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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgcttccacttcttttaccccttagtaatggtaaatcagagtctcattttgaacattaaaataattatcctgatctcgttttgacagAGGAACCCCTCAAATCGAGGTCACATTCGAAGTGGACGCCAACGGTATTCTTAATGTGAAAGCAGAGGACAAGGCGAGTGGTAAATCAGAGAAGATTACT

Basic information

species Arabidopsis thaliana
transcript AT5G28540.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G28540.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G114793_T01 (Zea mays), 3'ss of exon 7
gtttgcttccacttcttttaccccttagtaatggtaaatcagagtctcattttgaacattaaaataattatcctgatctcgttt--tga------cagAGGAACCCCTCAAATCGAGGTCACATTCGAAGTGGACGCCAACGGTATTCTTAATGTGAAAGCAGAGGACAAGGCGAGTGGTAAATCAGAGAAGATTACT
    |    ||  |     |  ||  ||      ||||| |    ||| ||||||  | |  |  ||| |  |   | | || |  |||      ||| || || || || |||||||| || ||||| ||||||||||||||||| || || ||||| || ||||||||||  |  || || || |||||||| || 
----gtgagcagctaccggagtccggag-----ataaattatta-ctctttttgatgaatggacgaatgaatccagtgttgtctgatgaactgtgcagGGGCACACCCCAGATCGAGGTGACCTTCGAGGTGGACGCCAACGGTATCCTAAACGTGAAGGCGGAGGACAAGGGCACGGGCAAGTCGGAGAAGATCACG

upper sequence: AT5G28540.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G415007_T01 (Zea mays), 3'ss of exon 7
gtttgcttccacttcttttaccccttagtaatggtaaatcagagtctcattttgaacattaaaataattatcctgatctcgttttgacagAGGAACCCCTCAAATCGAGGTCACATTCGAAGTGGACGCCAACGGTATTCTTAATGTGAAAGCAGAGGACAAGGCGAGTGGTAAATCAGAGAAGATTACT
||  | | |  || ||  |     |    |||||   ||  || ||   | |||     | ||  ||||   |||            ||| || || || || |||||||| || ||||| ||||||||||||||||| || || ||||| || ||||||||||  |  || || || |||||||| || 
gtgcgttgctgctgctcatctttttgttgaatggccgatt-gaatccagtgttgtctgatgaacgaattgaactgt----------gcagGGGCACACCCCAGATCGAGGTGACCTTCGAGGTGGACGCCAACGGTATCCTGAACGTGAAGGCGGAGGACAAGGGCACGGGCAAGTCGGAGAAGATCACG

upper sequence: AT5G28540.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA08G02940.1 (Glycine max), 3'ss of exon 7
gtttgcttccacttcttttaccccttagtaatggtaaatcagagtctcat-tttgaacattaaaataattatcc-tgatctcgtttt----------gacagAGGAACCCCTCAAATCGAGGTCACATTCGAAGTGGACGCCAACGGTATTCTTAATGTGAAAGCAGAGGACAAGGCGAGTGGTAAATCAGAGAAGATTACT
||||| | ||     |  |    |   ||  |     || |  |   ||| | | ||  |||  | | | ||   || | |  | ||           |||| || ||||||||||| || || || |||||||| || |||||||| ||||| |||||||| ||||| |||||||  | |||||||||||| ||||| || 
gtttgttacctgcgttgatgatgcagtgtcctctctcattattgctccatatattaatgttagtaaattcattggtggtattatatttgggtaattgaacagGGGCACCCCTCAAATTGAAGTGACCTTCGAAGTTGATGCCAACGGCATTCTAAATGTGAAGGCAGAAGACAAGGGAACTGGTAAATCAGAAAAGATCACC

upper sequence: AT5G28540.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA05G36600.1 (Glycine max), 3'ss of exon 7
gtttgcttccacttcttttaccccttagtaatggtaaatcagagtctcattttgaacattaaaataattatc--ctgatctcgt--tttgacagAGGAACCCCTCAAATCGAGGTCACATTCGAAGTGGACGCCAACGGTATTCTTAATGTGAAAGCAGAGGACAAGGCGAGTGGTAAATCAGAGAAGATTACT
||||  | ||   | |  |    |   ||  |     |  |  |    ||||      |  || | |||      | || | ||  ||  |||| || ||||||||||| || || || |||||||| || |||||||| ||||| |||||||| ||||| |||||||  | |||||||||||| ||||| || 
gtttattacctgctttgatgatgcagtgtcctctctcaatattgctcaatttaatgtttgtaattcattggtattttatttggtaattgaacagGGGTACCCCTCAAATTGAAGTGACCTTCGAAGTTGATGCCAACGGCATTCTAAATGTGAAGGCAGAAGACAAGGGCACTGGTAAATCAGAAAAGATCACC

upper sequence: AT5G28540.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA05G36620.1 (Glycine max), 3'ss of exon 7
gtttgcttccacttcttttaccccttagtaatggtaaatcagagtctcattttgaacattaaaataattatc--ctgatctcgt--tttgacagAGGAACCCCTCAAATCGAGGTCACATTCGAAGTGGACGCCAACGGTATTCTTAATGTGAAAGCAGAGGACAAGGCGAGTGGTAAATCAGAGAAGATTACT
||||| | ||   | |  |    |   ||  |     |  |  |    ||||      |  || | |||      | || | ||  ||  |||| || || |||||||| || || || |||||||| || |||||||| ||||| |||||||| ||||| |||||||  | |||||||||||| ||||| || 
gtttgttacctgctttgatgatgcagtgtcctctctcaatattgctcaatttaatgtttgtaattcattggtattttatttggtaattgaacagGGGTACGCCTCAAATTGAAGTGACCTTCGAAGTTGATGCCAACGGCATTCTAAATGTGAAGGCAGAAGACAAGGGCACTGGTAAATCAGAAAAGATCACC

upper sequence: AT5G28540.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA08G02960.1 (Glycine max), 3'ss of exon 7
gtttgcttccacttcttttaccccttagtaatggtaaatcagagtctcattttgaacattaaaataattatcctg--atctcgt--tttgacagAGGAACCCCTCAAATCGAGGTCACATTCGAAGTGGACGCCAACGGTATTCTTAATGTGAAAGCAGAGGACAAGGCGAGTGGTAAATCAGAGAAGATTACT
||||| || |   | |  |    ||         || |   |    ||| ||      |  || | |||    ||  || | ||  ||  |||| || ||||||||||| || || || |||||||| || || || || ||||| |||||||| ||||| |||||||  | |||||||||||| ||||| || 
gtttgtttgctgctttcatgatactagtgtcctctacagatgttgttcaattgatgtttgtaactcattggtatgttatgttgtaattgaacagGGGTACCCCTCAAATTGAAGTGACCTTCGAAGTTGATGCAAATGGCATTCTAAATGTGAAGGCAGAAGACAAGGGCACTGGTAAATCAGAAAAGATAACA

upper sequence: AT5G28540.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv02s0025g02140.t01 (Vitis vinifera), 3'ss of exon 7
gtttgcttccacttcttttaccccttagtaatggtaaatcagagtctcattttgaaca----ttaaaataattatcctgatctcgttttga-cagAGGAACCCCTCAAATCGAGGTCACATTCGAAGTGGACGCCAACGGTATTCTTAATGTGAAAGCAGAGGACAAGGCGAGTGGTAAATCAGAGAAGATTACT
    | || |    | | | | |   |    |  |  |  | | ||  | | |   ||    || |  | || |||    ||   | |||| ||| |||||||| ||||| || ||||| || ||||| ||||| || ||||| || ||||| || || ||||||||||  |  ||||||||||||||||| || 
----gtttgcgaaacctgtccactccaactcttctgtaaaatactcctactgtaggcagaaattgatgtgataatctgattcctatgttgaacagGGGAACCCCACAAATTGAAGTCACGTTTGAAGTTGACGCAAATGGTATCCTAAATGTCAAGGCTGAGGACAAGGGCACGGGTAAATCAGAGAAGATCACC

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|164031759|gb|ES015154.1|ES015154
EST:     TGCAGGCTACTCGGGAAATTCGACCTCAATGGAATCCCACCGGCCCCAAG                         GGGAACCCCTCCAAATCGAGGTCACATT
genomic: TGCAGGCTACTCGGGAAATTCGACCTCAATGGAATCCCACCGGCCCCAAGgtttgcttcc ... gttttgacagAGGAACCCCTC-AAATCGAGGTCACATT
EST: gi|164130321|gb|ES103219.1|ES103219
EST:     TGCAGGCTACTCGGGAAATTCGACCTCACTGGAGTCCCACCGGCCCCAAG                         AGGAACCCCTCAAAT
genomic: TGCAGGCTACTCGGGAAATTCGACCTCAATGGAATCCCACCGGCCCCAAGgtttgcttcc ... gttttgacagAGGAACCCCTCAAAT
EST: gi|164227113|gb|ES126337.1|ES126337
EST:     TGCAGGCTACTCGGGAAATTCGACCTCAATGGAATCCCACCGGCCCCAAG                         AGGAACCCCTCAAATCG
genomic: TGCAGGCTACTCGGGAAATTCGACCTCAATGGAATCCCACCGGCCCCAAGgtttgcttcc ... gttttgacagAGGAACCCCTCAAATCG
EST: gi|164125383|gb|ES103149.1|ES103149
EST:     TGCAGGCTACTCGGGAAATTCGACCTCAATGGAATCCCACCGGCCCCAAG                         AGGAACCCCTCAAATCGAGGTCACATTCGAAGTGG
genomic: TGCAGGCTACTCGGGAAATTCGACCTCAATGGAATCCCACCGGCCCCAAGgtttgcttcc ... gttttgacagAGGAACCCCTCAAATCGAGGTCACATTCGAAGTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatcagagtctcattttgaacattaaaataattatcctgatctcgttttgacagAGGAACCCCTCAAATCGAGGTCACATTCGAAGTGGACGCCAACGGTATTCTTAATGTGAAAGCAGAGGACAAGGCGAGTGGTAAATCAGAGAAGATTACT
                                   tcctgat  putative branch site (score: 3)
                                         tctcgtttt  CT-rich tract
         tctcattttgaacatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgcttccacttcttttaccccttagtaatggtaaatcagagtctcattttgaacattaaaataattatcctgatctcgttttgacagAGGAACCCCTCAAATCGAGGTCACATTCGAAGTGGACGCCAACGGTATTCTTAATGTGAAAGCAGAGGACAAGGCGAGTGGTAAATCAGAGAAGATTACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA