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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggagtagtgaaagtaatatactactttgctgggtacagtattctctgtcttgtcgatttggttttatgatgatcctctgttgcttctaattatcctctcagGCTATAAGGGATGGTGCAGATGCTGTCATTGCGGTTGGAGGTGATGGAACACTTCATGAG

Basic information

species Arabidopsis thaliana
transcript AT2G46090.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G46090.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os03g03400.2 (Oryza sativa), 3'ss of exon 3
gtaaggagtagtgaaagtaatatactactttgctgggtacagtattctctgtcttgtcgatttggttttatgatgatcctctgttgcttctaattatcctctcagGCTATAAGGGATGGTGCAGATGCTGTCATTGCGGTTGGAGGTGATGGAACACTTCATGAG
       || ||| | |   | | |||         |||    ||| |   | |   |  ||||||||| |  | |   | |||   |  | || ||  | | ||||| ||| |||||| || ||||| || ||||| ||||| |||||||||||||||||||||
-------gt-gtgtatgggct-tcctatagctgccagtatccaattgttaatttcccct-tttggttttcttgttacaatgtgtgtatgatgatgatgatgt-agGCTGTAAAGGATGGGGCTGATGCCGTGATTGCTGTTGGTGGTGATGGAACACTTCATGAG

upper sequence: AT2G46090.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G382537_T01 (Zea mays), 3'ss of exon 4
gtaaggagtagtgaaagtaatatactactttgctgggtacagtattctctgtcttgtcgatttggttttatgatgatcctctgttgcttctaattatcctctcagGCTATAAGGGATGGTGCAGATGCTGTCATTGCGGTTGGAGGTGATGGAACACTTCATGAG
            |   ||    |  | | |||     ||| |  ||| |   || | ||| |    ||||   | | |  ||| || |  ||    | |||| ||||||||| |||||| || |||||||| || || |||||||||||||| || |||||||||
------------gtgcgtg-cgtgttcccttgtcaaatactgggttccc---ctcggcgacta---tttactctaagca-ctggtgatgatatgcttactct-agGCTATAAAGGATGGGGCTGATGCTGTGATCGCTGTTGGAGGTGATGGTACGCTTCATGAG

upper sequence: AT2G46090.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G089860_T02 (Zea mays), 3'ss of exon 3
gtaaggagtagtgaaagtaatatactactttgctgggtacagtattctctgtcttgt--cgatttggttttatgatgatcctctgttgcttctaattatcctctcagGCTATAAGGGATGGTGCAGATGCTGTCATTGCGGTTGGAGGTGATGGAACACTTCATGAG
     | |              |    | |||    ||  | ||   ||    | ||  | ||||  | | |  |    |   || || | |||||||   |   ||||||||| |||||| |  ||||| || || || |||||||||||||| ||||||||||||
-----gtgcgtgcgtgactgcgtgtccccttgtcaagtgtactaggttccacttggtaactatttaatctaagca----ctggtgatg-tcctaattactgt---agGCTATAAAGGATGGGGTTGATGCCGTGATAGCTGTTGGAGGTGATGGTACACTTCATGAG

upper sequence: AT2G46090.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA09G39010.1 (Glycine max), 3'ss of exon 3
gtaaggagtagtgaaagtaatatactactttgctgggtacagtat---tctctgtcttgtcgatttggttttatgatgatcctctgttgcttctaattatcctctcagGCTATAAGGGATGGTGCAGATGCTGTCATTGCGGTTGGAGGTGATGGAACACTTCATGAG
                          | ||||  | ||     ||   |   | |  |||| |||   |   |||| | |  |   | | |     |   |     ||||||||||||| || || ||||| |||||||| ||||||||||||||||| |||||||||
-----------------------gtcagtttggagtgtttgagataagttggttttatgtcaattgcttccaatga-gttgttaaatcgttgtccttgcactatgtagGCTATAAGGGAGGGGGCTGATGCCGTCATTGCTGTTGGAGGTGATGGAACTCTTCATGAG

upper sequence: AT2G46090.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA18G47330.1 (Glycine max), 3'ss of exon 3
gtaaggagtagtgaaagtaatatactactttgctgggtacagtattc-tctgtcttgtcg-atttggttttatgatgatcctctgttgcttctaattatcctctcagGCTATAAGGGATGGTGCAGATGCTGTCATTGCGGTTGGAGGTGATGGAACACTTCATGAG
                         || ||||  | ||     ||   |  || || ||  |  || ||  |    | |  |   |||||     |  ||     ||||||||||||| || || |||||||||||||| |||||||| |||||||| |||||||| 
----------------------ggttagtttggagtgtttgagataagttggttttatctcagctgattccaatgagttgttgaattgctgtccttgttctatgtaGGCTATAAGGGAGGGGGCTGATGCTGTCATTGCTGTTGGAGGAGATGGAACTCTTCATGA-

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|116407738|gb|EG450330.1|EG450330
EST:     GTGAATTATTAACATCGGGTCCTTCTCATGCCATTGACATTACAAGAGAG                         GCTATAAGGGATGGTGCAGATGCTGTCATTGCGGTTGGAGGTGATGGAACA
genomic: GTGAATTATTAACATCGGGTCCTTCTCATGCCATTGACATTACAAGAGAGgtaaggagta ... atcctctcagGCTATAAGGGATGGTGCAGATGCTGTCATTGCGGTTGGAGGTGATGGAACA
EST: gi|86060582|gb|DR356339.1|DR356339
EST:     GTGAATTATTAACATCGGGTCCTTCTCATGCCATTGACATTACAAGAGAG                         GCTATAAGGGATGGTGCAGATGCTGTCATTGCGGTTGGAGGTGATGGAACA
genomic: GTGAATTATTAACATCGGGTCCTTCTCATGCCATTGACATTACAAGAGAGgtaaggagta ... atcctctcagGCTATAAGGGATGGTGCAGATGCTGTCATTGCGGTTGGAGGTGATGGAACA
EST: gi|86060583|gb|DR356340.1|DR356340
EST:     GTGAATTATTAACATCGGGTCCTTCTCATGCCATTGACATTACAAGAGAG                         GCTATAAGGGATGGTGCAGATGCTGGTCATTGCGGTTGGAGGTGATGGAAC
genomic: GTGAATTATTAACATCGGGTCCTTCTCATGCCATTGACATTACAAGAGAGgtaaggagta ... atcctctcagGCTATAAGGGATGGTGCAGATGCTG-TCATTGCGGTTGGAGGTGATGGAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcttgtcgatttggttttatgatgatcctctgttgcttctaattatcctctcagGCTATAAGGGATGGTGCAGATGCTGTCATTGCGGTTGGAGGTGATGGAACACTTCATGAG
                                     ttctaat  putative branch site (score: 2)
                                           ttatcctctc  CT-rich tract
                                     ttctaattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggagtagtgaaagtaatatactactttgctgggtacagtattctctgtcttgtcgatttggttttatgatgatcctctgttgcttctaattatcctctcagGCTATAAGGGATGGTGCAGATGCTGTCATTGCGGTTGGAGGTGATGGAACACTTCATGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA