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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactcgtatgctgtctgcattggagctgctattgattttgtctttaaaaacttccttcaatttttcaaaaatcttcatccaacagttttttacttaatacttgacatctagGCTTGAGAATACATTGAACTATGGCCTTGAGAGGGTTTGGGCTATTGGACACATTAAAGGTTCACGCCG

Basic information

species Arabidopsis thaliana
transcript AT1G79990.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM2G443953_T01 (Zea mays), 3'ss of exon 9
gtaactcgtatgctgtctgcattggagctgctattgattttgtctttaaaaactt-ccttcaatttttcaaaaatcttcatccaacagttttttacttaatacttgacatctagGCTTGAGAATACATTGAACTATGGCCTTGAGAGGGTTTGGGCTATTGGACACATTAAAGGTTCACGCCG
                   | ||| ||||  || |  ||||   ||  ||   |  | ||  ||||     |||| |      |||| | |  |   |  | |||| | | |||||||||||||||| | ||||||||||||||  | ||||||||  | ||  |||| || || |||||  |
-------------gacagaccttgaagcttttactctttttaggttacaagtttaacttttcatttcatggaaatttggtagtaacattgtgattggtgct-cttgtcttttagGCTTGAGAATACACTTAACTATGGCCTTGAACGAGTTTGGGCATTAGGTTACATGAAGGGCTCACGAAG

upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM2G419984_T01 (Zea mays), 3'ss of exon 7
gtaactcgtatgctgtctgcattggagctgctattgattttgtctttaaaaacttccttcaatttttcaaaaatcttcatccaacagttttttacttaatacttgacatctagGCTTGAGAATACATTGAACTATGGCCTTGAGAGGGTTTGGGCTATTGGACACATTAAAGGTTCACGCCG
| ||   ||    |       |  || | || | |  | |||   || | ||  || |       | |  | || ||| |      ||||| ||  |   |||   | | ||| |||||||| ||| | ||||||||||||||||| || |||||| ||||| |||| || || ||  |  |
ggaaaatgttctatactaatttctgaac-gccacttgtgttgctctttataatctcata------tcctgagatgttcttt-----gttttatatcttgaactattc-tgtagACTTGAGAACACACTAAACTATGGCCTTGAGAGAGTCTGGGCTGTTGGATACATGAAGGGGTCTAGAAG

upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM2G095348_T02 (Zea mays), 3'ss of exon 7
gtaactcgtatgctgtctgcattggagctgctattgattttgtctttaaaaacttccttcaatttttcaaaaatcttcatccaacagttttttacttaatacttgacatctagGCTTGAGAATACATTGAACTATGGCCTTGAGAGGGTTTGGGCTATTGGACACATTAAAGGTTCACGCCG
  |  || ||| |||  ||  |  ||| ||||  |  | ||    || | || |||     ||  | | ||  | ||| |      ||||| |||||   |||     | ||| |||||||| ||| | ||||||||||||||||| || |||||| ||||| |||| || || ||| |  |
--atatcctatactggttgagtccgag-tgctgcttgtgttactctttataatttc-----ataatcctaaggtgttcttt-----gttttatactttgaactatttttgtagACTTGAGAACACACTAAACTATGGCCTTGAGAGAGTCTGGGCTGTTGGATACATGAAGGGATCAAGAAG

upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM2G000645_T02 (Zea mays), 3'ss of exon 8
gtaactcgtatgctgt-ctgcattggagctgctattgattttgtctttaaaaacttccttcaatttttcaaaaatcttcatccaacagttttttacttaatacttgacatctagGCTTGAGAATACATTGAACTATGGCCTTGAGAGGGTTTGGGCTATTGGACACATTAAAGGTTCACGCCG
 |      | | || | |||  ||      || | |  | |||   || | ||  || | |          | || ||| |      ||||| ||  |   |||   | | ||| |||||||| ||| | ||||||||||||||||| || |||||| ||||| |||| || || ||  |  |
ctggaaaatgttctatactgatttctgaacgccacttgtgttgctctttataatctcatcctg--------agatgttcttt-----gttttatatcttgaactattc-tgtagACTTGAGAACACACTAAACTATGGCCTTGAGAGAGTCTGGGCTGTTGGATACATGAAGGGGTCTAGAAG

upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA07G03890.1 (Glycine max), 3'ss of exon 8
gtaactcgtatgct-gtctgcattggagctgctattgattttgtctttaaaaacttccttcaatttttcaaaaatcttcatccaacagttttttacttaatacttgacatctagGCTTGAGAATACATTGAACTATGGCCTTGAGAGGGTTTGGGCTATTGGACACATTAAAGGTTCACGCCG
 | ||  || |    |  | ||    |  |  | ||||  |||   |||   |  |  | || |  |    |||| || ||      ||  |  | |   | ||||      ||||||||||| |||||||||||||| ||||| || ||||||||||||||| |  | || |||||||||||
-ttacatgtttttaagatttcaccaaaattagt-ttgaaattgagattatggatatattccagtcatctttaaatttttat-----ggtggtgcaatc--tgcttg-----cagGCTTGAGAACACATTGAACTATGGTCTTGAAAGAGTTTGGGCTATTGGATATCTGAAGGGTTCACGCCG

upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 8
gtaactcgtatgctgtctgcattggagctgctattgattttgtctttaaaaacttccttcaatttttcaaaaatct-tcatccaacagttttt-tactta-atacttgacatctagGCTTGAGAATACATTGAACTATGGCCTTGAGAGGGTTTGGGCTATTGGACACATTAAAGGTTCACGCCG
               | | |||   |  |    |||| ||    ||| |||  |  ||   ||| |  | | |||| ||||     | ||||| |  ||   || |   | |  ||||||||||| |||||||||||| | ||||| || ||||||||||||||| || | || |||||||| ||
--------------tttttcataacatttctccttgaatta--ttttgaaatatatctgagattatggatatatctgtcatttttaaatttttatggttgtgtaatatgcttgcagGCTTGAGAACACATTGAACTATAGTCTTGAAAGAGTTTGGGCTATTGGATACCTGAAGGGTTCACGTCG

upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 8
gtaactcgtatgctgtctgcattggagctgctattgattttgtctttaa--aaacttccttcaatttttcaaaaatcttcatccaacagttttttacttaatacttgacatctagGCTTGAGAATACATTGAACTATGGCCTTGAGAGGGTTTGGGCTATTGGACACATTAAAGGTTCACGCCG
             |  | |  ||  ||||| || | | |||   |  ||  | ||||  |   || | |   || ||| |||   |   ||| |   | |||   |  | |  ||||||||||| ||||| |||||||| ||||| || || |||||||||||| || | ||  |||| || ||
------------tttacagtttttaagctgttactaaatttagttggaagtatactttgtaagatatatactaattctccattttaatttttatggttcaat---ttgcttgcagGCTTGAGAACACATTAAACTATGGTCTTGAAAGAGTCTGGGCTATTGGATACTTGAAGAGTTCTCGTCG

upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 8
gtaactcgtatgctgtctgca---ttggagctgctattgattttgtctttaaaaacttccttcaatttttcaaaaatcttcatccaacagttttttacttaatacttgacatctagGCTTGAGAATACATTGAACTATGGCCTTGAGAGGGTTTGGGCTATTGGACACATTAAAGGTTCACGCCG
 ||  |  | | | || | ||   ||  ||||| || | | |  ||  ||  ||   |      |||||  || |      ||  |  | || |  | ||   | |  |  |  ||||||||||| ||||| |||||||| ||||| || || |||||||||||| || | ||  |||| || ||
ctattttattt-ccgtttacagtttttaagctgatactaaat--gtagttggaagtat------attttggaaga-----tatatactaattctccattt--caatgtatttgcagGCTTGAGAACACATTAAACTATGGTCTTGAAAGAGTCTGGGCTATTGGATACTTGAAGAGTTCTCGTCG

upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 8
gtaactcgtatgctgtctgcattgg-agctgctat-tgattttgtctttaaaaacttccttcaatttttcaaaaatcttcatccaacagttttttacttaatacttgacatctagGCTTGAGAATACATTGAACTATGGCCTTGAGAGGGTTTGGGCTATTGGACACATTAAAGGTTCACGCCG
        | | ||   || | ||  || || ||  |||||    ||||| |   ||     | | |||    ||| | |  |  || |    ||  | | ||  |       ||||| ||||| || ||||| ||||| ||||| || ||||||||| ||||| |||| ||||||||||||||
----tgttttttcttaatgtagtgatagatgatagatgattaaacctttagag--ttatgctagtcttt----aatttccgacagactgaaccttcttcattaacta-----cagGCTCGAGAACACGTTGAATTATGGTCTTGAAAGAGTTTGGGCTGTTGGATACATGAAAGGTTCACGCCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaatttttcaaaaatcttcatccaacagttttttacttaatacttgacatctagGCTTGAGAATACATTGAACTATGGCCTTGAGAGGGTTTGGGCTATTGGACACATTAAAGGTTCACGCCG
                                          acttgac  putative branch site (score: 4)
                             ttttttacttaatact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaactcgtatgctgtctgcattggagctgctattgattttgtctttaaaaacttccttcaatttttcaaaaatcttcatccaacagttttttacttaatacttgacatctagGCTTGAGAATACATTGAACTATGGCCTTGAGAGGGTTTGGGCTATTGGACACATTAAAGGTTCACGCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG