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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactaaattaaactatatctagatagtattaatgaccttcaattttctatagtaatcacattttgcttatattatacagGGCTTATTGAATTAGCCATAAAGAGAAACTGCTTGATCGGTGGTGATGACTTCAAGAGTGGTCAGACCAAGATGAAGTCTGTCCTCGTCGATTTCCTTGT

Basic information

species Arabidopsis thaliana
transcript AT5G10170.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G10170.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os10g22450.1 (Oryza sativa), 3'ss of exon 5
-------------------------gtaac-taaattaa--actatatctagatagtatta-atgaccttcaattttctatagtaatcacattttgcttatat-tatacagGGCTTATTGAATTAGCCATAAAGAGAAACTGCTTGATCGGTGGTGATGACTTCAAGAGTGGTCAGACCAAGATGAAGTCTGTCCTCGTCGATTTCCTTGT
                           | | |  |||||  || |   | ||| | | ||  ||||    |   ||  ||   | |  |   | |||| ||   |  |||||||| || ||  | ||||| ||||  ||||   ||||||| || || |||||||||||||| ||||||||||||||||| ||||||||||| ||||| ||
gtgcgccgcccgccgtctgctagctacatcctccattaacgacgacgacgagacattgtttcatgaatcccg--ttcttaggttgacgatgatgtgctgatgcatggacagGGCTGATCGAGCTCGCCATCAAGAAGAACTCGGTGATCGGCGGCGACGACTTCAAGAGTGGGCAGACCAAGATGAAGTCCGTCCTCGTCGACTTCCTCGT

upper sequence: AT5G10170.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os03g09250.2 (Oryza sativa), 3'ss of exon 5
gtaactaaattaaactatatctagatagtattaatgaccttcaattttctatagtaatcacat-tttgcttatattatacagGGCTTATTGAATTAGCCATAAAGAGAAACTGCTTGATCGGTGGTGATGACTTCAAGAGTGGTCAGACCAAGATGAAGTCTGTCCTCGTCGATTTCCTTGT
        ||  || | | | |  | |||| || ||   || | |||   |   | ||  | | |||| |||   | ||||||||| || ||  | || || ||||  |||||| |||| ||||||||||| ||||||||||| ||||| ||||||||||||||| | || |||||||| ||
------gtatgtaattttctgtgtagagtagta-tgcggtttattttctcaggttcatggcttatttgtttactgtgtacagGGCTGATCGATCTTGCTATTAAGAACAACTGCCTGATTGGTGGTGATGATTTCAAGAGTGGACAGACAAAGATGAAGTCTGTCTTGGTTGATTTCCTAGT

upper sequence: AT5G10170.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G155242_T01 (Zea mays), 3'ss of exon 5
-----------------------gtaactaaattaaactatatctagatagta----ttaatgaccttcaattttctatagtaatcacattttgcttatattatac----agGGCTTATTGAATTAGCCATAAAGAGAAACTGCTTGATCGGTGGTGATGACTTCAAGAGTGGTCAGACCAAGATGAAGTCTGTCCTCGTCGATTTCCTTGT
                         | ||  ||     |  || |   |   |    || |||   ||  ||||    |   |  |  ||| | | | |   ||      |||||| |||||  | || ||||| |  ||||||||||| |||||||| |||||||||||||| |||||||||||||| |||||| | ||||||||||||||
gtgcgtggtttggtgtgtttgcaaaagcttcatggtgttgcatttctgttccaaagtttcatggtgttgtatttctgttccaaggcttattatacctgttgcatgttcgtagGGCTGATTGATCTTGCTATAAAAAACAACTGCTTGATTGGTGGTGACGACTTCAAGAGTGGACAGACCAAGATGAAATCTGTCTTGGTCGATTTCCTTGT

upper sequence: AT5G10170.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G004528_T03 (Zea mays), 3'ss of exon 5
--gtaactaaattaaactatatctagatagtattaatgaccttcaattttctatagtaatcacattttgcttatatta----tacagGGCTTATTGAATTAGCCATAAAGAGAAACTGCTTGATCGGTGGTGATGACTTCAAGAGTGGTCAGACCAAGATGAAGTCTGTCCTCGTCGATTTCCTTGT
  ||   ||  ||    | |  | | |  || |||  |   | ||  | | |  |  || |  ||| | ||| | | |    |  |||||| |||||  | || || ||||  |||||| ||||||||||||| |||||||||||||| |||||||||||||| || ||||| || ||||| |||||
gtgtgtttagtttggtgtgttcccaaa--gttttatggtgttgcatctctgttcaaaaaacttattatacttgtttcatgtttgtagGGCTGATTGATCTTGCTATCAAGAACAACTGCCTGATCGGTGGTGACGACTTCAAGAGTGGGCAGACCAAGATGAAATCGGTCCTGGTTGATTTTCTTGT

upper sequence: AT5G10170.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G392513_T02 (Zea mays), 3'ss of exon 3
------------------gtaactaaattaaactatatctagatagtattaatgaccttcaattttctatagtaatcacattttgc---ttatat-tatacagGGCTTATTGAATTAGCCATAAAGAGAAACTGCTTGATCGGTGGTGATGACTTCAAGAGTGGTCAGACCAAGATGAAGTCTGTCCTCGTCGATTTCCTTGT
                  ||   ||  ||    | | | |  | ||| ||| ||   ||  ||||    |   |  |  ||| | |   ||  || | |  |||||| |||||  | || || ||||  |||||| ||||||||||||| |||||||||||||| |||||||||||||| || ||||| || || ||||| ||
aacacttttgtgcctggtgtgtttagtttgg--tgtgtttgcaaagtttta-tggtgttgcatttctgttcaaagacttattatacgtgttgcatgtttgtagGGCTGATTGATCTTGCTATCAAGAACAACTGCCTGATCGGTGGTGACGACTTCAAGAGTGGGCAGACCAAGATGAAATCAGTCCTAGTTGAATTCCTAGT

upper sequence: AT5G10170.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G392513_T01 (Zea mays), 3'ss of exon 1
--gtaactaaattaaactatatctagatagtattaatgaccttcaattttctatagtaatcacattttgc---ttatat-tatacagGGCTTATTGAATTAGCCATAAAGAGAAACTGCTTGATCGGTGGTGATGACTTCAAGAGTGGTCAGACCAAGATGAAGTCTGTCCTCGTCGATTTCCTTGT
  ||   ||  ||    | | | |  | ||| ||| ||   ||  ||||    |   |  |  ||| | |   ||  || | |  |||||| |||||  | || || ||||  |||||| ||||||||||||| |||||||||||||| |||||||||||||| || ||||| || || ||||| ||
gtgtgtttagtttgg--tgtgtttgcaaagtttta-tggtgttgcatttctgttcaaagacttattatacgtgttgcatgtttgtagGGCTGATTGATCTTGCTATCAAGAACAACTGCCTGATCGGTGGTGACGACTTCAAGAGTGGGCAGACCAAGATGAAATCAGTCCTAGTTGAATTCCTAGT

upper sequence: AT5G10170.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G145638_T02 (Zea mays), 3'ss of exon 1
--gtaactaaattaaactatatctagatagtattaatgaccttcaattttct----atagtaatcacattttgcttatattatacagGGCTTATTGAATTAGCCATAAAGAGAAACTGCTTGATCGGTGGTGATGACTTCAAGAGTGGTCAGACCAAGATGAAGTCTGTCCTCGTCGATTTCCTTGT-
  ||   ||  ||    | | | |  | ||| |||  |   | || || | |    | | | || | | ||     || || |  |||||| |||||  | || || ||||  |||||| ||||||||| ||| |||||||||||||| |||||||||||||| || ||||| || ||||||||||| 
gtgtgtttagtttgg--tgtgtttgcaaagttttatggtgttgcatttctgttcaaagacttattatacttgttgcatgtt-tgtagGGCTGATTGATCTTGCTATCAAGAACAACTGCCTGATCGGTGTTGACGACTTCAAGAGTGG-CAGACCAAGATGAAATCAGTCCTGGTTGATTTCCTTGTT

upper sequence: AT5G10170.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G177461_T01 (Zea mays), 3'ss of exon 5
gtaactaaattaaactatatctagatagtattaatgaccttcaattttctatagtaatcacattttgcttatattatacagGGCTTATTGAATTAGCCATAAAGAGAAACTGCTTGATCGGTGGTGATGACTTCAAGAGTGGTCAGACCAAGATGAAGTCTGTCCTCGTCGATTTCCTTGT
     |   |    ||  | ||| | | | |||      |  | ||   | | ||| | |  ||  | | ||     |||||||| || ||  | |||||||| |  || |   |||| || || || ||||| |||||||| ||||||||||||||||||||  | ||||||||||| ||
----gtgcgtagcgctgca-ctacaaaattttacatgtgtgtatttgcttgt-gtagtaatgttcagttcatgc---acagGGCTGATGGAGCTTGCCATAAAAAAGAATTCGGTGATAGGAGGCGACGACTTTAAGAGTGGGCAGACCAAGATGAAGTCTGTGTTGGTCGATTTCCTCGT

upper sequence: AT5G10170.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA18G02210.4 (Glycine max), 3'ss of exon 5
----gtaactaaattaaactatatctagatagtattaatgaccttcaattttctatagtaatcacattttgcttatattata-----cagGGCTTATTGAATTAGCCATAAAGAGAAACTGCTTGATCGGTGGTGATGACTTCAAGAGTGGTCAGACCAAGATGAAGTCTGTCCTCGTCGATTTCCTTGT
    |   ||    |  |      |   | |   | |||    |  | || |    | |  | |  ||| | || | || |      ||||||| |||||  | |||||   ||| |||   ||||| ||||| |||||||||||||||||||||||||| ||||| |||||  | || ||||| |||||
gttggatgcttgcctttatgtcccccccacaacttaaattgtttgtatttatgctaatttgtgaactttggtttgtgttgttgtcatcagGGCTGATTGATCTTGCCATCGCGAGGAACACTTTGATTGGTGGAGATGACTTCAAGAGTGGTCAGACCAAAATGAAATCTGTGTTGGTTGATTTTCTTGT

upper sequence: AT5G10170.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA05G31450.2 (Glycine max), 3'ss of exon 5
-gtaactaaattaaactatatctagatagtattaatgaccttcaattttctatagtaatcacatt--------ttgctt---atattatacagGGCTTATTGAATTAGCCATAAAGAGAAACTGCTTGATCGGTGGTGATGACTTCAAGAGTGGTCAGACCAAGATGAAGTCTGTCCTCGTCGATTTCCTTGT
  | | ||      | |||   ||  | |  ||| | |  || | || |  | | |||  | |||        ||||||    | ||   ||||||| |||||  | ||||| ||||| ||| | ||||| || || |||||||| ||||||||||||||||| ||||| |||||  | || |||||||||||
gttcattattgattattattattatgtgg-gttattaaattttatttatgcaaaataaataaattggtgaattttgctttgtgttttcgtcagGGCTGATTGATCTGGCCATCAAGAGGAACAGTTTGATTGGAGGAGATGACTTTAAGAGTGGTCAGACCAAAATGAAATCTGTGTTGGTGGATTTCCTTGT

upper sequence: AT5G10170.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv07s0031g00920.t01 (Vitis vinifera), 3'ss of exon 5
-----------------------------gtaactaaattaaactatatctagatagtattaatgaccttcaattttctatagtaatcacattttgcttatattatacagGGCTTATTGAATTAGCCATAAAGAGAAACTGCTTGATCGGTGGTGATGACTTCAAGAGTGGTCAGACCAAGATGAAGTCTGTCCTCGTCGATTTCCTTGT
                             || |      | || |     ||||  |      | | ||      |  | | ||  |||   ||||  | | ||   ||||||| ||||| || || || ||||| ||  | ||||| ||||| ||||| || ||||||||||| ||||||||||| |||||  | || |||||||||||
gttcttaatctgaaattttccttttctatgtgaaggttatgaattcatcatagagggggcgtctaatctcactcatgtttttgttgtcaatctttgtatgtctt---cagGGCTGATTGATTTGGCTATTAAGAGGAATAGTTTGATTGGTGGGGATGATTTTAAGAGTGGTCAAACCAAGATGAAATCTGTATTGGTGGATTTCCTTGT

upper sequence: AT5G10170.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S267_10V6.1 (Physcomitrella patens), 3'ss of exon 5
gtaactaaattaaact----atatctagatagtattaatgaccttcaattttct-atagtaatcacattttgcttatatt--------------atacagGGCTTATTGAATTAGCCATAAAGAGAAACTGCTTGATCGGTGGTGATGACTTCAAGAGTGGTCAGACCAAGATGAAGTCTGTCCTCGTCGATTTCCTTGT
|  ||| | |  | |     | | || |||    |      ||   ||||  || |||    | ||| |  | |||| |                | ||||  | ||||| |  ||  || |||  || |   | || || ||||||||||||||||| || || ||||||||||| ||||| || || || ||||| ||
gcgacttattcgagcatctgaaaccttgatgaggtctgcttccgaaaattccctcataaacttaacagtgcgtttatgtatatcgggaactttggtgcagGCGTAATTGAGTACGCTGTAGAGAAGAAATCTCTTATTGGCGGTGATGACTTCAAGAGCGGACAAACCAAGATGAAATCTGTGCTTGTGGACTTCCTCGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtattaatgaccttcaattttctatagtaatcacattttgcttatattatacagGGCTTATTGAATTAGCCATAAAGAGAAACTGCTTGATCGGTGGTGATGACTTCAAGAGTGGTCAGACCAAGATGAAGTCTGTCCTCGTCGATTTCCTTGT
  tattaat  putative branch site (score: 2)
                                   attttgcttatattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaactaaattaaactatatctagatagtattaatgaccttcaattttctatagtaatcacattttgcttatattatacagGGCTTATTGAATTAGCCATAAAGAGAAACTGCTTGATCGGTGGTGATGACTTCAAGAGTGGTCAGACCAAGATGAAGTCTGTCCTCGTCGATTTCCTTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG