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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacaaaatgcaactaatgatagttacttttctgaaggaaatggtgctgacgatataagtttttgtaaccagGGTGAGTATCCATGAAGCCATGGAACAACAGAGTATTAGTATATCGAAGGCAGGAATAGTTACTTCTCTTCAAGCTCGTTGCTCTGTTATTGCTGCAGCT

Basic information

species Arabidopsis thaliana
transcript AT1G44900.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G44900.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os11g29380.1 (Oryza sativa), 3'ss of exon 11
gta-acaaaatgcaact--aatgatagttacttttctgaagg-aaatggtgctgac--gatataagtttttgtaa-----ccagGGTGAGTATCCATGAAGCCATGGAACAACAGAGTATTAGTATATCGAAGGCAGGAATAGTTACTTCTCTTCAAGCTCGTTGCTCTGTTATTGCTGCAGCT
|||     ||| | | |   || ||   | |||||  | |   |  |  |  || |   | |||  ||| | | |      |||||||||||| ||||| |||||||| ||||| ||||| |||||||| ||||| ||||| || || || ||||||||||| |||  ||||||||||||||| 
gtatgtgtaataccatttggataatgtgtgcttttaagcatttatgttctattgccctaagatatctttctcttattgtttcagGGTGAGTATTCATGAGGCCATGGAGCAACAAAGTATCAGTATATCAAAGGCCGGAATTGTCACATCCCTTCAAGCTCGGTGCAGTGTTATTGCTGCAGCA

upper sequence: AT1G44900.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G139894_T02 (Zea mays), 3'ss of exon 11
-----gta-acaaaatgcaacta-atgatagttacttttctgaaggaaatggtgctgacgatataagttt-ttgtaac-----cagGGTGAGTATCCATGAAGCCATGGAACAACAGAGTATTAGTATATCGAAGGCAGGAATAGTTACTTCTCTTCAAGCTCGTTGCTCTGTTATTGCTGCAGCT
      || || |  || |  |  |||     | || ||   |      |  | |  |  || ||| ||| || | |      |||||| ||||| |||||||| ||||| ||||||||||| |||||||| || |||||||| || || |||||||||||| | |||  |||||||||||| || 
gtatgatataccatttgtatttggatgtcctgtgctatttaaatttctgtattaccaaaaatgtaattttcttctgattgtttcagGGTAAGTATTCATGAAGCTATGGAGCAACAGAGTATCAGTATATCAAAAGCAGGAATCGTCACATCTCTTCAAGCTAGATGCAGTGTTATTGCTGCGGCA

upper sequence: AT1G44900.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA17G03920.1 (Glycine max), 3'ss of exon 10
--------------------------------------gtaacaaaatgcaactaatgatagttacttt-tctgaaggaaatggtgctgac----gatataagtttttgtaaccagGGTGAGTATCCATGAAGCCATGGAACAACAGAGTATTAGTATATCGAAGGCAGGAATAGTTACTTCTCTTCAAGCTCGTTGCTCTGTTATTGCTGCAGCT
                                       | |||   |  |||||   |   | || |  | |  |  || |     ||||     || ||  ||||||| ||||||||||||||||||||||||||||| || |||||||| || ||||| || || ||||| ||||| |||||||| || || ||||||||||||||||| || 
gtaagaaaatcaatcttgtaattatttgaattttcctaattacattgttaaactac--accttcacatgatatacaaaaactatccttgaccattaatttatatttttgttaccagGGTGAGTATCCATGAAGCCATGGAGCAGCAGAGTATAAGCATATCAAAAGCTGGAATTGTTACATCTCTTCAGGCACGCTGCTCTGTTATTGCTGCTGCA

upper sequence: AT1G44900.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA07G36680.1 (Glycine max), 3'ss of exon 10
gtaacaaaatgcaactaatga--tagttacttttctgaaggaaatggt----gctgacga----------tataagtttttgtaaccagGGTGAGTATCCATGAAGCCATGGAACAACAGAGTATTAGTATATCGAAGGCAGGAATAGTTACTTCTCTTCAAGCTCGTTGCTCTGTTATTGCTGCAGCT
|||| |||||  | ||  | |     | | |||||| ||  | ||  |      |||  |          | ||  ||||||| ||||||||||| ||||||||||||||||| || |||||||| || ||||| || || ||||| ||||| |||||||| || || || |||||||||||||| || 
gtaagaaaattgaccttgtaaatccttgagttttcttaattacattattatccttgatcattaatttatatttatatttttgttaccagGGTGAGCATCCATGAAGCCATGGAGCAGCAGAGTATAAGCATATCAAAAGCTGGAATTGTTACATCTCTTCAGGCACGCTGTTCTGTTATTGCTGCGGCA

upper sequence: AT1G44900.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv01s0150g00390.t01 (Vitis vinifera), 3'ss of exon 10
gtaacaaaatgcaactaatgatagtt---------acttttctgaaggaaatggtgc----tgacgatataagtttttgta----accagGGTGAGTATCCATGAAGCCATGGAACAACAGAGTATTAGTATATCGAAGGCAGGAATAGTTACTTCTCTTCAAGCTCGTTGCTCTGTTATTGCTGCAGCT
||||  ||||| |  |    ||| ||         | |    || |  || | ||      |||  |   |||||| | |     |  || ||||| ||||| ||||| |||||||| ||||||||||| ||||| ||||| || || || |||||||| || ||||| |||||||| |||||||| || 
gtaaggaaatgtatgtgcgtatattttggtacttcaatcccttgcaaaaatttgtatcatgtgaacaagaaagtttatatcctctattagAGTGAGCATCCACGAAGCAATGGAACAGCAGAGTATTAGCATATCAAAGGCTGGGATTGTCACTTCTCTCCAGGCTCGCTGCTCTGTCATTGCTGCTGCA

upper sequence: AT1G44900.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: PP1S28_266V6.1 (Physcomitrella patens), 3'ss of exon 10
--------------------------------------------------------------------------gtaacaaaatgcaactaatgata-gttacttttctgaaggaaatggtgctgacgatataagtttttgtaaccagGGTGAGTATCCATGAAGCCATGGAACAACAGAGTATTAGTATATCGAAGGCAGGAATAGTTACTTCTCTTCAAGCTCGTTGCTCTGTTATTGCTGCAGCT
                                                                           ||  |||| ||  ||  ||||  | | || ||      |||    |  ||  || ||  | ||||||    ||||||||||| ||||| || |||||||| ||||| || |||||||| |||||||| || || |||||  | ||||| || ||| |||||||||||||||| 
gtgcagtccctttctggagatgcatttttcataaccatttgtatacagttcttgaaactctcaattgccaagccttagaaaaacgctcct--tgatgtgctgctatttcatctgaagactttgtg-tgaaattcgattttgt--ttagGGTGAGTATTCATGAGGCTATGGAACAGCAGAGCATCAGTATATCTAAGGCAGGCATTGTGACTTCGTTGCAAGCCCGGTGCGCTGTTATTGCTGCAGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatagttacttttctgaaggaaatggtgctgacgatataagtttttgtaaccagGGTGAGTATCCATGAAGCCATGGAACAACAGAGTATTAGTATATCGAAGGCAGGAATAGTTACTTCTCTTCAAGCTCGTTGCTCTGTTATTGCTGCAGCT
                           tgctgac  putative branch site (score: 2)
                                          tttttgt  putative PPT
                                   atataagtttttgtaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacaaaatgcaactaatgatagttacttttctgaaggaaatggtgctgacgatataagtttttgtaaccagGGTGAGTATCCATGAAGCCATGGAACAACAGAGTATTAGTATATCGAAGGCAGGAATAGTTACTTCTCTTCAAGCTCGTTGCTCTGTTATTGCTGCAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT