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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acgaaaattgctgatttactaaaggtgagcgtaatatattatgaaaatgatgattgtaccattatgcctaataagcctaaactcataatacactctacagCTTCATGATGTAATTGATCTTGTCATTCCAAGAGGCAGCAATAAGCTGGTTTCACAAATCAAGACATCAACTAAGATCCCTGTTCTTGGTCATGCTG

Basic information

species Zea mays
transcript AC203754.4_FGT008
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC203754.4_FGT008 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os05g38150.1 (Oryza sativa), 3'ss of exon 11
acgaaaattgctgatttactaaaggtgagcgtaa---tatattatgaaaatgatgattgtaccattatgcctaataagcctaaactcataatacactctacagCTTCATGATGTAATTGATCTTGTCATTCCAAGAGGCAGCAATAAGCTGGTTTCACAAATCAAGACATCAACTAAGATCCCTGTTCTTGGTCATGCTG
                        |||   | ||   |||||| | |||  | ||||  ||||| | || ||||         || | ||||||||| | |||||| ||||||| ||||||||||||||||||||||| || |||||||| || || ||||||||| | ||||||||||| ||||||||||| |||||||
----------------------gtgtgtatgcaattctatattttcaaagcgttgatactaccaatttggctaa---------acccgtaatacactgtgcagCTTGATGATGTCATTGATCTTGTCATTCCAAGAGGAAGTAATAAGCTTGTCTCTCAAATCAAGGCGTCAACTAAGATTCCTGTTCTTGGGCATGCTG

upper sequence: AC203754.4_FGT008 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA01G24530.1 (Glycine max), 3'ss of exon 13
acgaaaattgctgatttactaaaggtgagcgtaatatattatgaaaatgatgattgta-ccattatgcc-taataagcctaaactcataatacactcta-cagCTTCATGATGTAATTGATCTTGTCATTCCAAGAGGCAGCAATAAGCTGGTTTCACAAATCAAGACATCAACTAAGATCCCTGTTCTTGGTCATGCTG
                       | ||    | |  || ||  |||   ||  |  ||   ||| |     |||        ||| || |||| || |  |||||| |||||||||| ||||| ||  | || |||||||| |||||||| ||||| |||||||||  |||||| || || |||||||||||||||||||
-----------------------gttggatatcac-tagtaaaaaataaatcctcataattattgttttacaatggtttgtcacttattatactctgtctcagCTTGATGATGTAATAGATCTAGTGGTCCCTAGAGGCAGTAATAAGCTTGTTTCTCAAATCAAGGAATCAACAAAAATTCCTGTTCTTGGTCATGCTG

upper sequence: AC203754.4_FGT008 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA18G03830.1 (Glycine max), 3'ss of exon 12
------acgaa--aattgctgatttactaaaggtgagcgtaatatattatgaaaatgatgattgtaccattatgcctaataagcctaaactcataatacactctacagCTTCATGATGTAATTGATCTTGTCATTCCAAGAGGCAGCAATAAGCTGGTTTCACAAATCAAGACATCAACTAAGATCCCTGTTCTTGGTCATGCTG
      || ||  |  |  | |||||  |    |   | |  |   ||   | | || |   | || ||  |   |||   ||  |  | || || |   || | ||| |  |||||||||||||||| || ||||||||||||||||| || || ||  | || |||||||  || ||||| || ||||| || |||||||| |
gtgaatacaaagtagatattcatttatgatttatagtcctgctcactttgaacattggtacctttaaca--aaagctag--agtttgcattc-tacttttcttt-cagTTGGATGATGTAATTGATCTAGTGATTCCAAGAGGCAGCAACAAACTTGTCACTCAGATCAAGAGTTCCACTAAAATTCCTGTCCTGGGTCATGCAG

upper sequence: AC203754.4_FGT008 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA02G41850.1 (Glycine max), 3'ss of exon 9
acgaaaattgctgatttactaaaggtgagcgtaatatattatgaaaatgatgattgtaccattatgcctaataagcctaaactcataatacactctacagCTTCATGATGTAATTGATCTTGTCATTCCAAGAGGCAGCAATAAGCTGGTTTCACAAATCAAGACATCAACTAAGATCCCTGTTCTTGGTCATGCTG
              |  |||||   | || | |   || | | |   | || |     |  ||   | |||  |     | ||    ||  |   | |||||  |||||||||| ||||| || ||||||||||||||||| || || ||||| || |||||||  || ||||| || |||||| | ||||||||||
-------------gtgaactaa---tcagtggagcttaatttcagtttcataacc---ctgttcaccttaagcattggcacctttctatttaaatttcagCTGGATGATGTAATCGATCTGGTGATTCCAAGAGGCAGCAACAAACTTGTTTCTCAGATCAAGAGTTCCACTAAAATTCCTGTTTTAGGTCATGCTG

upper sequence: AC203754.4_FGT008 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA03G12240.1 (Glycine max), 3'ss of exon 12
acgaaaattgctgatttactaaaggtgagcgtaatatattatgaaaatgatgattgtaccattatgcctaataagcctaaactcataatacactctacagCTTCATGATGTAATTGATCTTGTCATTCCAAGAGGCAGCAATAAGCTGGTTTCACAAATCAAGACATCAACTAAGATCCCTGTTCTTGGTCATGCTG
         | ||  | |  |   || |    |||| ||  | ||||| ||  || ||| || ||   | |     ||||  | ||| |        |||||| |||||||||| ||||| ||  | || |||||||| |||||||| ||||| |||||||||  |||||| || || |||||||||||||||||||
---------gttggat-atcactagtaaaa--aataaatcctcaaaattattgttttacaatgatttgtca-----ctaa--ttatactctgtct--cagCTTGATGATGTAATAGATCTAGTGGTCCCTAGAGGCAGTAATAAGCTTGTTTCTCAAATCAAGGAATCAACAAAAATTCCTGTTCTTGGTCATGCTG

upper sequence: AC203754.4_FGT008 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA18G40770.1 (Glycine max), 3'ss of exon 13
acgaaaattgctgatttactaaaggtgagcgtaatatattatgaaaatgatgattgtaccattatgcctaataagcctaaactcataatacact-ctacagCTTCATGATGTAATTGATCTTGTCATTCCAAGAGGCAGCAATAAGCTGGTTTCACAAATCAAGACATCAACTAAGATCCCTGTTCTTGGTCATGCTG
                                         | ||| |  | |   |    || |    ||| |   | |||| || ||||  | | ||||||| |||| || || ||||||||  | || |||||||| || || || ||||| |||||||||   || || ||||| |||||||||||||||||||
----------------------------------------gtaaaattcctaaa-atttatttgtctgaaatgattttcaactaattatactttgccacagcttgatgacgtgatagATCTTGTGGTCCCCAGAGGCAGTAACAAACTTGTTTCTCAAATCAAGGATTCCACAAAGATTCCTGTTCTTGGTCATGCTG

upper sequence: AC203754.4_FGT008 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA14G07120.1 (Glycine max), 3'ss of exon 9
acgaaaattgctgatttactaaaggtgagcgtaatatattatgaaaatgatgattgtaccattatgcctaataagcctaaactcataatacactctacagCTTCATGATGTAATTGATCTTGTCATTCCAAGAGGCAGCAATAAGCTGGTTTCACAAATCAAGACATCAACTAAGATCCCTGTTCTTGGTCATGCTG
              |  |||||   | || | |   || | | ||  | || |   |       |     ||  |||     | |  |   |   | |||||  |||| ||||||||||| || ||||||||||||||||| || || ||||| ||||||||||  || ||||| || |||||| | ||||| ||||
-------------gtgaactaa---tcagtggagcttaatttcaatttcataagcctgttcactttaagcattggccacctttaaatacttaaatttcagCTGGATGACGTAATTGATCTGGTGATTCCAAGAGGCAGCAACAAACTTGTTTCTCAAATCAAGAGTTCCACTAAAATTCCTGTTTTAGGTCACGCTG

upper sequence: AC203754.4_FGT008 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA07G16510.1 (Glycine max), 3'ss of exon 9
acgaaaattgctgatttactaaaggtgagcgtaatatattatgaaaatgatgat-tgtaccattatgcctaataagcctaaactcataatacact-ctacagCTTCATGATGTAATTGATCTTGTCATTCCAAGAGGCAGCAATAAGCTGGTTTCACAAATCAAGACATCAACTAAGATCCCTGTTCTTGGTCATGCTG
                                         | ||| |  | |  | ||  | | ||   ||| |   |  ||| || ||||  | | ||||||| |||| || || ||||||||  | || |||||||| |||||||| || || |||||||||    |||| ||||| |||||||||||||||||||
----------------------------------------gtaaaattcctaaaatttattagtctga--aatgattttccactaatcatactttgccacagcttgatgacgtgatagATCTTGTGGTCCCCAGAGGCAGTAATAAGCTTGTCTCTCAAATCAAGGGTACAACAAAGATTCCTGTTCTTGGTCATGCTG

upper sequence: AC203754.4_FGT008 (Zea mays), 3'ss of exon 11
lower sequence: AT3G55610.2 (Arabidopsis thaliana), 3'ss of exon 12
acgaaaattgctgatttactaaaggtgagcgtaatatattatgaaaatgatgattgtaccattatgcctaataagcctaaactcata-atacactctacagCTTCATGATGTAATTGATCTTGTCATTCCAAGAGGCAGCAATAAGCTGGTTTCACAAATCAAGACATCAACTAAGATCCCTGTTCTTGGTCATGCTG
       |       |   || |  |||  |  |  |       || |||| |   |    | |    || |    |  | |   || ||      |||||||| |||| || ||||||||||| || |||||||||||||| ||||| ||||| ||||| || |  || || || ||||| || || || |||||||
------gtaagcagatagatacatatgaatggcaagt-ccccagaagtgattagc-ttttttcacttatactggaacccaccatttacatttttggtacagCTTGATGACGTTATTGATCTTGTGATCCCAAGAGGCAGCAACAAGCTTGTTTCTCAAATAAAAAACTCGACGAAAATCCCAGTGCTAGGCCATGCTG

upper sequence: AC203754.4_FGT008 (Zea mays), 3'ss of exon 11
lower sequence: Vv13s0019g02360.t01 (Vitis vinifera), 3'ss of exon 12
------------acgaaaattgctgatttactaaaggtgagcgtaatatattatgaaaatgatgattgtaccattatgcctaataagcctaaactcataatacactctacagCTTCATGATGTAATTGATCTTGTCATTCCAAGAGGCAGCAATAAGCTGGTTTCACAAATCAAGACATCAACTAAGATCCCTGTTCTTGGTCATGCTG
             |  | | || | ||| | ||      | | |  |  | | | | |||| ||||   |  | |     |    |  |   | |  |  |     || |||||| ||||||| || || ||||| || ||||||||||||||||| || ||||| ||||| |||   ||||| || || |||||||| || |||||||
gtgagctgatgtgctgagaatgatcattga-tagttaaaaacatt-tgaactttcagaatggtgatatgaaaaatggatgttcacactcagtatttttgttttgtgctccagCTTGATGATGTGATCGACCTTGTAATCCCAAGAGGCAGCAATAAACTTGTTTCTCAAATAAAGGATTCAACAAAAATTCCTGTTCTGGGCCATGCTG

upper sequence: AC203754.4_FGT008 (Zea mays), 3'ss of exon 11
lower sequence: Vv08s0007g01060.t01 (Vitis vinifera), 3'ss of exon 12
acgaaaattgctgatttactaaaggtgagcgtaatatattatgaaaatgatgattgtaccattatgcctaataagcctaaactcataatacact--ctacagCTTCATGATGTAATTGATCTTGTCATTCCAAGAGGCAGCAATAAGCTGGTTTCACAAATCAAGACATCAACTAAGATCCCTGTTCTTGGTCATGCTG
                       |  | |  | | ||   ||     ||||| || |  ||| ||   |  |     | ||||  |  ||      |  |||||| ||||||| || |||||||| || || ||||||||||| || || ||||| |||||||||   |||||||| ||||||||||||||||||||||
-----------------------gtggggattgagattggatatgtttgatggtt-tttcataataggt--tggttattaacttgttttagttctgccccagCTTGATGATGTCATAGATCTTGTGATCCCTAGAGGCAGCAACAAACTCGTTTCTCAAATCAAGGATTCAACTAAAATCCCTGTTCTTGGTCATGCTG

upper sequence: AC203754.4_FGT008 (Zea mays), 3'ss of exon 11
lower sequence: EFJ17662 (Selaginella moellendorffii), 3'ss of exon 12
acgaaaattgctgatttactaaaggtgagcgtaatatattatgaaaatgatgattgtaccattatgcctaataagcctaaactcataatacactctacagCTTCATGATGTAATTGATCTTGTCATTCCAAGAGGCAGCAATAAGCTGGTTTCACAAATCAAGACATCAACTAAGATCCCTGTTCTTGGTCATGCTG
                                                  | | | |||  |  |||    | |||      || ||  |     | |||||| | ||||| ||||| || || || |||||||| |||||||| || |||||||||||||||   || || || || ||||| || || ||||| |
-------------------------------------------------gtaactatactttcgtgct--gttagctcgt-ttcttaccatgggtttcagCTTGACGATGTTATTGACCTCGTTATACCAAGAGGAAGCAATAAACTTGTTTCACAAATCAAGGAGTCTACGAAAATTCCTGTGCTGGGCCATGCCG

upper sequence: AC203754.4_FGT008 (Zea mays), 3'ss of exon 11
lower sequence: EFJ29127 (Selaginella moellendorffii), 3'ss of exon 12
acgaaaattgctgatttactaaaggtgagcgtaatatattatgaaaatgatgattgtaccattatgcctaataagcctaaactcataatacactctacagCTTCATGATGTAATTGATCTTGTCATTCCAAGAGGCAGCAATAAGCTGGTTTCACAAATCAAGACATCAACTAAGATCCCTGTTCTTGGTCATGCTG
                                                  | | | |||  || |||    | |||      || ||  |     | |||||| | ||||| ||||| || || || |||||||| |||||||| || |||||||||||||||   || || || || ||||| || || ||||| |
-------------------------------------------------gtaactatacttttgtgct--gttagctcgt-ttcttaccatgggtttcagCTTGACGATGTTATTGACCTCGTTATACCAAGAGGAAGCAATAAACTTGTTTCACAAATCAAGGAGTCTACGAAAATTCCTGTGCTGGGCCATGCCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgatgattgtaccattatgcctaataagcctaaactcataatacactctacagCTTCATGATGTAATTGATCTTGTCATTCCAAGAGGCAGCAATAAGCTGGTTTCACAAATCAAGACATCAACTAAGATCCCTGTTCTTGGTCATGCTG
                             gcctaaa  putative branch site (score: 3)
                                     tcataata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acgaaaattgctgatttactaaaggtgagcgtaatatattatgaaaatgatgattgtaccattatgcctaataagcctaaactcataatacactctacagCTTCATGATGTAATTGATCTTGTCATTCCAAGAGGCAGCAATAAGCTGGTTTCACAAATCAAGACATCAACTAAGATCCCTGTTCTTGGTCATGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - tgctgat
- - - - - - - - - - - - - - - - - - - - - - - -tgatgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - tgtacca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tatgcct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaactca