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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtgttttctctttaatattcagtcaatcttaatttcttttattcacacatcaggctttaatattgatctgttttggggacatttgctttggaacacagATCTTGTTTGTCATATCAAAGCCTGATGTGTTCAAGAGTCCAGCATCAGACACATATGTGATCTTTGGAGAGGCGAAGATCGAGGATTTGAGCTCTCAGA

Basic information

species Arabidopsis thaliana
transcript AT3G12390.1
intron # 3
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 3
lower sequence: LOC_Os01g71230.2 (Oryza sativa), 3'ss of exon 3
gtttgtgttttctctttaatattcagtcaatcttaatttcttttattcacacatcaggctttaatattgatctgttttggggacatttgctttggaacac-agATCTTGTTTGTCATATCAAAGCCTGATGTGTTCAAGAGTCCAGCATCAGACACATATGTGATCTTTGGAGAGGCGAAGATCGAGGATTTGAGCTCTCAGA
      ||   ||  |||||      |    | |  |||||| ||  | ||||  |   ||  |||    |   |||||   |  ||| |  || |  || ||||  |||| ||||| || || || ||||| |||||||| |||   |||||||| || || ||||| || |||||||||||||||||| ||||||| ||| 
------gtgagctgcttaatcactgttatgccattgtttcttgtaggctcacagaattgttatataccattgcattttgcttaacttttccctgcactaccagATTCTGTTCGTCATCTCTAAACCAGATGTCTTCAAGAGCCCAAACTCAGACACCTACGTCATCTTCGGTGAGGCGAAGATCGAGGATCTGAGCTCGCAGC

upper sequence: AT3G12390.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os05g31000.1 (Oryza sativa), 3'ss of exon 3
----gtttgtgttttctctttaatattcagtcaatcttaat--ttcttttattcacacatcaggctttaatattgatctgttttggggacatttgctttggaacacagATCTTGTTTGTCATATCAAAGCCTGATGTGTTCAAGAGTCCAGCATCAGACACATATGTGATCTTTGGAGAGGCGAAGATCGAGGATTTGAGCTCTCAGA
    | ||  |  | |||||    ||  || |||||| |||  |||| ||| |   |   | |   || || ||   || |||      | |||||     |   |||||| | |||||||| || || || ||||| |||||||| ||  |||| ||||| ||||| || ||||| ||||| |||||||||||  ||||||| ||| 
gtgagcttacgactgctctt----atctagccaatctaaatagttctattagttggattcctg---ttgatgtttg-ctattt------cttttgcccc--atttcagATCCTTTTTGTCATCTCCAAACCGGATGTCTTCAAGAGCCCTACATCCGACACCTATGTCATTTTTGGCGAGGCCAAGATCGAGGACCTGAGCTCGCAGC

upper sequence: AT3G12390.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G465333_T01 (Zea mays), 3'ss of exon 3
gtttgtgttttctctttaatattcagtcaatcttaatt--tcttttattcacacatcagg------ctttaatattgatctgttttggggacatttgc---tttggaacacagATCTTGTTTGTCATATCAAAGCCTGATGTGTTCAAGAGTCCAGCATCAGACACATATGTGATCTTTGGAGAGGCGAAGATCGAGGATTTGAGCTCTCAGA
    ||  ||   |    | | |  | | ||||| |||  | | |   | |||    |        ||||| | |||    | |     || |  |||   | |    | |||||  |||||||||| || ||||| |||||||||||||| ||    ||||||||||| || || || || ||||| |||||||||||  | ||||| ||| 
----gtaattcaccacgcaaact-ggcctatctttattgttgtctggctaacatggtatatattatctttattgttgtctggctaacatgataaatgcacatatttttcccagATACTGTTTGTCATCTCGAAGCCAGATGTGTTCAAGAGCCCGAACTCAGACACATACGTCATATTCGGCGAGGCCAAGATCGAGGACCTCAGCTCCCAGC

upper sequence: AT3G12390.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv13s0067g00710.t01 (Vitis vinifera), 3'ss of exon 3
-------------------------gtttgtgttttctctttaatattcag--tcaatct--taatttcttttattcacacatcaggctttaatattga--tctgttttggggacatttgctttggaaca-cagATCTTGTTTGTCATATCAAAGCCTGATGTGTTCAAGAGTCCAGCATCAGACACATATGTGATCTTTGGAGAGGCGAAGATCGAGGATTTGAGCTCTCAGA
                         || | | ||  |   ||  |   ||    | ||||  | | | ||||| | | | | |  | | |   | |  |  |||||| |     |  ||  |       | ||||||||||||||||||||||| || ||||| |||||||| ||| ||||||| |||||||| || ||||| ||||| ||||| || || |||||||| ||| 
gttagtttccctctcttttctttgtgtgtatattcccctcttgctccccatgccccatctgcttaatccttttgtcctc-cttttgtcctccctttgaacttctgttgtaatctcggttattacttgctatcagATCTTGTTTGTCATATCAAAACCAGATGTCTTCAAGAGCCCAACATCAGATACATATGTCATTTTTGGCGAGGCAAAGATTGAAGACTTGAGCTCACAGC

upper sequence: AT3G12390.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv08s0040g00600.t01 (Vitis vinifera), 3'ss of exon 3
------------------------gtttgtgttttctctttaatattcagtcaatcttaatttcttttat-tcacacatcaggctttaatattgatctgttttggggacatttgctttgga-------acacagATCTTGTTTGTCATATCAAAGCCTGATGTGTTCAAGAGTCCAGCATCAGACACATATGTGATCTTTGGAGAGGCGAAGATCGAGGATTTGAGCTCTCAGA
                        | ||   |||| | ||| || ||  | | ||  | |  ||||| || |||    ||   || |  ||   |||| ||    | |  ||| || |||        |  |||||  | |||||||| || ||||| |||||||||||||| ||| | |||||||| ||||| || ||||| ||||| ||||| ||||||||||| || ||  
gtcagtttctctttgcccactgttgattactttttatttttcatgttgggcctattgtcacctctttaatatcaggtttctttctattttac-aatctattgaaagca-gtttactatggtttttattattcagATTCTCTTTGTCATCTCGAAGCCAGATGTGTTCAAGAGCCCAACTTCAGACACTTATGTAATATTTGGCGAGGCAAAGATTGAGGATTTGAGTTCACAAC

upper sequence: AT3G12390.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S10_319V6.1 (Physcomitrella patens), 3'ss of exon 3
gtttgtgttttctctttaatattcagtcaatcttaatttcttttattcacacatcaggctttaatattgatctgttttggggacatttgctttggaac--acagATCTTGTTTGTCATATCAAAGCCTGATGTGTTCAAGAGTCCAGCATCAGACACATATGTGATCTTTGGAGAGGCGAAGATCGAGGATTTGAGCTCTCAGA
   | | |     || || | ||||||    ||||  |   | |  || |  |  ||   |  ||  ||   ||  ||  |  || | | | |  ||    |||||| | || || || ||    ||||||||||||||||| || ||||||||||| ||  | |||||||| || || ||||| ||||| ||||| |||||  
aaatatctccgaactgtatttttcagt-gtgcttatctgtgtctggtctctgaaaagcaatgtattctg--ttggcttacgaccaat-gttgtaaaatttgcagATCCTCTTCGTGATCTCCGCTCCTGATGTGTTCAAGAGCCCTGCATCAGACACGTACATTATCTTTGGCGAAGCCAAGATTGAGGACTTGAGTTCTCAAC

upper sequence: AT3G12390.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S539_1V6.1 (Physcomitrella patens), 3'ss of exon 3
gtttgtgttttctctttaatattcagtcaatcttaatttcttttattcacacatcaggctttaatattgatctgttttggggacatttgctttggaac--acagATCTTGTTTGTCATATCAAAGCCTGATGTGTTCAAGAGTCCAGCATCAGACACATATGTGATCTTTGGAGAGGCGAAGATCGAGGATTTGAGCTCTCAGA
 | |   ||   ||||||      | || |  |    |||||| |    |     | |    ||| |  ||   ||    | |  ||     || |||   |||||| | ||||| || || |||||||||||||||||||| || ||||||||||| || || ||||| || ||||| ||||| ||||||||||| |||||  
-tataccttcaatctttatcgcagattctacata---ttctttcagatccttgagatgtcagaatttcaatagcttgcaagtaacttcatcgtgcaacttgcagATCCTCTTTGTGATCTCGAAGCCTGATGTGTTCAAGAGCCCTGCATCAGACACTTACGTAATCTTCGGCGAGGCAAAGATTGAGGATTTGAGTTCTCAAT

upper sequence: AT3G12390.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S156_120V6.1 (Physcomitrella patens), 3'ss of exon 2
gtttgtgttttctctttaatattcagtcaatcttaatttcttttattcacacatcaggctttaatattgatctgttttggggacatttgctttggaa--cacagATCTTGTTTGTCATATCAAAGCCTGATGTGTTCAAGAGTCCAGCATCAGACACATATGTGATCTTTGGAGAGGCGAAGATCGAGGATTTGAGCTCTCAGA
 ||    |    |||     | |    ||||  || |||   |||| ||  ||  ||  |||   |    |   || ||    | |||| |||||||  | |||||  | ||||| || || ||||| ||||| |||||||| || || || |||||  || | |||||||||||||| ||||||||||||||||| || ||| 
-ttaacttcaattctgcttgaattgtgcaataatagtttgagttatcca-gcaatagatttt--cacctgtggcttatgctttcttttgttttggaattcgcagATTCTTTTTGTGATCTCTAAGCCCGATGTATTCAAGAGCCCTGCCTCTGACACCCATATCATCTTTGGAGAGGCCAAGATCGAGGATTTGAGTTCGCAGC

upper sequence: AT3G12390.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S122_100V6.1 (Physcomitrella patens), 3'ss of exon 3
gtttgtgttttctctttaatattcagtcaatcttaatttcttttattcacacatcaggctttaatattg-atctgttttggggacatttgct-ttggaaca-cagATCTTGTTTGTCATATCAAAGCCTGATGTGTTCAAGAGTCCAGCATCAGACACATATGTGATCTTTGGAGAGGCGAAGATCGAGGATTTGAGCTCTCAGA
    | | ||   |  |  | ||   |    ||| | |    | |||   |  | ||  ||   ||||    || |  ||    |  | |||  |     | ||||| ||||| || || || |||||||| ||||||||||| |||||||| ||  |  |  | |||||||||||||||||||| |||||||||||||| ||  
----gcgattctccaattgttttattttccccttgaatctggtgatttcgaagttag-tttcgttattctgcctctaatgtatgctctggctgctaatgtatcagATTTTGTTCGTAATCTCGAAGCCTGACGTGTTCAAGAGCCCAGCATCTGATGCTCACATCATCTTTGGAGAGGCGAAGATTGAGGATTTGAGCTCACAAC

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|124749604|gb|EH839734.1|EH839734
EST:     ACCCATCACTGGTGTTAGCCGAGTCACCGTCAAAAAGAGCAAGAAT                         ATCTTGTTTGTCATATCAAAGCCTGATGTG
genomic: ACCCATCACTGGTGTTAGCCGAGTCACCGTCAAAAAGAGCAAGAATgtttgtgttt ... tggaacacagATCTTGTTTGTCATATCAAAGCCTGATGTG
EST: gi|124734160|gb|EH825562.1|EH825562
EST:     TCACCGTCAAAAAGAGCAAGAAT                         ATCTTGTTTGTCATATCAAAGCCTGATGTGTTCAAGAGTCCAGCATCAGAC
genomic: TCACCGTCAAAAAGAGCAAGAATgtttgtgttt ... tggaacacagATCTTGTTTGTCATATCAAAGCCTGATGTGTTCAAGAGTCCAGCATCAGAC
EST: gi|116471411|gb|EG514003.1|EG514003
EST:     TGAAACCCATCACTGGTGTTAGCCGAGTCACCGTCAAAAAGAGCAAGAAT                         ATCTTGTTTGTCATATCAAAGCCTGATGTGTTCAAGAGTCCAGCATCAGAC
genomic: TGAAACCCATCACTGGTGTTAGCCGAGTCACCGTCAAAAAGAGCAAGAATgtttgtgttt ... tggaacacagATCTTGTTTGTCATATCAAAGCCTGATGTGTTCAAGAGTCCAGCATCAGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacacatcaggctttaatattgatctgttttggggacatttgctttggaacacagATCTTGTTTGTCATATCAAAGCCTGATGTGTTCAAGAGTCCAGCATCAGACACATATGTGATCTTTGGAGAGGCGAAGATCGAGGATTTGAGCTCTCAGA
                 tattgat  putative branch site (score: 3)
                                      tttgcttt  putative PPT
            tttaatattgatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtgttttctctttaatattcagtcaatcttaatttcttttattcacacatcaggctttaatattgatctgttttggggacatttgctttggaacacagATCTTGTTTGTCATATCAAAGCCTGATGTGTTCAAGAGTCCAGCATCAGACACATATGTGATCTTTGGAGAGGCGAAGATCGAGGATTTGAGCTCTCAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT