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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttggaaaatgcacaatgtgtttatcttcaaatgtgatgcttttgagttcattccattagtatttgatgaaccaagtttgtatgtatgtgtgttttgcagACTATTCCGGTTAACCCGAAACCATTCTTGAACAACTTGACCGGCAAGACTGTTATCGTCAAGCTTAAATGGGGAATGGAATACAAAG

Basic information

species Arabidopsis thaliana
transcript AT4G30220.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G30220.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os11g43620.1 (Oryza sativa), 3'ss of exon 1
gttggaaaatgcacaatgtgtttatcttcaaatgtgatgcttttgagttcattccattagtatttgatgaaccaagtttgtatgtatg---tgtgtttt---gcagACTATTCCGGTTAACCCGAAACCATTCTTGAACAACTTGACCGGCAAGACTGTTATCGTCAAGCTTAAATGGGGAATGGAATACAAAG
     ||  | |||| ||  |||   |  ||  |  |||   ||  |||| ||  ||   | |||  ||  |     ||  ||| |||   ||| | ||   ||||||| |||| |||||||| ||||| |||||||||||| |||| || ||| |||| || ||||| ||||| ||||| |||||||||||||
---acaatgtacacattgaatttgcttgtaacag--atggaatttcgttctttttatacatctttcctgttctgctctta-atggatggattgtttcttaatgcagACTGTTCCAGTTAACCCAAAACCTTTCTTGAACAACCTGACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAG

upper sequence: AT4G30220.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os02g08090.1 (Oryza sativa), 3'ss of exon 1
-gttggaaaatgcacaatgtgtttatcttcaaatgtgatgcttttgagttcattccattagtatttgatgaaccaagtttgtatgtatgtgtgttt-tgcagACTATTCCGGTTAACCCGAAACCATTCTTGAACAACTTGACCGGCAAGACTGTTATCGTCAAGCTTAAATGGGGAATGGAATACAAAG
   ||   | |   ||  || || |  | |||  ||| ||| |     | |||    |   || |   | |   |   ||    |  ||| | |   |||||||| | || ||||||||||| || |||||||||||| |||| || ||| |||| || ||||| ||||| ||||| |||||||||||||
tcatgatgattattcatggtattcagttccaa--gtggtgcctccatatacatcttgtctatactcttttatatactattaatggattgtttctaaatgcagACTGTGCCAGTTAACCCGAAGCCTTTCTTGAACAACCTGACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAG

upper sequence: AT4G30220.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA20G21250.1 (Glycine max), 3'ss of exon 1
-gttggaaaatgcacaatgt----gtttatcttcaaatgtgatgcttttgagttcattccattagtatttgatgaaccaagtttgtatgtatgtgtgttttgcagACTATTCCGGTTAACCCGAAACCATTCTTGAACAACTTGACCGGCAAGACTGTTATCGTCAAGCTTAAATGGGGAATGGAATACAAAG
 | ||    ||   |||||      || |   |  || || |  |  |    || |||       |||||  | |   |   | || |   |||   |||||||||||||||| |||||||| || || ||||||||||| ||||| || ||| | || || || || || || ||||||||||| ||||| |
agctgagcgattt-caatgctcacattgagtgtagaaggtcacacaatgtgattaattgtgcct-tattttttaatttattctggtcttcctgt---ttttgcagACTATTCCAGTTAACCCCAAGCCTTTCTTGAACAATTTGACTGGGAAGCCCGTAATTGTGAAACTCAAGTGGGGAATGGAGTACAAGG

upper sequence: AT4G30220.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA17G07060.1 (Glycine max), 3'ss of exon 1
----------------------------------------------------------------------------gttggaaaatgcacaatgtgt-ttatcttcaaatgtgatgcttttgagttcattccatta---gtatttgatgaaccaa---gtttgtatgtatgtgtgttttgcagACTATTCCGGTTAACCCGAAACCATTCTTGAACAACTTGACCGGCAAGACTGTTATCGTCAAGCTTAAATGGGGAATGGAATACAAAG
                                                                              ||    ||   |||||  |  |  |||  | ||||  |    | |    ||   ||||   ||   | ||   | ||    |||   |    |||| ||||||||||||| || ||||| || || || ||||||||||| ||||| || ||| |||| || || || || || ||||||||||| ||||| |
gtgagtaccttcttcttgcactccctttacttaatcatcttccatttatttcattcacttaacctgcatcttcataactgagtgattt-caatgcttgctcgctttgagtgtgtagaaggtcacacgatgtgattaattgtgccttattttctaatttattttcgtcctcgtgttttttgcagACTATACCAGTTAATCCCAAGCCTTTCTTGAACAATTTGACTGGGAAGCCTGTAATTGTGAAACTGAAGTGGGGAATGGAGTACAAGG

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|164122869|gb|ES158654.1|ES158654
EST:     TTTGTTCTCCCAGATCTTCGTTTCGTCTCTTCGTTCTCAAACTCATGGC-                         ACTATTCCGGTTAA
genomic: TTTGTTCTCCCAGATCTTCGTTTCGTCTCTTCGTTCTCAAACTCATGGCGgtaagtttcg ... tgttttgcagACTATTCCGGTTAA
EST: gi|164043348|gb|EL969191.1|EL969191
EST:     CTCAAACTCATGGCG                         ACTATTCCGGTTTAACCCGAAACCATTCTTGAACAACTTGACCGGCAAGAC
genomic: CTCAAACTCATGGCGgtaagtttcg ... tgttttgcagACTATTCCGG-TTAACCCGAAACCATTCTTGAACAACTTGACCGGCAAGAC
EST: gi|164088729|gb|EL992373.1|EL992373
EST:     AAACTCATGGCG                         ACTATTCCGGTTAACCCGAAACCATTCTTGAACAACTTGACCGGCAAGACT
genomic: AAACTCATGGCGgtaagtttcg ... tgttttgcagACTATTCCGGTTAACCCGAAACCATTCTTGAACAACTTGACCGGCAAGACT
EST: gi|19741076|gb|AU226429.1|AU226429
EST:     AGATCTTCGTTTCGTCTCTTCGTTCTCAAACTCATGG-G                         ACTATTCCGGTTAACCCGAAACCATTCTTGAACAACTT-ACCGGCAAGACT
genomic: AGATCTTCGTTTCGTCTCTTCGTTCTCAAACTCATGGCGgtaagtttcg ... tgttttgcagACTATTCCGGTTAACCCGAAACCATTCTTGAACAACTTGACCGGCAAGACT
EST: gi|124722681|gb|EH814083.1|EH814083
EST:     TTTGTTCTCCCAGATCTTCGTTTCGTCTCTTCGTTCTCAAACTCATGGCG                         ACTATTCCGGTTAACCCGAAACCATTCTTGAACAACTTGACCGGCAAGACT
genomic: TTTGTTCTCCCAGATCTTCGTTTCGTCTCTTCGTTCTCAAACTCATGGCGgtaagtttcg ... tgttttgcagACTATTCCGGTTAACCCGAAACCATTCTTGAACAACTTGACCGGCAAGACT
EST: gi|19874858|gb|AU235689.1|AU235689
EST:     AGATCTTCGTTTCGTCTCTTCGTTCTCAAACTCATGGCG                         ACTATTCCGGTTAACCCGAAACCATTCTTGAACAACTTGACCGGCAAGACT
genomic: AGATCTTCGTTTCGTCTCTTCGTTCTCAAACTCATGGCGgtaagtttcg ... tgttttgcagACTATTCCGGTTAACCCGAAACCATTCTTGAACAACTTGACCGGCAAGACT
EST: gi|86080133|gb|DR375890.1|DR375890
EST:     TTTGTTCTCCCAGATCTTCGTTTCGTCTCTTCGTTCTCAAACTCATGGCG                         ACTATTCCGGTTAACCCGAAACCATTCTTGAACAACTTGACCGGCAAGACT
genomic: TTTGTTCTCCCAGATCTTCGTTTCGTCTCTTCGTTCTCAAACTCATGGCGgtaagtttcg ... tgttttgcagACTATTCCGGTTAACCCGAAACCATTCTTGAACAACTTGACCGGCAAGACT
EST: gi|124722203|gb|EH813605.1|EH813605
EST:     TTTGTTCTCCCAGATCTTCGTTTCGTCTCTTCGTTCTCAAACTCATGGCG                         ACTATTCCGGTTAAACCCG
genomic: TTTGTTCTCCCAGATCTTCGTTTCGTCTCTTCGTTCTCAAACTCATGGCGgtaagtttcg ... tgttttgcagACTATTCCGGTTAA-CCCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttcattccattagtatttgatgaaccaagtttgtatgtatgtgtgttttgcagACTATTCCGGTTAACCCGAAACCATTCTTGAACAACTTGACCGGCAAGACTGTTATCGTCAAGCTTAAATGGGGAATGGAATACAAAG
                atttgat  putative branch site (score: 5)
          attagtattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggaaaatgcacaatgtgtttatcttcaaatgtgatgcttttgagttcattccattagtatttgatgaaccaagtttgtatgtatgtgtgttttgcagACTATTCCGGTTAACCCGAAACCATTCTTGAACAACTTGACCGGCAAGACTGTTATCGTCAAGCTTAAATGGGGAATGGAATACAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - gaaaatg
- - - - - - - - - - - - -cttcaaa
- - - - - - - - - - - - - - - - - - - gcttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaccaag