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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgagtttctgttgcatttagctctttttgaatatctctctctctctaaatattataagtttgctcatatatttggcgttttctttaacatacagCTTCTCTGGGTTAATCTGATAATGGACACTCTTGGAGCATTGGCTTTGGCTACTGAACCACCCACTGATCACCTCATGGGGAGGCCTCCAGTTGGCAGAA

Basic information

species Arabidopsis thaliana
transcript AT5G57110.1
intron # 28
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G57110.2 (Arabidopsis thaliana), 3'ss of exon 28
lower sequence: LOC_Os02g08010.1 (Oryza sativa), 3'ss of exon 10
-gtttgagtttctgttgcatttagctctttttgaatatctctctctctctaaatattataagtttgctcatatatttggcgt---tttctttaacatacagCTTCTCTGGGTTAATCTGATAATGGACACTCTTGGAGCATTGGCTTTGGCTACTGAACCACCCACTGATCACCTCATGGGGAGGCCTCCAGTTGGCAGAA
 |    | | |  ||   | | |  |     |   || || | |   | |  |  |    |  | ||| | || |||  | |   ||| ||    ||  ||||||| ||||| ||||| || |||||||| ||||| ||| | || ||||||||||||||||| || || || || |||  | |||| || |||||  | |
ggggaaattgttagtgaaaatgaaattaagatacttaactgtattgatttgcacgtcggcacatggctga-atgttttacttccgtttgttgttgatttagCTTCTTTGGGTCAATCTCATTATGGACACACTTGGTGCACTTGCATTGGCTACTGAACCACCAACAGACCAACTTATGAAGCGGCCACCTGTTGGACGGA

upper sequence: AT5G57110.2 (Arabidopsis thaliana), 3'ss of exon 28
lower sequence: GRMZM5G893864_T01 (Zea mays), 3'ss of exon 6
--gtttgagtttctgttgcatttagctctttttgaatatctc-tctctctctaaatattataagtttgctcatatatttggcgttttctttaacatacagCTTCTCTGGGTTAATCTGATAATGGACACTCTTGGAGCATTGGCTTTGGCTACTGAACCACCCACTGATCACCTCATGGGGAGGCCTCCAGTTGGCAGAA
       ||||  |  || |   ||     ||  | |||      ||| | | ||  ||  |      |  ||||      | |||| |||   ||||||||||||||||||||||| || |||||||| || || ||  | |||||||||||||||||||| || ||||| || ||| || |||| ||||||||  | |
caaaccaagttgttaatgaacaaagtgtagttaaagtattaagcttctatttgaaagttggacaccaacaaatattagcttccttttgttttttatacagCTTCTCTGGGTTAATCTCATCATGGACACACTCGGTGCTCTTGCTTTGGCTACTGAACCACCAACAGATCAACTTATGAGGCGGCCACCAGTTGGACGGA

upper sequence: AT5G57110.2 (Arabidopsis thaliana), 3'ss of exon 28
lower sequence: GLYMA17G06520.1 (Glycine max), 3'ss of exon 29
gtttgagtttctgttgcatttagctctttttgaatatctctctctctctaaatattataagtttgctcatatatttggcgttttctttaacatacagCTTCTCTGGGTTAATCTGATAATGGACACTCTTGGAGCATTGGCTTTGGCTACTGAACCACCCACTGATCACCTCATGGGGAGGCCTCCAGTTGGCAGAA
|||||  ||    |||  | || ||  |||    |  |||  |   ||  ||   |||   | ||  | ||||  |     ||  |||| || ||||||||||||||| ||||| || ||||| |||||||||||||| || ||||| ||||||||||| ||||||  ||| ||||       ||||   ||  |||
gtttgctttctatttgtctctaactggtttgtgctccctcatttattcagaaggctatccttatgaac-tatacct--tcattaatttatca-acagCTTCTCTGGGTAAATCTTATCATGGATACTCTTGGAGCATTAGCCTTGGCAACTGAACCACCAACTGATTCCCTGATGGATCAAAGTCCAAAGGGTCGAA

upper sequence: AT5G57110.2 (Arabidopsis thaliana), 3'ss of exon 28
lower sequence: GLYMA13G00420.1 (Glycine max), 3'ss of exon 27
gtttgagtttctgttgcatttagctctttttgaatatctctctctctctaaatattataagtttgc-tcatatatttggcgttttctttaacatacagCTTCTCTGGGTTAATCTGATAATGGACACTCTTGGAGCATTGGCTTTGGCTACTGAACCACCCACTGATCACCTCATGGGG-AGGCCTCCAGTTGGCAGAA
|||||| ||    |||  | || |   |||    |  |||  |   ||  ||   |||   | ||    |||  ||      |||||  |     |||||||||||||| ||||| || ||||| |||||||||||||| || ||||| |||||||| || ||||||   || ||||   |   | | |   | || | 
gtttgatttctatttgtctctaaccggtttgtgctccctcatttattcagaaggctatccttatgaactataccttcattaatttctcaa-----cagCTTCTCTGGGTAAATCTTATCATGGATACTCTTGGAGCATTAGCCTTGGCAACTGAACCGCCAACTGATTCTCTGATGGATCAAAGCCCTAAGGGTCAAA-

upper sequence: AT5G57110.2 (Arabidopsis thaliana), 3'ss of exon 28
lower sequence: GLYMA09G06890.1 (Glycine max), 3'ss of exon 26
gtttgagtttctgttgcatttagctctttttgaatatctctctctctctaaatattataagt--ttgctcatatatttggcgttttctttaacatacagCTTCTCTGGGTTAATCTGATAATGGACACTCTTGGAGCATTGGCTTTGGCTACTGAACCACCCACTGATCACCTCATGGGGAGGCCTCCAGTTGGCAGAA
  |||| |||||      |||     || | |  |||     | | |  |   |  || ||   |    |  | || ||  | ||||| ||      ||||||| ||||| ||||| || ||||| ||||| |||||  ||||  |||| ||||||||||| ||||||||||||||||   |  ||||||| ||  |||
-gttgactttct------ttttttctttctaggttatgctcatgtattaagtcaggatgagccatgatgctaaaatctgttgctttctcta-----tagCTTCTTTGGGTGAATCTTATCATGGATACTCTGGGAGCGCTGGCCCTGGCAACTGAACCACCAACTGATCACCTCATGGATCGAACTCCAGTGGGTCGAA

upper sequence: AT5G57110.2 (Arabidopsis thaliana), 3'ss of exon 28
lower sequence: GLYMA15G18180.1 (Glycine max), 3'ss of exon 26
gtttgagtttctgttgcatttagctctttttgaatatctctctctctctaaat-attataagtttgctcat--atatttggcgttttctttaacatacagCTTCTCTGGGTTAATCTGATAATGGACACTCTTGGAGCATTGGCTTTGGCTACTGAACCACCCACTGATCACCTCATGGGGAGGCCTCCAGTTGGCAGAA
         |    |   |||  |||||| |   |    ||| |    ||| | |  || |||     |||  | || ||  | ||||| ||      ||||||| ||||| ||||| || ||||| ||||| |||||| | ||  |||| ||||||||||| ||||||||||||||||   |  | ||||| ||  |||
--------gttgactttctttttctctttctaggttatgctcacgtattaagtcaggatgagtcatgacattaaaatctgttgctttctcta-----tagCTTCTTTGGGTAAATCTTATCATGGATACTCTGGGAGCACTAGCCCTGGCAACTGAACCACCAACTGATCACCTCATGGATCGATCCCCAGTGGGTCGAA

upper sequence: AT5G57110.2 (Arabidopsis thaliana), 3'ss of exon 28
lower sequence: Vv11s0052g00320.t01 (Vitis vinifera), 3'ss of exon 29
gtttgagtttctgttgcattta--gctctttttgaatatctctctctctctaaatattataagtttgctcatatatttggcgttttctttaacatacagCTTCTCTGGGTTAATCTGATAATGGACACTCTTGGAGCATTGGCTTTGGCTACTGAACCACCCACTGATCACCTCATGGGGAGGCCTCCAGTTGGCAGAA
      |||  ||   ||   |  |||   | |  |  |  |  |     ||  |  | | | |||| | |  | | ||  || | ||||  | ||||||| |||||||||||||| || ||||| |||||||||||| | || ||||| ||||||||||| || |||||||| |||   ||||||||||||||  |||
------gttggtggcccacccattgctgcctcttgagttgacagttctattatgtcgtctca-tttgtttaactctgtgttgtctactttg-cttacagCTCCTCTGGGTTAATCTTATCATGGATACTCTTGGAGCACTTGCATTGGCCACTGAACCACCAACAGATCACCTGATGCACAGGCCTCCAGTTGGTCGAA

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|164000954|gb|ES067481.1|ES067481
EST:     CCGCTGTGCTAG                         CTTCTCTGGGTTAATCTGATAATGGACACTCTTGGAGCATTGGCTTTGGC
genomic: CCGCTGTGC-AGgtttgagttt ... taacatacagCTTCTCTGGGTTAATCTGATAATGGACACTCTTGGAGCATTGGCTTTGGC
EST: gi|86081055|gb|DR376812.1|DR376812
EST:     ATGTTGTAGCTGCTATTTCGAGTGGTGACGTTCCACTTACCGCTGTGCAG                         CTTCTCTGGGTTAATCTGATAATGGACACTCTTGGAGCATTGGCTTTGGCT
genomic: ATGTTGTAGCTGCTATTTCGAGTGGTGACGTTCCACTTACCGCTGTGCAGgtttgagttt ... taacatacagCTTCTCTGGGTTAATCTGATAATGGACACTCTTGGAGCATTGGCTTTGGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctctctaaatattataagtttgctcatatatttggcgttttctttaacatacagCTTCTCTGGGTTAATCTGATAATGGACACTCTTGGAGCATTGGCTTTGGCTACTGAACCACCCACTGATCACCTCATGGGGAGGCCTCCAGTTGGCAGAA
                                          ctttaac  putative branch site (score: 3)
                                    cgttttcttt  CT-rich tract
      taaatattataagttt  TA-rich tract