGCCGCAAGGCCATGCTGAAGCTTGGCATGAAGCCCATCACTGGTGTCAGCCG

upper sequence: AT3G12390.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G000923_T02 (Zea mays), 3'ss of exon 2
ttttcaaataatctttgcgttgact-tgtgttgatagacatg-tttgtggaacttaatgttatcatctattttattcttgttgattggtgattggaaaacagGACTAGATGGAGAGGCAGGAGGTAAGTCAAAACAAAGCAGAAGTGAGAAGAAGAGTCGCAAAGCCATGCTCAAGCTTGGCATGAAACCCATCACTGGTGT---------
        |   |||||  ||  || | ||||  ||    || | |||| |||  |||   | || ||      |  ||||    |  | ||       |  ||| ||| || || ||  | || |||||||| |||||||| |||||||||||||| ||||| |||||||| |||||||||||||| ||||||||||||||         
------tgtgcgctttgaatttgctgtctgtttttatctctggtatgtgaaac--aattacaacacctgacaagtatttgtctcattttcatcttt---cgcgacaagaagGGGATGCCAGTGGCAAGTCAAAGCAAAGCAGGAGTGAGAAGAAGAGCCGCAAGGCCATGCTGAAGCTTGGCATGAAGCCCATCACTGGTGTCAGCCGCGT

upper sequence: AT3G12390.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA03G27570.1 (Glycine max), 3'ss of exon 2
ttttcaaataatctttgcgttgacttgtgttgatagacatgtttgtggaacttaatgttatcatctattttat--tcttgttg--attggtgattggaaaacagGACTAGATGGAGAGGCAGGAGGTAAGTCAAAACAAAGCAGAAGTGAGAAGAAGAGTCGCAAAGCCATGCTCAAGCTTGGCATGAAACCCATCACTGGTGT
| |   ||| |  ||    |||   | |  |    | ||||    || | |   |||     ||| | || |   ||||   |  ||| ||| ||  |   |||||||||| || || |||   |||| ||| || || | ||||||||| |||||||||||||| || ||||| || ||||| ||||||||  | || |||||
tgtctgaatgag-ttaatattgttattttctttctg-catgaac-tgaagccacatggacagatccaattcacaatcttagaggaatttgtg-ttctattgcagGACTAGAAGGTGATGCATCTGGTAGGTCCAAGCAGACCAGAAGTGAAAAGAAGAGTCGCAAGGCAATGCTTAAACTTGGAATGAAACCTGTAACAGGTGT

upper sequence: AT3G12390.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA19G30540.1 (Glycine max), 3'ss of exon 2
--ttttcaaataatctttgcgttgacttgtgttgatagacatgtttgtggaact-taatgttatcatctattttattcttgttgattggtgattggaaaacagGACTAGATGGAGAGGCAGGAGGTAAGTCAAAACAAAGCAGAAGTGAGAAGAAGAGTCGCAAAGCCATGCTCAAGCTTGGCATGAAACCCATCACTGGTGT
   | ||  |     ||    ||||  | | |   |  |||||    || | ||  || | ||    | |||  | |||     ||| ||| ||  |   |||||||||| || || |||   |||| ||| || || | ||||||||| |||||||||||||| || ||||| || ||||| ||||||||  |||| |||||
ttctgtctgactgagttaatattgatattt-tcattgtacatgaac-tgaagctacaaagatagttccaattacaatctcaggaatttgtg-ttctattgcagGACTAGAAGGTGATGCATCTGGTAGGTCGAAGCAGACCAGAAGTGAAAAGAAGAGTCGCAAGGCAATGCTTAAACTTGGAATGAAACCTGTCACAGGTGT

upper sequence: AT3G12390.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA03G27580.1 (Glycine max), 3'ss of exon 2
ttttcaaataatctttgcgttgacttgtgttgatagacatgtttgtggaacttaatgttatc-atctatttta--ttcttgttgattggtgattggaaaacagGACTAGATGGAGAGGCAGGAGGTAAGTCAAAACAAAGCAGAAGTGAGAAGAAGAGTCGCAAAGCCATGCTCAAGCTTGGCATGAAACCCATCACTGGTGT------
      ||||  ||   | ||   |  |||| ||    |  |   | ||| ||||  | ||  ||  | || |   |||   | ||| ||  |      | | | | ||| || || |||   |||| ||| || || | |||||| || |||||||||||||| || |||||||| ||||| ||||||||  |||| |||||      
------aata--ctgcactttatttcatgtt-atttttacatgaattgaagttaaaatgatggatacaattcaatctctgagtaatttgtattctatttaaatgtcaagAAGGTGATGCATCTGGTAGGTCCAAGCAGACCAGAAGCGAAAAGAAGAGTCGCAAGGCAATGCTCAAACTTGGAATGAAACCTGTCACAGGTGTCAGTCG

upper sequence: AT3G12390.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA03G27580.2 (Glycine max), 3'ss of exon 2
ttttcaaataatctttgcgttgacttgtgttgatagacatgtttgtggaacttaatgttatcatctattttattcttgttgattggtgattggaaaacagGACTAGATGGAGAGGCAGGAGGTAAGTCAAAACAAAGCAGAAGTGAGAAGAAGAGTCGCAAAGCCATGCTCAAGCTTGGCATGAAACCCATCACTGGTGT---------
      | |   ||||   |    || | || | |   ||    ||  || | |  | ||  ||  | | |   ||   | ||| ||  |      | | | | ||| || || |||   |||| ||| || || | |||||| || |||||||||||||| || |||||||| ||||| ||||||||  |||| |||||         
------actgcactttatttcatgttatttttacatgaattgaagttaaaatgatggatacaattcaatct---ctgagtaatttgtattctatttaaatgtcaagaagGTGATGCATCTGGTAGGTCCAAGCAGACCAGAAGCGAAAAGAAGAGTCGCAAGGCAATGCTCAAACTTGGAATGAAACCTGTCACAGGTGTCAGTCGTGT

upper sequence: AT3G12390.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA19G30550.1 (Glycine max), 3'ss of exon 2
ttttcaaataatctttgcgttgacttgtgttgatagacatgtttgtggaact-taatgttatcatctattt-tattcttgttg--attggtgattggaaaacagGACTAGATGGAGAGGCAGGAGGTAAGTCAAAACAAAGCAGAAGTGAGAAGAAGAGTCGCAAAGCCATGCTCAAGCTTGGCATGAAACCCATCACTGGTGT
 | ||  |     ||    ||||  | |  |  |  |||||    || | ||  || | ||    | ||||  | |||    |  ||| ||| ||  |   |||||||||| || || |||   |||| ||| || || | ||||||||| |||||||||||||| || ||||| || ||||| ||||||||  |||| |||||
-tgtctgactgagttaatattgatattttctt-tgtacatgaac-tgaagctacaaagatagatccaatttacaatctcagaggaatttgtg-ttctattgcagGACTAGAAGGTGATGCATCTGGTAGGTCGAAGCAGACCAGAAGTGAAAAGAAGAGTCGCAAGGCAATGCTTAAACTTGGAATGAAACCTGTCACAGGTGT

upper sequence: AT3G12390.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EDO97954 (Chlamydomonas reinhardtii), 3'ss of exon 1
-----ttttcaaataatctttgcgttgacttgtgttgatagacatgtttgtgg-aacttaatgttatcatctattttattcttgttgattggtgattggaaaacagGACTAGATGGAGAGGCAGGAGGTAAGTCAAAACAAAGCAGAAGTGAGAAGAAGAGTCGCAAAGCCATGCTCAAGCTTGGCATGAAACCCATCACTGGTGT---
        ||      | |  || | | |  | | ||  ||   |  ||  |    |  |  |  ||  |  |  |    | |||    || ||  || | |  ||||   | ||| |  |   | || |||      || ||| | || ||||||||||| ||||| |||||||  ||||| |||||||| ||| ||||||| ||   
gctcagcgtctggcgctgtcggc-tgggcgagcgatgccagctttagtttcgtcggcccacagggatgctgaacatggcgcatgtgtgatgttggctgcagATGAGGA--GGGTGGCGCTGGCCGCGGCAAG------CAGAGCCGCAGCGAGAAGAAGAGCCGCAAGGCCATGCAGAAGCTGGGCATGAAGCCCGTCACTGGCGTGAC

upper sequence: AT3G12390.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S122_100V6.1 (Physcomitrella patens), 3'ss of exon 2
-----------ttttcaaataatctttgcgttgacttgtgttgatagacatgtttgtggaacttaatgttatcatctattttattcttgttgattggtgattggaaa---acagGACTAGATGGAGAGGCAGGAGGTAAGTCAAAACAAAGCAGAAGTGAGAAGAAGAGTCGCAAAGCCATGCTCAAGCTTGGCATGAAACCCATCACTGGTGT
             ||| ||    | |  | |||    ||   |  |       |     |  | | | | ||  | |||  | | |   |    ||  | ||| | |    ||||   ||| ||   | | | |||||||||||| || ||| |  |||||||||||||  | || |||||||  |||||||||||||||||  || | || ||
gtgaagaagcccattctaactcccatcac-ttgctgcgttcagtgaatttcaatcaacaagataattttcattttatataatctccaactcatgtgaagtttgaacatctgcagGCGAAGACGGTCTGACTGCAGGTAAGTCAAAGCAGAGCCGTGGTGAGAAGAAGAGCAGGAAGGCCATGCAAAAGCTTGGCATGAAACCAGTCCCCGGCGT

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|125310045|gb|EL324130.1|EL324130
EST:     CGAAGACGATGACTCTGATGACGATGATAAGGATGATGACGAGGCTGATG                         GACTAGATGGAGAGGCAGGAGGTAAGTCAA
genomic: CGAAGACGATGACTCTGATGACGATGATAAGGATGATGACGAGGCTGATGgtaaaagctt ... tggaaaacagGACTAGATGGAGAGGCAGGAGGTAAGTCAA
EST: gi|116471411|gb|EG514003.1|EG514003
EST:     ACTCTGATGACGATGATAAGGATGATGACGAGGCTGATG                         GACTAGATGGAGAGGCAGGAGGTAAGTCAAAACAAAGCAGAAGTGAGAAGA
genomic: ACTCTGATGACGATGATAAGGATGATGACGAGGCTGATGgtaaaagctt ... tggaaaacagGACTAGATGGAGAGGCAGGAGGTAAGTCAAAACAAAGCAGAAGTGAGAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggaacttaatgttatcatctattttattcttgttgattggtgattggaaaacagGACTAGATGGAGAGGCAGGAGGTAAGTCAAAACAAAGCAGAAGTGAGAAGAAGAGTCGCAAAGCCATGCTCAAGCTTGGCATGAAACCCATCACTGGTGT
                               tgttgat  putative branch site (score: 4)
      ttaatgttatcatcta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttcaaataatctttgcgttgacttgtgttgatagacatgtttgtggaacttaatgttatcatctattttattcttgttgattggtgattggaaaacagGACTAGATGGAGAGGCAGGAGGTAAGTCAAAACAAAGCAGAAGTGAGAAGAAGAGTCGCAAAGCCATGCTCAAGCTTGGCATGAAACCCATCACTGGTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - caaataa
- - - - - - - - - - - - - - - - - - - -tgtttgt
- - - - - - - - - - - - - - - - - - - - - - - - aacttaa