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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattttatcaagatcctgctgtcattcctgtaaacaagcaccatgcagcaatttgtatttttatgacttacaatgtcttccctctgtgtgatagTGAGGATCCTGAGATTCACTTCAAGTACATCGAAGCAGCTGCCAAGACTGGTCAAATAAAGGAGGTTGAGCGTGTGACTAGAGAGTCTAACTTTTATGAT

Basic information

species Arabidopsis thaliana
transcript AT3G11130.1
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 20
gtaattttatcaagatcctgctgtcattcctgtaaacaagcaccatgcagcaatttgtatttt-tatgacttac---aatgtc-ttccctctgtgtgatagTGAGGATCCTGAGATTCACTTCAAGTACATCGAAGCAGCTGCCAAGACTGGTCAAATAAAGGAGGTTGAGCGTGTGACTAGAGAGTCTAACTTTTATGAT
              |     ||     |  |||  | | |  | | |||    |||||  ||    || |  ||   ||| || |||  |   |   | ||||||||||| || ||||| ||||| ||||| ||||||||||| | |||||| || || || || ||||| ||||| || || || || ||||||||||||
------------gtagttaactactcctgatgttgatatgtgcgaagcaat--tttgtccttaacgtggcgcaccttaatatcgttctttacattcaacagTGAGGATCCAGATATTCATTTCAAATACATAGAAGCAGCTGCTAGGACTGGACAGATCAAAGAAGTTGAACGTGTAACCAGGGAATCCAACTTTTATGAT

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 20
gtaattttatcaagatcctgctgtcattcctgtaaacaagcaccatgcagcaatttgtatttt-tatgacttac---aatgtc-ttccctctgtgtgatagTGAGGATCCTGAGATTCACTTCAAGTACATCGAAGCAGCTGCCAAGACTGGTCAAATAAAGGAGGTTGAGCGTGTGACTAGAGAGTCTAACTTTTATGAT
              |     ||     |  |||  | | |  | | |||    |||||  ||    || |  ||   ||| || |||  |   |   | ||||||||||| || ||||| ||||| ||||| ||||||||||| | |||||| || || || || ||||| ||||| || || || || ||||||||||||
------------gtagttaactacacctgatgttgatatgtgcgaagcaat--tttgtccttaacgtggcgcaccttaatatcgttctttacattcaacagTGAGGATCCAGATATTCATTTCAAATACATAGAAGCAGCTGCTAGGACTGGACAGATCAAAGAAGTTGAACGTGTAACCAGGGAATCCAACTTTTATGAT

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 18
gtaattttatcaagatcctgctgtcattcctgtaaacaagcaccatgcagcaat-ttgtattttt----atgacttacaatgtc------ttccctctgtgtg-atagTGAGGATCCTGAGATTCACTTCAAGTACATCGAAGCAGCTGCCAAGACTGGTCAAATAAAGGAGGTTGAGCGTGTGACTAGAGAGTCTAACTTTTATGAT
||| ||   ||    ||||| |||   |  |    | | |   ||| |   ||| ||  |||| |    ||| | | || ||        ||  || | | |  ||||||||||||| || || || ||||| ||||| ||||||||||| |  ||||| || || || || ||||||||||| || ||||||||||| || ||||||
gtagttac-tcttactcctgatgttggtatttctta-aggtggcataccttaatattaaatttctcaacatggcatgcattgatattaaattttctttatattcatagTGAGGATCCAGATATCCATTTCAAATACATAGAAGCAGCTGCAAGAACTGGACAGATCAAAGAAGTTGAGCGTGTAACCAGAGAGTCTAATTTCTATGAT

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GRMZM2G430947_T01 (Zea mays), 3'ss of exon 6
gtaattttatcaagatcctgctgtcattcctgtaaacaagcaccatgcagcaatttgtatttttatgacttacaatgtcttccctctgtgtgatagTGAGGATCCTGAGATTCACTTCAAGTACATCGAAGCAGCTGCCAAGACTGGTCAAATAAAGGAGGTTGAGCGTGTGACTAGAGAGTCTAACTTTTATGAT
|||||||  ||  | |      |  || ||| |   |||      ||   |  | |  |  |  |  ||     | || |||  |   ||  | || ||||| || || || || ||||||||||| |||||||| || | |||||| ||||| || || ||||| ||||| || |||||||| ||||| ||||||
gtaatttc-tcttgttgacagcggaatgcctttct-caaattttgtgtgtctttctcaaaatgcaacacacctgaggt-ttctttacatgcaacagCGAGGACCCAGATATCCATTTCAAGTACATAGAAGCAGCAGCAAGGACTGGACAAATCAAAGAAGTTGAACGTGTAACCAGAGAGTCAAACTTCTATGAT

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 19
gtaattttatcaagatcctg---ctgtcattcctg-taaacaag---caccatgcagcaa--------tttgtatttttat-gacttacaatgtcttccctctg----tgtgatagTGAGGATCCTGAGATTCACTTCAAGTACATCGAAGCAGCTGCCAAGACTGGTCAAATAAAGGAGGTTGAGCGTGTGACTAGAGAGTCTAACTTTTATGAT
||||||   |||   |  |    ||||  |  ||| |   ||||     ||||     ||        | | |  | | ||   || | | | | ||||| ||     || || |||||||||||||| |||||||| |||||||| ||||||||||| |||||||| ||||| || ||||||||||||||||||||||| || |  || ||||||
gtaattccttcatttttatagaactgttttggctggtgggcaagtgatgccatttgtaaaggggatgttgtctgatatcatcagctaatatttttttccccctaaacttgggacagTGAGGATCCTGACATTCACTTTAAGTACATTGAAGCAGCTGCAAAGACTGGACAAATCAAAGAGGTTGAGCGTGTGACTAGAGAATCAAGTTTCTATGAT

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 19
gtaattttatcaagatcct---gctgtcattcctg-taaacaag-----caccatgca----gcaatttgtatttttatgacttacaatgtcttccctctg--tgtgatagTGAGGATCCTGAGATTCACTTCAAGTACATCGAAGCAGCTGCCAAGACTGGTCAAATAAAGGAGGTTGAGCGTGTGACTAGAGAGTCTAACTTTTATGAT
|||| | | ||| | |  |    ||||  |  ||| |  |||||     ||   || |    | |  |||| |  |     || | | | | ||||||     || || |||||||||||||| ||||||||||||||||| || ||||| || |||||||| ||||| || ||||||||||||||||||||||| || |  |||||||||
gtaactctttcatgtttttagaactgttttggctggtggacaagtgatgcaatttgtaaaggggatattgtctgctatcagctaatatttttttccctgaacttgggacagTGAGGATCCTGACATTCACTTCAAGTACATTGAGGCAGCAGCAAAGACTGGACAAATCAAAGAGGTTGAGCGTGTGACTAGAGAATCAAGTTTTTATGAT

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 20
gtaattttatca---------agatcctgctgtcattcctgtaaacaagcaccatgcagcaatttgtatttttatgacttac----aatgtct-tccctctgtgtgata-------gTGAGGATCCTGAGATTCACTTCAAGTACATCGAAGCAGCTGCCAAGACTGGTCAAATAAAGGAGGTTGAGCGTGTGACTAGAGAGTCTAACTTTTATGAT
|||||| | |||         | | | || | |  |    ||||   | | |  |  |   |  | |  |   |||  || |     |||| | | |||||   | |||       ||||||||||||| |||||||| |||||||| || ||||| || |||||||||||||| |||||||||||||||||||| ||||| || || || ||||||
gtaattctttcatttggaaaaaaaacttgtttttctgttggtaattgacctcattttattgagatattgtccgatgtatttctgctgatgtatgttcctctaaataatatggaacagTGAGGATCCTGACATTCACTTTAAGTACATTGAGGCAGCAGCAAAGACTGGTCAAATCAAGGAGGTTGAGCGTGTGACAAGAGAATCAAATTTCTATGAT

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 20
gtaattttatca---------agatcctgctgtcattcctgtaaacaagcaccatgcagc--aatttgtatt---tttatgacttacaatgtct-tccctctgtgtgata-------gTGAGGATCCTGAGATTCACTTCAAGTACATCGAAGCAGCTGCCAAGACTGGTCAAATAAAGGAGGTTGAGCGTGTGACTAGAGAGTCTAACTTTTATGAT
|||||| | |||         | |  ||  | |   |  ||  || |  |  |||  |    |  |  |||    | |||  ||    |||| | | |||||   | |||       ||||||||||||| |||||||| |||||||| || ||||| || |||||||||||||| |||||||||||||||||||| ||||| || || || ||||||
gtaattctttcatttggaaaaaaaaacttgtttttctgttggtaatagacctcatttaattgagatattatccaatgtatttctgctgatgtatgttcctctaaataatatggaacagTGAGGATCCTGATATTCACTTTAAGTACATTGAGGCAGCGGCAAAGACTGGTCAAATCAAGGAGGTTGAGCGTGTGACAAGAGAATCAAATTTCTATGAT

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 20
gtaattt---tatcaagatcctgctgtcattcctgtaaacaagcaccatgcagcaatttgtatttttatgacttacaatgtcttccctctgtgtgatagTGAGGATCCTGAGATTCACTTCAAGTACATCGAAGCAGCTGCCAAGACTGGTCAAATAAAGGAGGTTGAGCGTGTGACTAGAGAGTCTAACTTTTATGAT
|||||||   ||  |||      || |  || || ||     |   ||| || |   || | |  || | |  |    |   ||   |   ||  | |||||||||||||| |||||||||||||| || ||||| ||||| || ||||| ||||| ||||||||||||||||||||| |||| || ||||| ||||||
gtaatttgtttagtaaggaagaactttgctttctttaggtgcggtacatccaacttattttgtgattttcatatcgttttcttttggttcatggaacagTGAGGATCCTGACATTCACTTCAAGTATATTGAAGCTGCTGCTAAAACTGGACAAATTAAGGAGGTTGAGCGTGTGACTCGAGAATCAAACTTCTATGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accatgcagcaatttgtatttttatgacttacaatgtcttccctctgtgtgatagTGAGGATCCTGAGATTCACTTCAAGTACATCGAAGCAGCTGCCAAGACTGGTCAAATAAAGGAGGTTGAGCGTGTGACTAGAGAGTCTAACTTTTATGAT
                         gacttac  putative branch site (score: 2)
                                  tgtcttccctctgt  putative PPT
          aatttgtatttttatg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattttatcaagatcctgctgtcattcctgtaaacaagcaccatgcagcaatttgtatttttatgacttacaatgtcttccctctgtgtgatagTGAGGATCCTGAGATTCACTTCAAGTACATCGAAGCAGCTGCCAAGACTGGTCAAATAAAGGAGGTTGAGCGTGTGACTAGAGAGTCTAACTTTTATGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG