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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatcttttagactttttgaacaaggcttttctgtttatggttttgtttcgtggattcgtaattggtttactataatatttggtagGATTGCGAAAGATCCTCACTTCGAAAGACTACCTTGTATACACAAAGGGACATATGCTGATGACTGTCTCGTTGACAGAGTTACTCAG

Basic information

species Arabidopsis thaliana
transcript AT2G46230.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G46230.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA13G38690.2 (Glycine max), 3'ss of exon 6
----------gtaaatcttttagactttttgaacaaggcttttctgt--ttatggttttgtttcgtggattcgtaattggtttactataatatttggtagGATTGCGAAAGATCCTCACTTCGAAAGACTACCTTGTATACACAAAGGGACATATGCTGATGACTGTCTCGTTGACAGAGTTACTCAG
           |  |||  | |  ||  | ||  || |   || | |  || | | ||   ||  ||| |   |   |   |  || | |||  |   |||||||| || |||||||  || || ||| |||  ||||  || |||||||| |||||||||||||| || ||||| ||||||||||||
ttcttgtatgatttatccctcaatctagtagagaaaaggaattatattattcttgcttcaatttctgggtgtatttatttatcccttttatacataacagGATTGCCAAGGATCCTCGATTTGAGAGAATACTATGTACTCATAAAGGGACCTATGCTGATGACTGCCTTGTTGAGAGAGTTACTCAG

upper sequence: AT2G46230.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA12G31740.1 (Glycine max), 3'ss of exon 6
---------gtaaatcttttagacttttt---gaacaaggcttttctgtttatggttttgtttcgtggattcgtaattggtttactataatatttggtagGATTGCGAAAGATCCTCACTTCGAAAGACTACCTTGTATACACAAAGGGACATATGCTGATGACTGTCTCGTTGACAGAGTTACTCAG
          | |    | |  |  |  |   ||| | |  || | |  || | | ||   ||  ||| |   |   |   |  || | |||  |   |||||||| || |||||||  || || ||| |||  ||||  || |||||||| |||||||||||||| || ||||| ||||||||||||
atttcttgtatgatctatctcaatctagtagagaaaaggaattatattcttcttgcttcaatttttgggtgtatttatttatcccttttatacataacagGATTGCCAAGGATCCTCGATTTGAGAGAATACTATGTACTCATAAAGGGACCTATGCTGATGACTGCCTTGTTGAGAGAGTTACTCAG

upper sequence: AT2G46230.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA03G41500.1 (Glycine max), 3'ss of exon 4
----------gtaaatcttttagactttttgaacaaggcttttctgt--ttatggttttgtttcgtggattcgtaattggtttac--tataatatttggtagGATTGCGAAAGATCCTCACTTCGAAAGACTACCTTGTATACACAAAGGGACATATGCTGATGACTGTCTCGTTGACAGAGTTACTCAG
             ||| | | || ||  | |   ||     || |    || | ||||    |  ||| |  |||||   || ||  |   |||| || ||||||||| || |||||||  || || ||| |||  ||||  || |||||||  ||||||||||||||||| ||||| ||||||||||||
tcttcaagtaagcaatttctcagtctagtagggaaaataaattataatgttctagtttcagctgctgggt--gtaatcatttaacccttctatatgtgatagGATTGCAAAGGATCCTCGATTTGAGAGAATACTCTGTACTCATAAAGGGATGTATGCTGATGACTGTCTTGTTGAGAGAGTTACTCAG

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|86084884|gb|DR380643.1|DR380643
EST:     GTCATGGCTGAGTTAGAGAAGTTAGGTCAGAAGTATCGTGTAGCTCTAAG                         GATTGCGAAAGATCCTCACTTCGAAAGACTACCTTGTATRCMCAWAGGGAC
genomic: GTCATGGCTGAGTTAGAGAAGTTAGGTCAGAAGTATCGTGTAGCTCTAAGgtaaatcttt ... tatttggtagGATTGCGAAAGATCCTCACTTCGAAAGACTACCTTGTATACACAAAGGGAC
EST: gi|86051132|gb|DR346887.1|DR346887
EST:     GTCATGGCTGAGTTAGAGAAGTTAGGTCAGAAGTATCGTGTAGCTCTAAG                         GATTGCGAAAGATCCTCACTTCGAAAGACTACCTTGTATACACAAAGGGAC
genomic: GTCATGGCTGAGTTAGAGAAGTTAGGTCAGAAGTATCGTGTAGCTCTAAGgtaaatcttt ... tatttggtagGATTGCGAAAGATCCTCACTTCGAAAGACTACCTTGTATACACAAAGGGAC
EST: gi|86051135|gb|DR346890.1|DR346890
EST:     GTCATGGCTGAGTTAGAGAAGTTAGGTCAGAAGTATCGTGTAGCTCTAAG                         GATTGCGAAAGAT
genomic: GTCATGGCTGAGTTAGAGAAGTTAGGTCAGAAGTATCGTGTAGCTCTAAGgtaaatcttt ... tatttggtagGATTGCGAAAGAT
EST: gi|164194553|gb|EL979547.1|EL979547
EST:     TCAGAAGTATCGTGTAGCTCTAAG                         GATTGCGAAAGATCCTCACTTCGAAAGACTACCTTGTATACACAAAGGGAC
genomic: TCAGAAGTATCGTGTAGCTCTAAGgtaaatcttt ... tatttggtagGATTGCGAAAGATCCTCACTTCGAAAGACTACCTTGTATACACAAAGGGAC
EST: gi|86051134|gb|DR346889.1|DR346889
EST:     TCATGGCTGAGTTAGAGAAGTTAGGTCAGAAGTATCGTGTAGCTCTAAAG                         GATTGCGAAAGATCCTCACTTCGAAAGA
genomic: TCATGGCTGAGTTAGAGAAGTTAGGTCAGAAGTATCGTGTAGCTCTAA-Ggtaaatcttt ... tatttggtagGATTGCGAAAGATCCTCACTTCGAAAGA
EST: gi|47829180|gb|CK118864.1|CK118864
EST:     GTCATGGCTGAGTTAGAGAAGTTAGGTCAGAAGTATCGTGTAGCTCTAAG                         GATTGCGAAAGATCCTCACTTCGAAAGACTACCTTGTATACACAAAGGGAC
genomic: GTCATGGCTGAGTTAGAGAAGTTAGGTCAGAAGTATCGTGTAGCTCTAAGgtaaatcttt ... tatttggtagGATTGCGAAAGATCCTCACTTCGAAAGACTACCTTGTATACACAAAGGGAC
EST: gi|86080730|gb|DR376487.1|DR376487
EST:     GTCATGGCTGAGTTAGAGAAGTTAGGTCAGAAGTATCGTGTAGCTCTAAG                         GATTGCGAAAGATCCTCACTTCGAAAGACTACCTTGTATACACAAAGGGAC
genomic: GTCATGGCTGAGTTAGAGAAGTTAGGTCAGAAGTATCGTGTAGCTCTAAGgtaaatcttt ... tatttggtagGATTGCGAAAGATCCTCACTTCGAAAGACTACCTTGTATACACAAAGGGAC
EST: gi|163977883|gb|ES138240.1|ES138240
EST:     GTCATGGCTGAGTTAGAGAAGTTAGGTCAGAAGTATCGTGTAGCTCTAAG                         GATTGCGAAAG
genomic: GTCATGGCTGAGTTAGAGAAGTTAGGTCAGAAGTATCGTGTAGCTCTAAGgtaaatcttt ... tatttggtagGATTGCGAAAG
EST: gi|164216203|gb|EL970219.1|EL970219
EST:     TCGTGTAGCTCTAAG                         GATTGCGAAAGATCCTCACTTCG-AAGACTACCTTGTATACACAAAGGGAC
genomic: TCGTGTAGCTCTAAGgtaaatcttt ... tatttggtagGATTGCGAAAGATCCTCACTTCGAAAGACTACCTTGTATACACAAAGGGAC
EST: gi|47828370|gb|CK118054.1|CK118054
EST:     GTCATGGCTGAGTTAGAGAAGTTAGGTCAGAAGTATCGTGTAGCTCTAAG                         GATTGCGAAAGATCCTCACTTCGAAAGACTACCTTGTATACACAAAGGGAC
genomic: GTCATGGCTGAGTTAGAGAAGTTAGGTCAGAAGTATCGTGTAGCTCTAAGgtaaatcttt ... tatttggtagGATTGCGAAAGATCCTCACTTCGAAAGACTACCTTGTATACACAAAGGGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtttatggttttgtttcgtggattcgtaattggtttactataatatttggtagGATTGCGAAAGATCCTCACTTCGAAAGACTACCTTGTATACACAAAGGGACATATGCTGATGACTGTCTCGTTGACAGAGTTACTCAG
                            taattggtttactata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatcttttagactttttgaacaaggcttttctgtttatggttttgtttcgtggattcgtaattggtttactataatatttggtagGATTGCGAAAGATCCTCACTTCGAAAGACTACCTTGTATACACAAAGGGACATATGCTGATGACTGTCTCGTTGACAGAGTTACTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT