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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACGAGCTAGCTCTAAAACAAATCTAGAACGAGGAATCTACGTTAAGCATTTCAAAAACATTCCTATGGCTGACATGGAGATTGTGCTTgtaagtttctgttcttgtcttctttccttttgcatcgctggattttgtagcgaaaattgcaaactagctgcaataacattaatgtcttgtgcag

Basic information

species Arabidopsis thaliana
transcript AT3G19340.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G19340.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: LOC_Os12g29550.1 (Oryza sativa), 5'ss of exon 9
ACGAGCTAGCTCTAAAACAAATCTAGAACGAGGAATCTACGTTAAGCATTTCAAAAACATTCCTATGGCTGACATGGAGATTGTGCTTgtaagtttctgttcttgtctt----ctttccttttgcatcgctgg-attttgtagcgaaaattgcaa--actagctgcaa--taacattaatgt---cttgtgcag
  | ||  |  |||| || || |  || |||||||| |  || ||||||||||| || || || |||||||||||||| ||||| |||||||| |      || |  ||          | | ||||   | | || || |||| | |  ||       ||||    |  | | ||| |      ||| |||||
GAGGGCAGGTACTAAGACTAAGCCTGATCGAGGAATATTTGTAAAGCATTTCAAGAATATCCCAATGGCTGACATGGAAATTGTTCTTgtaagatgaatcactagagttgagataaatgtgtagcatttttagcatcttttagctatatctgtggctgttagcaaggacctgaaattgaaacttacttttgcag

upper sequence: AT3G19340.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA19G27800.1 (Glycine max), 5'ss of exon 9
ACGAGCTAGCTCTAAAACAAATCTAGAACGAGGAATCTACGTTAAGCATTTCAAAAACATTCCTATGGCTGACATGGAGATTGTGCTTgtaagtttctgttcttgtctt-ctttccttttgcatcgctggattttgtagcgaaaattgc-----aaactagctgcaataacatt----aatgtcttgt------gcag
  |||| ||  | ||| ||||   |||||||||||| || || |||||||||||||||||||| |||||||| ||||| || || ||||| |||| |     ||||    ||||   |   |||  ||   |||| |  | ||  || |      || ||   | |||||| ||    ||   |||||      ||||
GAGAGCCAGAACCAAATCAAAAGAAGAACGAGGAATATATGTGAAGCATTTCAAAAACATTCCAATGGCTGATATGGAAATAGTTCTTgtgagttacctcatttgtgaagcttttaatgaacatt-ctaatttttattactaactttcccccaacaaatacaagtaataaccttggtcaagaacttgttacttggcag

upper sequence: AT3G19340.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA16G05180.1 (Glycine max), 5'ss of exon 9
ACGAGCTAGCTCTAAAACAAATCTAGAACGAGGAATCTACGTTAAGCATTTCAAAAACATTCCTATGGCTGACATGGAGATTGTGCTTgtaagtttctgttcttgt----cttc---------tttccttttgcatcgctggattttgtagcgaaaattgcaa--actagctgcaat--aacattaatgtcttgtgcag
  |||| ||    ||| ||||   |||||||||||| || || |||||||||||||||||||| ||||| || ||||| || || ||||| |||| |     ||||    |||          || |  |||  ||  ||   |||       | || | |||  | || |     |  |  | |  |  |||| ||||
GGGAGCCAGAAACAAATCAAAAGAAGAACGAGGAATATATGTGAAGCATTTCAAAAACATTCCAATGGCCGATATGGAAATAGTTCTTgtgagttacctcatttgtgaagcttttaaaggacattccaatttttattactaactttccccctaacaaatacaagtaataaccttggtcaagaacttgttacttg-gcag

upper sequence: AT3G19340.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: Vv14s0068g01000.t01 (Vitis vinifera), 5'ss of exon 9
ACGAGCTAGCTCTAAAACAAATCTAGAACGAGGAATCTACGTTAAGCATTTCAAAAACATTCCTATGGCTGACATGGAGATTGTGCTTgtaagtttctgttc---ttgtcttctttccttttgcat---cgctggatttt--gtagcgaaaattgcaaactagctgcaataacattaatgtcttgtgcag--------------------------------------
 || ||  |  |   | |||| | ||| |||||||| || || |||||||||||||||||||| |||||||| ||||| || || || || ||||  |||     || ||| ||  ||  |  ||    | ||  || |   |||   ||| ||  ||     |     |  |   || || || |  |                                       
GCGGGCATGTACGGCAGCAAAACCAGAGCGAGGAATATATGTGAAGCATTTCAAAAACATTCCAATGGCTGATATGGAAATAGTCCTGgtgagttcttgtctgctttctctcctcccccctctcactcactctccatctcaggtatttaaagttttaattgcacctttttctctcaaaagttttctatacagctgttaacatgtcttgtaacattttcctttgagcag

upper sequence: AT3G19340.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: PP1S60_139V6.2 (Physcomitrella patens), 5'ss of exon 10
------------ACGAGCTAGCTCTAAAACAAATCTAGAACGAGGAATCTACGTTAAGCATTTCAAAAACATTCCTATGGCTGACATGGAGATTGTGCTTgtaagtt-tctgttcttgtcttctttccttttgcatcgctggattttgtagcgaaaattgcaaac--tagctgcaataacattaatgtcttgtgcag---
            ||     | |  | |  |      |||  |||  ||  || |   ||||||   ||| ||||||||||| ||||||||| |||| |||||||||| ||  | || || | ||          | ||       |   ||| |    || || |  ||  |   ||      | ||  |  | | |   
TGCCTCGAAACCACACCACATCCTTGATCCCCTGGGAGACAGAGCCATTCACATCCGGCATTTTCGAAATATTCCTATGGCAGACATGGAGCTTGTTCTTgtaagttgtcgatactcgtatgctcataacagttagcggcaagcctgagagctagtcatggaagcagtattttacattgtgggactgcgtattcctggaa

upper sequence: AT3G19340.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: PP1S140_106V6.1 (Physcomitrella patens), 5'ss of exon 10
------------ACGAGCTAGCTCTAAAACAAATCTAGAACGAGGAATCTACGTTAAGCATTTCAAAAACATTCCTATGGCTGACATGGAGATTGTGCTTgtaagtt-tctgttcttgtcttctttccttttgcatcgctggattttgtagcgaaaattgcaaacta----gctgcaataacattaatgtcttgtgcag--
            ||    ||    | |  ||  |   || || |  ||  || |   ||||||   |||||||||| |||| ||||||||| ||||||||||||||| ||  |   | |  |     | | |   ||  | | |   |   | ||   | |||| ||      |   |||   ||    | || | | |  
TGCTTCTAAACCACATCATATAATTGACCCACTTGGGGACCGGGCCATACACATCCGGCATTTTCGAAACATTCCTTTGGCAGACATGGAGCTTGTGCTTgtaagttgtcaatgtctatacttcacacctgtatgtc-ttaggtcagggtacaaagccttcaaaatatgcaagtatgatatattttgcattttcttcggtg

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|86055111|gb|DR350868.1|DR350868
EST:     ACGTTAAGCATTTCAAAAACATTCCTATGGCTGACATGGAGATTGTGCTT                         CCTGAGAAAAGAAACCCTGGACTGACTCCAATGGATTGGGTCAAATTTCTA
genomic: ACGTTAAGCATTTCAAAAACATTCCTATGGCTGACATGGAGATTGTGCTTgtaagtttct ... tcttgtgcagCCTGAGAAAAGAAACCCTGGACTGACTCCAATGGATTGGGTCAAATTTCTA




















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACGAGCTAGCTCTAAAACAAATCTAGAACGAGGAATCTACGTTAAGCATTTCAAAAACATTCCTATGGCTGACATGGAGATTGTGCTTgtaagtttctgttcttgtcttctttccttttgcatcgctggattttgtagcgaaaattgcaaactagctgcaataacattaatgtcttgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT