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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTTATTGAGTATAGGGCACATCCCTTTTGGATGCAAAAGTATTGTCCTTCACATGAGCGTGATGGAACTCCTCGGTGTTGCAGTTGTGAGCGAATGGAGgtcagttgttcgatatagcatttctgttaataggaaaataaatttaagaatctgattcgaaaaccagatgttgttctgtttttggctcatggtttcag

Basic information

species Arabidopsis thaliana
transcript AT4G36860.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G36860.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: LOC_Os12g40490.1 (Oryza sativa), 5'ss of exon 9
TCTTATTGAGTATAGGGCACATCCCTTTTGGATGCAAAAGTATTGTCCTTCACATGAGCGTGATGGAACTCCTCGGTGTTGCAGTTGTGAGCGAATGGAGgtcagttgttcgatatagcatttctgttaa--taggaaaataaatttaagaat-ctgattcgaaaaccagatgttgttctgtttttggctcatggtttcag-
 || || || ||  | |||||||| || |||||||||||||| |||||||| |||||   |||||| |||||| ||||||||||||||||  ||||||||||||||     ||| |||    ||  | |    ||       |  ||   | | ||  |||    |  |||       | ||||| | ||     ||  |  
GCTGATCGAATACCGAGCACATCCATTCTGGATGCAAAAGTACTGTCCTTCCCATGAAGATGATGGCACTCCTAGGTGTTGCAGTTGTGAAAGAATGGAGgtcagtgcagggatctagatcctcaatgagaccagtttccccagcttgtcacttcttgttcctggaa-agaaaccagccagtttt-gactaccatttggaaa

upper sequence: AT4G36860.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: LOC_Os03g42820.2 (Oryza sativa), 5'ss of exon 9
TCTTATTGAGTATAGGGCACATCCCTTTTGGATGCAAAAGTATTGTCCTTCACATGAGCGTGATGGAACTCCTCGGTGTTGCAGTTGTGAGCGAATGGAGgtcagt--tgttcgatatagcatttctgttaataggaaaataaatttaagaatctgattcgaaaaccagatgttgttctgtttt-tggctcatggtttcag
 |  ||||| ||| |||| ||||| || |||||||| |||||||||||| | |||||   |||| | |||||| |||| ||||||||||| |||||||||||  ||  | | | ||| |  | || |     |||  |   ||||  |||  || |  | | ||   | |  | |   ||||   |     |       ||
CCACATTGAATATCGGGCCCATCCTTTCTGGATGCAGAAGTATTGTCCTGCCCATGAAACTGATCGTACTCCTAGGTGCTGCAGTTGTGAACGAATGGAGgtttgtgctatcctataaaaaagttatacatgtagtgattcaaatggaagtgtcaggat-gtaactaacacttcggcatgttccctcaacaaaaaaaatag

upper sequence: AT4G36860.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GRMZM2G099328_T04 (Zea mays), 5'ss of exon 8
TCTTATTGAGTATAGGGCACATCCCTTTTGGATGCAAAAGTATTGTCCTTCACATGAGCGTGATGGAACTCCTCGGTGTTGCAGTTGTGAGCGAATGGAGgtcagttgttcgatatagcatttctgttaataggaaaataaatttaagaatctgattcgaaaaccagatgttgttctgtttttggc-tcatggtttcag-------
 || ||||| ||  | |||||||| || |||||||| ||||| |||||||| |||||   |||||| ||||||||||| ||||||||||| |||||||||||||||       | |   || ||||| |||  |        |||     |   ||||   |    || |  | || ||| | |   | | ||   ||        
CCTCATTGAATACCGAGCACATCCTTTCTGGATGCAGAAGTACTGTCCTTCCCATGAAGATGATGGCACTCCTCGGTGCTGCAGTTGTGAACGAATGGAGgtcagtaaa--agttttctatatctgtcaatgagt---cctgtttccctgttcaattcctga-ttggaagccgctcagttatggttattacggcaccacgacgagc

upper sequence: AT4G36860.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GRMZM2G342105_T02 (Zea mays), 5'ss of exon 4
TCTTATTGAGTATAGGGCACATCCCTTTTGGATGCAAAAGTATTGTCCTTCACATGAGCGTGATGGAACTCCTCGGTGTTGCAGTTGTGAGCGAATGGAGgtcagttgttcgatatagcatttctgttaataggaaaataaatttaagaatctg-attcgaaaaccagatgttgttctgtttttggctcatggtttcag-----
 || ||||| ||  |||| ||||| ||||||||||| |||||||||||||| |||||   |||||| || ||| |||| ||||||||||| ||||||||||| |||  |  | |     |  |    |||||   | ||| || ||   || |  ||    | |     | ||| |   ||  |     ||    |  |     
CCTCATTGAATACCGGGCCCATCCTTTTTGGATGCAGAAGTATTGTCCTTCCCATGAAAATGATGGTACACCTAGGTGCTGCAGTTGTGAACGAATGGAGgttagtgttatgtt----tacatacaataatatatatatatatatatatatatatatatatatatatattattgatggattcataaaaaataaaatgtggatcc

upper sequence: AT4G36860.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GRMZM2G017845_T02 (Zea mays), 5'ss of exon 6
TCTTATTGAGTATAGGGCACATCCCTTTTGGATGCAAAAGTATTGTCCTTCACATGAGCGTGATGGAACTCCTCGGTGTTGCAGTTGTGAGCGAATGGAGgtcagttgttcgatatagcatttctgttaataggaaaataaatttaagaatc-tgattcgaaaaccagatgt-tgttctgtttttggctcatg--gtttcag---------------------
 |||||||| |||||||||||||| || ||| | ||||| || ||||||||||||||    ||||| |||||  |||| || ||||||||  ||||||||||  |    |    ||    ||| | |||||  |    |      |    || || || ||| |     | | |||      ||||| ||||    || ||                      
CCTTATTGAATATAGGGCACATCCTTTCTGGGTACAAAAATACTGTCCTTCACATGAAATGGATGGTACTCCGAGGTGCTGTAGTTGTGAAAGAATGGAGgtaggccagttagcatg---tttttcttaatttggtcttgtgggcatatttcatggttagaagagagcctctgtgtgtgaaatttggatcatttcattccaacatggtttgttcacttaccag

upper sequence: AT4G36860.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA12G19010.1 (Glycine max), 5'ss of exon 6
TCTTATTGAGTATAGGGCACATCCCTTTTGGATGCAAAAGTATTGTCCTTCACATGAGCGTGATGGAACTCCTCGGTGTTGCAGTTGTGAGCGAATGGAGgtcagttgttcgatatagcatttctgttaataggaaaataaatttaagaatctgattcgaaaa----ccagatgttgttctgtttttggctcatggtttcag--------------------------------
||| ||||||||||| |||||||| || ||| | ||||| |||||||| || |||||||||||||| |||||||| ||||| || ||| |  || |||||||||||| |   | ||  ||  | | ||      |   |      || || | ||| |  |      |||  | |   ||  || || | |  ||  ||                                   
TCTCATTGAGTATAGAGCACATCCTTTCTGGCTACAAAAATATTGTCCATCGCATGAGCGTGATGGTACTCCTCGCTGTTGTAGCTGTCAAAGATTGGAGgtcagttatatcagatcacaaatttttttcataaattttgttaccaacaagcagatactgatgtatcccatctctcactcctttctttgtttttgtctttttcctttccgtatgaaactttccgatcatttcag

upper sequence: AT4G36860.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA02G06720.2 (Glycine max), 5'ss of exon 7
TCTTATTGAGTATAGGGCACATCCCTTTTGGATGCAAAAGTATTGTCCTTCACATGAGCGTGATGGAACTCCTCGGTGTTGCAGTTGTGAGCGAATGGAGgtcagttgttcgatatagcatt-tctgttaataggaaaataaatttaagaatctgattcgaaaa----ccagatgttgttctgtttttggctcatggtttcag--------------------------------
||| ||||||||||| |||||||| || ||| | ||||| |||||||| || |||||||||||||| |||||||| ||||| || ||| |  || |||||||||| | |   | ||  ||   | | ||  ||      |      || || | ||| |  |      |||  | |   ||  || || | |  ||  ||                                   
TCTCATTGAGTATAGAGCACATCCTTTCTGGCTACAAAAATATTGTCCATCGCATGAGCGTGATGGTACTCCTCGCTGTTGTAGCTGTCAAAGATTGGAGgtcagctatatcagatcacaaaattttttcgtaattttttgttaccaacaagcagatactgatgtatcccatctctcactcctttctttgtttttgtctttttcctttccgtatgaaactttccgatcagttcag

upper sequence: AT4G36860.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA16G25750.1 (Glycine max), 5'ss of exon 7
TCTTATTGAGTATAGGGCACATCCCTTTTGGATGCAAAAGTATTGTCCTTCACATGAGCGTGATGGAACTCCTCGGTGTTGCAGTTGTGAGCGAATGGAGgtcagttgttcgatatagcatttctgttaataggaaaataaatttaagaat--ctgattcgaaaaccagatgttgttc-tgtttttggctcatgg----tttcag---------
 || ||||||||||| |||||||| || |||   ||||| |||||||| || |||||| ||||||| |||||||| ||||| || ||| |  ||||||||||||||| |   |  |||||   |  || || |     |      || |||  || | ||        | | |||||  | |  ||  |  |||     || ||          
CCTCATTGAGTATAGAGCACATCCTTTCTGGCGACAAAAATATTGTCCATCGCATGAGGGTGATGGTACTCCTCGTTGTTGTAGCTGTCAAAGAATGGAGgtcagttatatcagctagcaaaacatttcatcgtttgttgttaccaacaatatctcactcctttctttgtttttgtttgtttccttttcatatgaaactttccaatcagtgcag

upper sequence: AT4G36860.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA01G38640.1 (Glycine max), 5'ss of exon 6
TCTTATTGAGTATAGGGCACATCCCTTTTGGATGCAAAAGTATTGTCCTTCACATGAGCGTGATGGAACTCCTCGGTGTTGCAGTTGTGAGCGAATGGAGgtcagttgttcgatatagcatttctgttaataggaaaataaatt-taagaatctgattcgaaaaccagatgttgttctgtttttggctcatggtttcag-------------------------
||| ||||||||||| || ||||| || ||| | ||||| || || || |||||||||| |||||| |||||||| ||||| || || ||  ||||||||||||||| |   |  |  ||  ||| || ||   |  || ||   | |||| || | |     | |   |    | ||   |      | || |  |                           
TCTCATTGAGTATAGAGCTCATCCTTTCTGGCTACAAAAATACTGCCCATCACATGAGCTTGATGGCACTCCTCGTTGTTGTAGCTGCGAAAGAATGGAGgtcagttatattagctcccaaatcttttcatcctattattaacaattagaagctaactgatggatcccttcccctcctccctccattccctg-tcccgttttcttgccttttcaatcagtgcag

upper sequence: AT4G36860.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA11G06650.2 (Glycine max), 5'ss of exon 3
TCTTATTGAGTATAGGGCACATCCCTTTTGGATGCAAAAGTATTGTCCTTCACATGAGCGTGATGGAACTCCTCGGTGTTGCAGTTGTGAGCGAATGGAGgtcagttgt-tcgat--------------atagcatttctgttaataggaaaataaatttaagaatctgattcgaaaaccagatgttgttctgtttttggctcatggtttcag---------
 || ||||||||||| || ||||| || ||| | ||||| || || || |||||||||| |||||| ||| |||| ||||| ||||| ||  |||||||||| |||| | | ||               ||   |||  | | |||  |||  ||| | |  ||  ||   ||     ||     |   | |    ||  ||     |||||          
CCTCATTGAGTATAGAGCTCATCCTTTCTGGCTACAAAAATACTGCCCATCACATGAGCTTGATGGCACTTCTCGTTGTTGTAGTTGCGAAAGAATGGAGgttagttatattgactcccaaatcttttcatcctattattatcaattagaagctaactgttggatccttcctctcctccccccattccctgtcccgttttcttgccttttcaatcaatgcag

upper sequence: AT4G36860.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: Vv04s0023g01040.t01 (Vitis vinifera), 5'ss of exon 11
TCTTATTGAGTATAGGGCACATCCCTTTTGGATGCAAAAGTATTGTCCTTCACATGAGCGTGATGGAACTCCTCGGTGTTGCAGTTGTGAGCGAATGGAGgtcagttgttcga---tatagcatttc--------tgttaataggaaaataaatttaagaatctgat---tcgaaaaccagatgttgttctgtttttggctcatggtttcag--------------------------
    |  |||||||| |||||||| || ||||||||| |||| ||||| |||||||||| ||||||||||||||||||||| |||||||| ||||  ||||| |||||   ||   || | | |  |        |  | |  | | ||    | |   |   |||    |  | ||| | |  |  |||| ||||| | |     ||||                            
AGAAACAGAGTATAGAGCACATCCTTTCTGGATGCAAGAGTACTGTCCCTCACATGAGCATGATGGAACTCCTCGGTGTTGTAGTTGTGAACGAACAGAGgttagttggaagaaaatacaacctcccatcccacatactcactgaagaaatcttctcgtagcttgacagattaacaactacagat--ttctatttttcgttttgtatttctttatagaaaatctgccaacccatgcag

upper sequence: AT4G36860.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: Vv04s0023g01030.t01 (Vitis vinifera), 5'ss of exon 8
TCTTATTGAGTATAGGGCACATCCCTTTTGGATGCAAAAGTATTGTCCTTCACATGAGCGTGATGGAACTCCTCGGTGTTGCAGTTGTGAGCGAATGGAGgtcagttgttcga---tatagcatttctgttaata------ggaaaataaatttaagaatctgattcgaaa-accagatgt----tgttctgtttttggctcatggtttcag---------------------
 |||||||||||||| |||||||| || |||||||||||||| ||||| ||||| |||| ||||||||||||||||||||| ||||||||  |||||||||| |||||   ||   || | |    |     | |      | | ||    | |   |   ||||   ||| | ||||| |    | ||   |||||||    |  ||   |                     
ACTTATTGAGTATAGAGCACATCCGTTCTGGATGCAAAAGTACTGTCCCTCACACGAGCATGATGGAACTCCTCGGTGTTGTAGTTGTGAAAGAATGGAGgttagttggaagaagatacaaccccccatcccacacacactgaagaaatcttcttgtagcttgatgataaacaacagatctctaatttttcttttttggtatttctttatggaaaatctgccaacccatgcag

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|164064005|gb|ES117914.1|ES117914
EST:     AACTCCTCGGTGTTGCAGTTGTGAGCGAATGGAG                         CCAAAAGATACAAAATATCTCATTCTTGATGATGGTCGAAAACTGTGTCTT
genomic: AACTCCTCGGTGTTGCAGTTGTGAGCGAATGGAGgtcagttgtt ... atggtttcagCCAAAAGATACAAAATATCTCATTCTTGATGATGGTCGAAAACTGTGTCTT
EST: gi|86086879|gb|DR382638.1|DR382638
EST:     CACATGAGCGTGATGGAACTCCTCGGTGTTGCAGTTGTGAGCGAATGGAG                         CCAAAAGATACAAAATATCTCATTCTTGATGATGGTCGAAAACTGTGTCTT
genomic: CACATGAGCGTGATGGAACTCCTCGGTGTTGCAGTTGTGAGCGAATGGAGgtcagttgtt ... atggtttcagCCAAAAGATACAAAATATCTCATTCTTGATGATGGTCGAAAACTGTGTCTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTTATTGAGTATAGGGCACATCCCTTTTGGATGCAAAAGTATTGTCCTTCACATGAGCGTGATGGAACTCCTCGGTGTTGCAGTTGTGAGCGAATGGAGgtcagttgttcgatatagcatttctgttaataggaaaataaatttaagaatctgattcgaaaaccagatgttgttctgtttttggctcatggtttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC