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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgtttatattcatgtttacaacatctagtttgtattctgatgctcaagcaagtctctgttactctatggtttgctttcggattcaacagcttcttgtagctgattatgctatgcagaaggcaaaacctgctaactttgatcatgggcactgcagGTGCAAGCTTACCTATATGATGGTTACTGGGAAGACATTGGTACTATAGAGGCATTTTATAACGCTAATCTTGGAATCACCAAGAAACCAGTTCCTGATT

Basic information

species Arabidopsis thaliana
transcript AT5G48300.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G48300.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os09g12660.2 (Oryza sativa), 3'ss of exon 4
gtgagtgtttatattcatgtttacaacatctag----tttgtattctgat----gctcaagca--agtctctgttactctatggtttgc---tttcggattcaacagcttcttgtagctgattatgctatgcagaaggca--------aaacctgctaactttgatcatgggcactgcagGTGCAAGCTTACCTATATGATGGTTACTGGGAAGACATTGGTACTATAGAGGCATTTTATAACGCTAATCTTGGAATCACCAAGAAACCAGTTCCTGATT
||  |   |  | || |   ||  | ||| |||    ||| ||| ||  |    | ||| ||   ||  | ||| |   | |||| ||     | | | | || ||  |  |   |  || |  | || | |  ||            |    |||| |   || | |||        |||||||||||||| |||||||||||||||||||||| |||||||||||||||||||| || || || ||  | || || ||||||||||| || || ||||
gtacgctatgctcttgaaacttgtagcatgtagggaatttttatccttctctcagttcatgctgtaggttttgtgaagtt-tggtatgtaaactgcagttacatcatttattgtgaaatgttacttctttacttaatttttactttgcatgtttgcttatgctgctaatgtatttgatagGTGCAAGCTTACTTATATGATGGTTACTGGGAAGATATTGGTACTATAGAGGCATTCTACAATGCCAACTTGGGGATAACCAAGAAACCTGTGCCAGATT

upper sequence: AT5G48300.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os08g25734.1 (Oryza sativa), 3'ss of exon 4
---------------------gtgagtgtttatattcat--gtttacaacatctagtttgtattctgatgctcaagcaagtctctgttact---ctatggt--ttgctttcggattcaacagcttctt--gtagctgattatgctatgcagaaggcaaaacctgctaactttgatcatgggcactgcagGTGCAAGCTTACCTATATGATGGTTACTGGGAAGACATTGGTACTATAGAGGCATTTTATAACGCTAATCTTGGAATCACCAAGAAACCAGTTCCTGATT
                     ||     ||| | ||| |  |||||  ||  ||  ||| |||  |  |   ||    |   ||| | |||    ||| ||  | || |  | | | ||   ||| ||   ||  ||    |  | |||   |       | |   || | |  |  ||    |||||||| ||||||||| | ||||||||||||||||||||||||||||| || |||||||| ||||| || ||||| ||||| || || || || || || ||||
gtatggaaagctcgctgtttagtagccttttgttttcttcagtttattactgctgcttt-tatgattgttagcatttgaccttctctcactgaaatattgtcatggcatatgtaataaattacttttttattacttgtaggtcatgtgctatatttgctgcttaagaa-tctatttttgttgtctgcagGTACAAGCTTACTTGTATGATGGTTACTGGGAAGACATTGGTACCATTGAGGCATTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATT

upper sequence: AT5G48300.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G106213_T01 (Zea mays), 3'ss of exon 4
-------------gtgagtgtttata-ttcatgtttacaacatctagtttgtattctgatgctcaagcaagtctctgttactctatggtttgctttcggattcaacagcttcttgtagct---gattatgctatgcagaag--gcaaaacctgctaactttgatcatgggcactgcagGTGCAAGCTTACCTATATGATGGTTACTGGGAAGACATTGGTACTATAGAGGCATTTTATAACGCTAATCTTGGAATCACCAAGAAACCAGTTCCTGATT
              ||||  ||  |  ||  | ||  | |  | | |||| |||  |  ||        | | |  |    ||  | |   | |||    |||| ||  || ||| || |   | |||  || |  || ||  || |    |||| |   || |  || |  |   |||||||||||||| |||||||||||||||||||||| ||||||||||| || ||||||||||| || ||  | ||||| |||||||| || || || ||||
gtatgctctgctcttgagctttcttggtttctcttctccagtttttgtttttatcattctggatttatga-tttgggcatttcggttgaaagattttaatttcatca-tttattgaagatttggcttagcctttttagtagttgctatgtttgcttatgatgttgttgtgttcaaaagGTGCAAGCTTACTTATATGATGGTTACTGGGAAGATATTGGTACTATTGAAGCATTTTATAATGCAAACTTGGGAATAACCAAGAAGCCTGTACCGGATT

upper sequence: AT5G48300.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G163437_T01 (Zea mays), 3'ss of exon 4
gtgagtgtttatattcatgtttacaacatctagtttgtattctgatgctcaagcaagtctctgttactctatggtttgctttcggattcaacagcttcttgtagctgattatgctatgcagaaggcaaaacctgctaactttgatcatgggcactgcagGTGCAAGCTTACCTATATGATGGTTACTGGGAAGACATTGGTACTATAGAGGCATTTTATAACGCTAATCTTGGAATCACCAAGAAACCAGTTCCTGATT
                                            |||||  || ||| ||  |    |   ||| |||  |   |     |  |      |     | |||  |  |  | || |  |    |    || ||  |  ||    |||||||| || ||||| |||||||||||||| |||||||| |||||||| || |||||||||||||| || ||  | ||||| |||||||| ||| | || ||||
-------------------------------------------catgct--agaaagcctaggcaggt---tgggttggctcaaggccggaggga-----gggaagggttacaccttttaaaatggta---tttaagaccttatttttgt---ctgcagGTTCAGGCTTATCTATATGATGGTTATTGGGAAGATATTGGTACAATTGAGGCATTTTATAATGCAAACTTGGGAATAACCAAGAAGCCAATACCAGATT

upper sequence: AT5G48300.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G068506_T03 (Zea mays), 3'ss of exon 4
gtgagtgtttatattcatgtttacaacatctagtttgtattctgatgctcaagcaagtctctgttactctatggtttgctttcggattcaacagcttcttgtagctgattatgctatgcagaaggcaaaacctgctaactttgatcatgggcactgcagGTGCAAGCTTACCTATATGATGGTTACTGGGAAGACATTGGTACTATAGAGGCATTTTATAACGCTAATCTTGGAATCACCAAGAAACCAGTTCCTGATT
                               || ||  | |   | ||  | ||| || |  |||     | ||   | |   |||   ||  | | | | |           |      |||   || ||||  ||  |||| |         ||||||| || ||||| || |||||||||||||||||||| || ||||| || | |||||||||||| || ||  | ||||| |||||||| ||| | || ||||
-------------------------------agctt--actagaaagcctaggcaggt-tgggttgtctcaaggcaggat---ggaaggaagggttgccttt-----------cagaatggaatttaagacct--tatttttgtt---------tgcagGTTCAGGCTTATCTGTATGATGGTTACTGGGAAGATATCGGTACCATTGCGGCATTTTATAATGCAAACTTGGGAATAACCAAGAAGCCAATACCAGATT

upper sequence: AT5G48300.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv12s0057g01480.t01 (Vitis vinifera), 3'ss of exon 4
gtgagtgtttatattcatgtttacaacatctagtttgtattctgatgctcaagcaagtctctgttactctatggtttgctttcggattcaacagcttcttgtagctgattatgctatgcagaaggcaaaacctgctaactttgatcatgggcactgcagGTGCAAGCTTACCTATATGATGGTTACTGGGAAGACATTGGTACTATAGAGGCATTTTATAACGCTAATCTTGGAATCACCAAGAAACCAGTTCCTGATT
                                            ||| |||    |   || | || || |   | |  |||    | ||   || |  |  ||   | | |  ||      || ||||   ||||         |||   | ||| |||||||||||||| | |||||||| |||||||||||||||||||| || ||||| ||||||||||||||| | || ||||| ||||| || || || ||||
-------------------------------------------tatgatcactggaaattccgataatc-aaaatgttattttatctgcatttgccttcttaagagaactttcata-----gagtcaaa--ttgctg--------cataatctctgtagGTGCAAGCTTACTTGTATGATGGCTACTGGGAAGACATTGGTACAATTGAGGCTTTTTATAACGCTAATTTGGGGATCACAAAGAAGCCGGTGCCAGATT

upper sequence: AT5G48300.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S2_337V6.1 (Physcomitrella patens), 3'ss of exon 4
gtgagtgtttatattcatgtttacaacatctagtttgtattctgatgctcaagcaagtctctgttactctatggtttgctttcggattcaacagcttcttgtagctgattatgctatgcagaaggcaaaacctgctaactttgatcatgggcactgcagGTGCAAGCTTACCTATATGATGGTTACTGGGAAGACATTGGTACTATAGAGGCATTTTATAACGCTAATCTTGGAATCACCAAGAAACCAGTTCCTGATT
                                                   |   || | ||| |     | |     |||||    ||| ||  | | | |   |  | |  | | | |    || |||  ||||||   |    |     |   |||||||| || ||| ||| |||||| ||||||||||| ||||| ||||| || || ||||| ||||| ||  | |||||||| ||||| || ||||||||||
---------------------------------------------------atttag-cgctgattaaagaagccgacctttcaacgtcatcatatgcctttcattcgtaactccaagtatcttgccaaa--tgctaatactaggta-----atatcagGTGCAGGCCTACTTATTTGATGGCTACTGGGAAGATATTGGAACTATTGAAGCTTTTTACAACGCAAACTTAGGAATCACGAAGAAGCCCGTTCCTGATT

upper sequence: AT5G48300.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S76_105V6.1 (Physcomitrella patens), 3'ss of exon 4
gtgagtgtttatattcatgtttacaacatctagtttgtattctgatgctcaagcaagtctctgttactctatgg-tttgctttcggattcaacagcttcttgtagctgattat-gctatgcagaaggcaaaacctgctaactttgatcatgggcactgcagGTGCAAGCTTACCTATATGATGGTTACTGGGAAGACATTGGTACTATAGAGGCATTTTATAACGCTAATCTTGGAATCACCAAGAAACCAGTTCCTGATT
                                                           |  | |   || ||  ||| | | |    ||| |   |    |||    ||  | | | | |  || |     ||||  ||  ||  |  |  |     ||||| ||||||||  | || ||||| ||||||||||| ||||| ||||| || ||||| || || || ||||| || ||||| |||||||| ||||||||||
----------------------------------------------------------gtagggtgagctgtgaatttccatacaacctcagccattggaggtaataaatagtagttgtacgtaatgt---tcctgagaagatttttgttctgtttatcagGTTCAAGCTTATTTGTACGATGGCTACTGGGAAGATATTGGAACTATTGAAGCATTCTACAATGCCAATCTGGGCATCACTAAGAAACCTGTTCCTGATT

upper sequence: AT5G48300.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S2_392V6.1 (Physcomitrella patens), 3'ss of exon 4
gtgagtgtttatattcatgtttacaacatctagtttgtattctgatgctcaagcaagtctctgttactctatggtttgctttcggattcaacagcttcttgtagctgattatgctatgcagaaggcaaaacctgctaactttgatcatgggcactgcagGTGCAAGCTTACCTATATGATGGTTACTGGGAAGACATTGGTACTATAGAGGCATTTTATAACGCTAATCTTGGAATCACCAAGAAACCAGTTCCTGATT
                                                   |  |        |  ||| |  | |||  |  | |    |       | | |           | | |      | ||   |  |     ||    || | ||  ||||| ||||| ||| | |||||||| |||||||||||||| |||||||| ||||| || || ||||| ||| | || ||||||||||| || || || ||||
--------------------------------------------------gaatattcggagatatctccaaaggttgtctgtgaacgtgatgttcagtggcaatgacccgcattgttc------ccaattgtattgtgactggat-tgtgtac--cagGTTCAAGCGTACTTGTATGATGGCTACTGGGAAGACATCGGTACTATCGAGGCTTTCTACAACGCGAATTTGGGCATCACCAAGAAGCCCGTGCCAGATT

upper sequence: AT5G48300.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ16157 (Selaginella moellendorffii), 3'ss of exon 4
gtgagtgtttatattcatgtttacaacatctagtttgtattctgatgctcaagcaagtctctgttactctatggtttgctttcggattcaacagcttcttgtagctgattatgctatgcagaaggcaaaacctgc-taactttgatcat-----gggcactgcagGTGCAAGCTTACCTATATGATGGTTACTGGGAAGACATTGGTACTATAGAGGCATTTTATAACGCTAATCTTGGAATCACCAAGAAACCAGTTCCTGATT
                                                                                                         || || |||| || ||    | ||||   | | ||||  |  ||     |  |  ||||||||||||| ||  | |||||||| |||||||||||||| || |||||||||||||||||  | || ||  | ||| |||| ||||| || |||||  | |
------------------------------------------------------------------------------------------------------gtttgtttttgctctgaagggatcgaaacgaacgtgacttaaacaatactctgttcgttgcagGTGCAAGCGTATTTGTATGATGGATACTGGGAAGACATAGGGACTATAGAGGCATTTTACCATGCCAACTTAGGATTCACAAAGAAGCCCGTTCCAAACT

upper sequence: AT5G48300.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ17026 (Selaginella moellendorffii), 3'ss of exon 4
gtgagtgtttatattcatgtttacaacatctagtttgtattctgatgctcaagcaagtctctgttactctatggtttgctttcggattcaacagcttcttgtagctgattatgctatgcagaaggcaaaacctgctaactttgatcatgggcactgcagGTGCAAGCTTACCTATATGATGGTTACTGGGAAGACATTGGTACTATAGAGGCATTTTATAACGCTAATCTTGGAATCACCAAGAAACCAGTTCCTGATT
                                                                                             | || || | |||    | |    | |     |   || |   |||  || || ||  |   |||||||||||| ||  | |||||||| |||||||||||||| || |||||||||||||||||  | || ||  | ||| |||| ||||| || |||||  | |
---------------------------------------------------------------------------------------------gtttgtttttgctctgaagggatcgaaacgaacgtgactta--aacaatgctc-tgttcgtcgcagGTGCAAGCGTATTTGTATGATGGATACTGGGAAGACATAGGGACTATAGAGGCATTTTACCATGCCAACTTAGGATTCACAAAGAAGCCCGTTCCAAACT

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|124995416|gb|EL067685.1|EL067685
EST:     ATGACTTTGGAAGTGAAGTCATTCCCGGTGCCACTTCCCTTGGACTGAGG                         GTGCAAGCTTACCTATATGATGGTTACTGGGAAGACATTGGTACTATAGA
genomic: ATGACTTTGGAAGTGAAGTCATTCCCGGTGCCACTTCCCTTGGACTGAGGgtgagtgttt ... ggcactgcagGTGCAAGCTTACCTATATGATGGTTACTGGGAAGACATTGGTACTATAGA
EST: gi|124864805|gb|EH949242.1|EH949242
EST:     ATGACTTTGGAAGTGAAGTCATTCCCGGTGCCACTTCCCTTGGACTGAGG                         GTGCAAGCTTACCTATATGA
genomic: ATGACTTTGGAAGTGAAGTCATTCCCGGTGCCACTTCCCTTGGACTGAGGgtgagtgttt ... ggcactgcagGTGCAAGCTTACCTATATGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgattatgctatgcagaaggcaaaacctgctaactttgatcatgggcactgcagGTGCAAGCTTACCTATATGATGGTTACTGGGAAGACATTGGTACTATAGAGGCATTTTATAACGCTAATCTTGGAATCACCAAGAAACCAGTTCCTGATT
                               taacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtgtttatattcatgtttacaacatctagtttgtattctgatgctcaagcaagtctctgttactctatggtttgctttcggattcaacagcttcttgtagctgattatgctatgcagaaggcaaaacctgctaactttgatcatgggcactgcagGTGCAAGCTTACCTATATGATGGTTACTGGGAAGACATTGGTACTATAGAGGCATTTTATAACGCTAATCTTGGAATCACCAAGAAACCAGTTCCTGATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA