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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttaacacaaaagagactaaatttgattagtcaatgtttattggtgttagcattagtacgtttggtatcggctcagatttgttgttaatttggtatcagGTTTTGAGCTTTGAAAAATGGTGAGAATCAGTGTGCTTAACGATGCTCTTAAGAGTATGTACAATGCTGAGAAGAGAGGGAAGAGGCAAGTCATGATCAG

Basic information

species Arabidopsis thaliana
transcript AT5G59850.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G59850.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G083497_T02 (Zea mays), 3'ss of exon 1
-ttttaacacaaaagagactaaatttgattagtcaatgtttattggtgttagcattagtac-gtttggtatcggctcagatttgttgttaatttggtatcagGTTTTGAGCTTTGAAAAATGGTGAGAATCAGTGTGCTTAACGATGCTCTTAAGAGTATGTACAATGCTGAGAAGAGAGGGAAGAGGCAAGTCATGATCAG-----------
   ||    |     |   || || | | | |  | | |  | || |  |  |   || || |  ||  |||    ||  |   |  ||   ||      ||||  | |           |||||||  |||||||||| |||||||| || |||   ||||||||||| |||||||| || |||||||| |||||||||||           
acctttggtcgtgctacg-tagatgtaaatggctatt-tcgaatgctactcactccagcacagcatgtgatccttacaattgcatctttttgttcacgcaagGTCATCA-----------TGGTGAGGGTCAGTGTGCTCAACGATGCGCTCAAGTCCATGTACAATGCAGAGAAGAGGGGCAAGAGGCAGGTCATGATCAGGCCGTCGTCCA

upper sequence: AT5G59850.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G328578_T01 (Zea mays), 3'ss of exon 1
----ttttaacacaaaagagactaaatttgattagtcaatgtttattggtgttagcattagtacgtttggtatcggctcagatttgttgttaatttggtatcagGTTTTGAGCTTTGAAAAATGGTGAGAATCAGTGTGCTTAACGATGCTCTTAAGAGTATGTACAATGCTGAGAAGAGAGGGAAGAGGCAAGTCATGATCAG----
      || |        | | |||||   | | |    |   |  || | ||    |  ||  ||  || ||  |  |    |   |||   | |    ||||||     |      |  ||||||||  |||||||||| || |||||||| |||   |||||||||||||| |||| ||||||  | || |||||||||||    
tgtacctttagttgtgttaca-taaatgcaaatggctgtttcct-ctgatattcttgtctgt--gtccggcatgagacccttatgactgtatctctttgttcagGTAAAAGGAC----AGCATGGTGAGGGTCAGTGTGCTCAATGATGCTCTCAAGTCCATGTACAATGCTGAAAAGATAGGGAAACGTCAGGTCATGATCAGGCCG
















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|152037907|gb|BP802584.2|BP802584
EST:     CTTTTGCTCCAGAGTTTTTGTGCGGCTGCCATTTTCGATTTCCAAAG                         GTTTTGAGCTTTGAAAAATGGTGAGAATCAGTGTGCTTAACGATGCTCTTA
genomic: CTTTTGCTCCAGAGTTTTTGTGCGGCTGCCATTTTCGATTTCCAAAGgttagagaga ... ttggtatcagGTTTTGAGCTTTGAAAAATGGTGAGAATCAGTGTGCTTAACGATGCTCTTA
EST: gi|164012934|gb|ES136205.1|ES136205
EST:     GCTCCAGAGTTTTTGTGCGGCTGCCATTTTCGATTTCCAAAG                         GTTTTGAGCTTTGAAAA-TGGTGAGAATCAGTGTG
genomic: GCTCCAGAGTTTTTGTGCGGCTGCCATTTTCGATTTCCAAAGgttagagaga ... ttggtatcagGTTTTGAGCTTTGAAAAATGGTGAGAATCAGTGTG
EST: gi|86052270|gb|DR348027.1|DR348027
EST:     GCGGCTGCCATTTTCGATTTCCAAAG                         GTTTTGAGCTTTGAAAAATGGTGAGAATCAGTGTGCTTAACGATGCTCTTA
genomic: GCGGCTGCCATTTTCGATTTCCAAAGgttagagaga ... ttggtatcagGTTTTGAGCTTTGAAAAATGGTGAGAATCAGTGTGCTTAACGATGCTCTTA
EST: gi|124749624|gb|EH839754.1|EH839754
EST:     GCTCCAGAGTTTTTGTGCGGCTGCCATTTTCGATTTCCAAAG                         GTTTTGAGCTTTGAAAAATGGTGAGAATCAGTGTG
genomic: GCTCCAGAGTTTTTGTGCGGCTGCCATTTTCGATTTCCAAAGgttagagaga ... ttggtatcagGTTTTGAGCTTTGAAAAATGGTGAGAATCAGTGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttagcattagtacgtttggtatcggctcagatttgttgttaatttggtatcagGTTTTGAGCTTTGAAAAATGGTGAGAATCAGTGTGCTTAACGATGCTCTTAAGAGTATGTACAATGCTGAGAAGAGAGGGAAGAGGCAAGTCATGATCAG
                                      tgttaat  putative branch site (score: 3)
                                atttgttgttaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttaacacaaaagagactaaatttgattagtcaatgtttattggtgttagcattagtacgtttggtatcggctcagatttgttgttaatttggtatcagGTTTTGAGCTTTGAAAAATGGTGAGAATCAGTGTGCTTAACGATGCTCTTAAGAGTATGTACAATGCTGAGAAGAGAGGGAAGAGGCAAGTCATGATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- -taacaca
- - - - - - - -gactaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cgtttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gatttgt