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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgactttctgtattttctgatcctaaatatgattcttgtgtccgcgtttgctagaaattcgtttgatgttccatttgttgattctttgaatgatatgtcaagATTATTAACGCTATAATGACGGGAAGAGATGTCCTGGTGATCATGGCAGCAGGTGGTGGGAAGAGTCTTTGCTATCAACTTCCAGCTATGCTTCGTGGTG

Basic information

species Arabidopsis thaliana
transcript AT1G31360.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G31360.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os11g48090.3 (Oryza sativa), 3'ss of exon 3
gtaagtgactttctgtattttctgatcctaaatatg-attcttgtgtccgcgtt--tgctagaaattcgtttgatgttccatttgttgattctttgaatgatatgtcaagATTATTAACGCTATAATGACGGGAAGAGATGTCCTGGTGATCATGGCAGCAGGTGGTGGGAAGAGTCTTTGCTATCAACTTCCAGCTATGCTTCGTGGTG
          | ||||     ||   |||| || |  || |        ||  |  ||||   | ||  ||| || || |||   || |  | |      |  | || |||| || || || || ||||  ||||||||||| ||||| || ||||| || ||||| |||||||| || ||||||||||| || ||| | |||| || ||
--------ggtactgttgagcctagccctagatgtacataccacaacttgctatactgcttacagtttcttt-attttgcatccttttaagcatattgcaacct-tccagATAATCAATGCCATCATGAGTGGAAGAGATGTACTGGTCATAATGGCTGCTGGTGGAGGGAAGAGCCTCTGCTATCAACTACCTGCTGTACTTCATGATG

upper sequence: AT1G31360.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G451856_T02 (Zea mays), 3'ss of exon 3
gtaagtgactttctgtattttctgatcctaaatatgattcttgtgtccgcgtttgctagaaattcgtttgatgttccatttgttgattctttgaatgatatgtcaagATTATTAACGCTATAATGACGGGAAGAGATGTCCTGGTGATCATGGCAGCAGGTGGTGGGAAGAGTCTTTGCTATCAACTTCCAGCTATGCTTCGTGGTG
   |       || |      |  |  |    |  |  |  |       | | |  || |  ||| | | || || ||    || |   |    ||  |   |  |||| ||||| ||  | ||||  ||||||||||| ||||| || |||||||| ||||| ||||||||||| || || || || |||||| | ||||||| ||
---aactttagtcaggggaaccaaacacccccttcgtattgtacagtttcctcttgtacagtttcctctcattttgcacccattaaacat----attctgcttatagATAATTAATGCAGTCATGAGTGGAAGAGATGTTCTGGTCATAATGGCAGCTGGTGGAGGGAAGAGTCTATGTTACCAGCTCCCAGCTGTACTTCGTGATG

upper sequence: AT1G31360.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA09G34860.1 (Glycine max), 3'ss of exon 2
gtaagtgactttctgtattttctgatcctaaat-atgattcttgtgtccgcgtttgctagaaattcgtttgatgttcca---tttgttgattctttg-aatgatatgtcaagATTATTAACGCTATAATGACGGGAAGAGATGTCCTGGTGATCATGGCAGCAGGTGGTGGGAAGAGTCTTTGCTATCAACTTCCAGCTATGCTTCGTGGTG
               || |    |    ||  | |||||| || | |  |  | |    | | |  |  |  ||    |   |||||| |    | | ||||        |||| ||||| || || ||||  ||||||||||| |||||||| ||||| ||||||||||| ||||| || ||||| || ||||| ||| | ||||||| ||
-----------atcataatcaagggctttagtttatgattttttt-ttggtatatatagggattgtgacttttgggtaaaactttgttaacaagtagtaatgtcgatgacagATAATTAATGCCATTATGAGTGGAAGAGATGTTCTGGTGATTATGGCTGCAGGTGGTGGCAAGAGCCTCTGCTACCAGCTTCCTGCTGTTCTTCGTGATG

upper sequence: AT1G31360.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv02s0087g00070.t01 (Vitis vinifera), 3'ss of exon 2
---gtaagtgactttctgtattttctgatcctaaatatgattcttgtgtccgcgtttgctagaaattcgtttgatgttccatttgttgattctttgaatgatatgtcaagATTATTAACGCTATAATGACGGGAAGAGATGTCCTGGTGATCATGGCAGCAGGTGGTGGGAAGAGTCTTTGCTATCAACTTCCAGCTATGCTTCGTGGTG
   || |   | ||| ||| |  | ||| |    | |   ||      |    |||  ||| | | | |||   || |  |       | || || |||  | |  | ||||||| || ||  | ||||  ||||| ||||| |||||||||||||| ||||||||||| ||||| ||||| || || ||||||||||| ||||||| ||
attgttataaaatttatgtttaatttgaac----acactgtttcaaaattt-tgttccctacacaat-gttcattgatttacaaac--aatcattcaat--ttttaccagATTATAAATGCAGTCATGAGTGGAAGGGATGTTCTGGTGATCATGGCTGCAGGTGGTGGTAAGAGCCTTTGTTACCAGCTTCCAGCTATACTTCGTGATG

upper sequence: AT1G31360.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S93_66V6.1 (Physcomitrella patens), 3'ss of exon 3
--gtaagtgactttctgtattttctgatcctaaatatgattcttgtgtccgcgtttgctagaaattcgtttgatgttccatttgttgattctttgaatgatatgtcaagATTATTAACGCTATAATGACGGGAAGAGATGTCCTGGTGATCATGGCAGCAGGTGGTGGGAAGAGTCTTTGCTATCAACTTCCAGCTATGCTTCGTGGTG
  |||| | |  |  |   | |   | | ||     ||||  |||||| |  | || |      |   ||  |  |  |  | ||  ||| ||||   | | || || ||| || || ||  ||||||  ||||| |||||  | || || |||||||||||||||||||||||||||||||| || || ||||||||| | |||  ||
ttgtaaatcaagtgatagctatcacggtact-----tgatatttgtgtacttggtttccgcttttaaattaaacttaaccgtggtatattttttg---gctgtgcca-gATCATAAATGCAGTAATGAGTGGAAGGGATGTAATCGTAATAATGGCAGCAGGTGGTGGGAAGAGTCTTTGCTACCAGCTCCCAGCTATGTTACGTACTG

upper sequence: AT1G31360.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ22718 (Selaginella moellendorffii), 3'ss of exon 1
gtaagtgactttctgtattttctgatcctaaatatgattcttgtgtccgcgtttgctagaaattcgtttgatgttccatttgttgattctttgaatgatatgtcaagATTATTAACGCTATAATGACGGGAAGAGATGTCCTGGTGATCATGGCAGCAGGTGGTGGGAAGAGTCTTTGCTATCAACTTCCAGCTATGCTTCGTGGTG
                                | |  ||||   ||   | |||  |     ||  ||   |||   |||||||      |||  || |   |  ||||| | |||||  | ||||     |   ||||  | ||  | ||||| ||||| || ||||||||||| |||||||| ||||||||| | || ||    |
-------------------------------gtctcgttctccagtttccttttttt---ttttttttgtgtgtgtgatttgtt-----cttgcttgctccttgcagATTGTAAACGCGCTGATGAGTAACAAGAATGTGGTCGTTGTTATGGCGGCAGGAGGAGGGAAGAGTCTGTGCTATCAGCTTCCAGCTCTTCTCCGGCCAG

upper sequence: AT1G31360.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ11578 (Selaginella moellendorffii), 3'ss of exon 1
gtaagtgactttctgtattttctgatcctaaatatgattcttgtgtccgcgtttgctagaaattcgtttgatgttccatttgttgattctttgaatgatatgtcaagATTATTAACGCTATAATGACGGGAAGAGATGTCCTGGTGATCATGGCAGCAGGTGGTGGGAAGAGTCTTTGCTATCAACTTCCAGCTATGCTTCGTGGTG
                  | ||     | |  |    || || |||     ||| ||     || || || |||   |||||||      |||  || |   |  ||||| | |||||  | ||||     |   ||||  | ||  | ||||| ||||| || ||||||||||| |||||||| ||||||||| | || ||    |
-----------------gtctcgttctccagtttccttttttttgttt---ttttctttccttttgtgtg-tgtgtgatttgtt-----cttgcttgctccttgcagATTGTAAACGCGCTGATGAGTAACAAGAATGTGGTCGTTGTTATGGCGGCAGGAGGGGGGAAGAGTCTGTGCTATCAGCTTCCAGCTCTTCTCCGGCCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgctagaaattcgtttgatgttccatttgttgattctttgaatgatatgtcaagATTATTAACGCTATAATGACGGGAAGAGATGTCCTGGTGATCATGGCAGCAGGTGGTGGGAAGAGTCTTTGCTATCAACTTCCAGCTATGCTTCGTGGTG
                            tgttgat  putative branch site (score: 4)
                                         aatgatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgactttctgtattttctgatcctaaatatgattcttgtgtccgcgtttgctagaaattcgtttgatgttccatttgttgattctttgaatgatatgtcaagATTATTAACGCTATAATGACGGGAAGAGATGTCCTGGTGATCATGGCAGCAGGTGGTGGGAAGAGTCTTTGCTATCAACTTCCAGCTATGCTTCGTGGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA