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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataaggcagtattctttacatctatggttctttctgattatccactaaattacatttcttctaaagtgattaaatacttagctgttataaacatgcattcagGTGTACCATCCAAATATTGATTTGGAAGGCAATGTCTGTCTGAACATTCTGCGTGAAGATTGGAAGCCTGTTCTCAACATCAACACCGTTATTTATGGCC

Basic information

species Zea mays
transcript GRMZM2G115939_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G115939_T04 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os10g11260.2 (Oryza sativa), 3'ss of exon 4
-----gtataaggc---agtattctttacatctatg-gttctttctgattatccactaaattacatttcttctaaagtgattaaatacttagctgttataaacatgcattcagGTGTACCATCCAAATATTGATTTGGAAGGCAATGTCTGTCTGAACATTCTGCGTGAAGATTGGAAGCCTGTTCTCAACATCAACACCGTTATTTATGGCC
     ||  ||| |    ||||    |    || |   | || | |  ||  ||| | ||| |  || | ||| ||   |||       ||    |||||| | ||||||||||| |||||||||||||||||||||||||| ||||| || ||||||||| ||||||||||||||||||||||||||||||||||||| |||||||||||||
gtgaagtgcaagaccaaggtataagatggggctttctatgctatatattttcccagtgaat-atgttgcctcttaaccaatt-----tctatgcattataa-cttgcattcagGTATACCATCCAAATATTGATTTGGAAGGAAATGTATGCCTGAACATTTTGCGTGAAGATTGGAAGCCTGTTCTCAACATCAACACTGTTATTTATGGCC

upper sequence: GRMZM2G115939_T04 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os10g11260.3 (Oryza sativa), 3'ss of exon 4
gtataaggcagtattctttacatctatggttctttctgattatccactaaattacatttcttctaaagtgattaaatacttagctgttataaacatgcattcagGTGTACCATCCAAATATTGATTTGGAAGGCAATGTCTGTCTGAACATTCTGCGTGAAGATTGGAAGCCTGTTCTCAACATCAACACCGTTATTTATGGCC
|||||||   |   | | ||   ||||   | || |   |          | ||  || | ||| ||   |||       ||    |||||| | ||||||||||| |||||||||||||||||||||||||| ||||| || ||||||||| ||||||||||||||||||||||||||||||||||||| |||||||||||||
gtataagatggggctttctatg-ctatatattttcccagt---------gaatatgttgcctcttaaccaatt-----tctatgcattataa-cttgcattcagGTATACCATCCAAATATTGATTTGGAAGGAAATGTATGCCTGAACATTTTGCGTGAAGATTGGAAGCCTGTTCTCAACATCAACACTGTTATTTATGGCC

upper sequence: GRMZM2G115939_T04 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA11G06830.1 (Glycine max), 3'ss of exon 4
-------gtataaggcagtattctttac----atctatggttct-ttctgattatccactaaattacatttcttctaaagtgattaaatacttagctgttataaa----catgcattcagGTGTACCATCCAAATATTGATTTGGAAGGCAATGTCTGTCTGAACATTCTGCGTGAAGATTGGAAGCCTGTTCTCAACATCAACACCGTTATTTATGGCC
       |     |    | || |||||    ||   || ||   || || | |     |   || | | |  | |    |  | | | | |||  |||   |      | |  ||  |||| || |||||||||||||| |||||||| ||||| ||||| |||||  | || ||||||||||| ||||| || || || ||||| || || |||||| 
gtaggatggtcttgattatcttttttactctaattcgtgctttagttttggtaagtgtgttgttttcttgttctgtttcatcttcataaatttatttgtagcattatctcgtatatgaagGTCTATCATCCAAATATTGACTTGGAAGGAAATGTTTGTCTCAACATCTTACGAGAAGATTGGAAACCTGTCCTTAATATAAACACTGTCATCTATGGCT

upper sequence: GRMZM2G115939_T04 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA01G38470.1 (Glycine max), 3'ss of exon 4
--------gtataaggcagtattctttac----atctatggttct-ttctgatta-tccactaaattacatttcttctaaagtgattaaatacttagctgttataaa----catgcattcagGTGTACCATCCAAATATTGATTTGGAAGGCAATGTCTGTCTGAACATTCTGCGTGAAGATTGGAAGCCTGTTCTCAACATCAACACCGTTATTTATGGCC
        || |     |   || ||| |    ||   || ||   || || | | |    |   ||    ||||  |  ||      ||   |||  |||   |      | |  || ||||| || |||||||||||||| |||||||| ||||| ||||| |||||  | || ||||||||||| ||||| || || || ||||| || || |||||| 
gtaggatggtcttgattatcttttttttctctaattcgtgctttagttttggtaagtgtgttgttttcttgttctgtttcagcatcataaattttatttgtagcattatctcctatatgcagGTCTATCATCCAAATATTGACTTGGAAGGAAATGTTTGTCTCAACATCTTACGAGAAGATTGGAAACCTGTCCTTAATATAAACACTGTCATCTATGGCT

upper sequence: GRMZM2G115939_T04 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA02G06580.1 (Glycine max), 3'ss of exon 6
-----------------------------------------------------gtataaggcagtattctttacatctatggttctttctgattatccactaaattacatttcttctaaagtgattaaatacttagctgttataaacatgcattcagGTGTACCATCCAAATATTGATTTGGAAGGCAATGTCTGTCTGAACATTCTGCGTGAAGATTGGAAGCCTGTTCTCAACATCAACACCGTTATTTATGGCC
                                                      | ||   || ||    ||  |||| || || | ||  |||      |        | | ||  ||||| ||||| || ||   ||| ||   |||  ||  |||| |||||||||||||| || |||||||| ||||| || || ||||| || || ||||||||||| ||||| ||||| || ||| |  | || || ||| 
gtaggaactaggagatcttggttatctttggtattattaactcattcttttttatgtacatca-tacgtgtttaatct-tgcttgtgtcatatttgtggtttttccttgtctgtttcaaagtcattaattaatt---tgtcatgt-catatatgtagGTCTACCATCCAAATATAGACTTGGAAGGAAATGTTTGCCTTAACATCCTACGAGAAGATTGGAAACCTGTCCTCAATATAAACTCTATCATCTACGGCT

upper sequence: GRMZM2G115939_T04 (Zea mays), 3'ss of exon 4
lower sequence: AT2G18600.1 (Arabidopsis thaliana), 3'ss of exon 4
gtataaggcagtattctttacatctatggttctttctgattatccactaaattacatttcttctaaagtgattaaatacttagctgttataaacatgcatt-cagGTGTACCATCCAAATATTGATTTGGAAGGCAATGTCTGTCTGAACATTCTGCGTGAAGATTGGAAGCCTGTTCTCAACATCAACACCGTTATTTATGGCC
                 |||    |    || || || | | ||       ||  || |  ||| |  || ||| | |    |||     |        ||  ||||||| ||||| ||||| ||| | ||||| || ||||||||||||||  |||||||||| ||||| || ||||||||||| ||||| ||||| || || |
----------------gttaggctt----tttttcctcagtctctgaagcgttttatgttgtctgatatgtttatacagaatgctaaagaatgtcaatgttgtagGTGTATCATCCGAATATCGATCTAGAAGGAAACGTCTGTCTGAACATCTTGCGTGAAGACTGGAAACCGGTTCTCAACATAAACACAGTTATCTACGGTC

upper sequence: GRMZM2G115939_T04 (Zea mays), 3'ss of exon 4
lower sequence: AT4G36800.1 (Arabidopsis thaliana), 3'ss of exon 4
gtataaggcagtattctttacatctatggttctttctgattatccactaaattacatttcttctaaagtgattaaatacttagctgttataaacatgcattcagGTGTACCATCCAAATATTGATTTGGAAGGCAATGTCTGTCTGAACATTCTGCGTGAAGATTGGAAGCCTGTTCTCAACATCAACACCGTTATTTATGGCC
   || | |  |  || ||  |  |    |   |  |    | |  |||  | | | | | | |    ||   |||  ||| | || | |         || |||| || ||||| ||||| ||||||||||| || || || ||||||||  |||||||||||||||| |||||||| ||||| ||||| ||||| || || |
--gtaggcctctcctccttttacatgccttatatagtttacagcttctacttcaaaat-cgtttgtgttgtagaaactctttgttggtttt----cttgtttagGTTTATCATCCCAATATCGATTTGGAAGGAAACGTTTGCCTGAACATCTTGCGTGAAGATTGGAAACCTGTTCTTAACATTAACACAGTTATCTACGGAC

upper sequence: GRMZM2G115939_T04 (Zea mays), 3'ss of exon 4
lower sequence: Vv18s0001g12010.t01 (Vitis vinifera), 3'ss of exon 3
--gtataaggcagtattctttacatctatggttctttctgattatccactaaattacatttcttctaaagtgattaaatacttagctgttataaacatgcatt-----cagGTGTACCATCCAAATATTGATTTGGAAGGCAATGTCTGTCTGAACATTCTGCGTGAAGATTGGAAGCCTGTTCTCAACATCAACACCGTTATTTATGGCC
  |   ||  |    |  |  |  | | |   | ||  |  |  |  ||||||||  | |  |  | | || ||     |  ||  || ||  |   ||   |     ||||| |||||||| || ||||| |||| ||| ||||||||||| |||||||| || || || ||||| ||||| || ||||| |||||  | || ||||| |
gtgggcaaaccccagtagtccatttttgttaatgttcattctcctttactaaattgtactattaatcatgttatcctgcaagtaattgctaacattgtgtcctacctgcagGTCTACCATCCTAACATTGACTTGGCAGGAAATGTCTGTCTTAACATTCTTCGGGAGGACTGGAACCCTGTCCTAAACATAAACACTATCATCTATGGAC

upper sequence: GRMZM2G115939_T04 (Zea mays), 3'ss of exon 4
lower sequence: Vv04s0023g01280.t01 (Vitis vinifera), 3'ss of exon 3
---------gtataaggc--agtattctttacatcta----tggttctttctgattatccactaaattacatttct-------tctaaagtgat---taa--atacttagctgttataaac-atgca---ttcagGTGTACCATCCAAATATTGATTTGGAAGGCAATGTCTGTCTGAACATTCTGCGTGAAGATTGGAAGCCTGTTCTCAACATCAACACCGTTATTTATGGCC
         | | ||     | | |  ||| | |||     || |||  | | || |    ||  ||   |||| |       | ||  ||| |   |||   |  | |  | | |||  | || ||   |  |||| |||||||| || ||||| |||||||| ||||| || || |||||| | || ||||||||||| ||||| || || || || ||  ||||||||||  
gtggagaaagcacaatctttaatttcttttgcttctggctctgtttcccttttatcagtttcttgatagtatttttgtccatatatatggtgttgtataatggtgttaaattctcatagtccatccaacttgtagGTCTACCATCCCAACATTGACTTGGAAGGAAATGTTTGCCTCAACATTTTACGAGAAGATTGGAAACCTGTCCTTAATATAAATACGATTATTTATGGAT

upper sequence: GRMZM2G115939_T04 (Zea mays), 3'ss of exon 4
lower sequence: PP1S61_126V6.1 (Physcomitrella patens), 3'ss of exon 4
--gtataaggcagtattctttacatctatggttctttctgattatccactaaattacatttcttctaaagtgattaaatacttagctgttataaacatgcattcagGTGTACCATCCAAATATTGATTTGGAAGGCAATGTCTGTCTGAACATTCTGCGTGAAGATTGGAAGCCTGTTCTCAACATCAACACCGTTATTTATGGCC
  ||| |   |   | |   || ||  ||| || |      | ||| |   |||   |    | || ||||  |||| |||||  ||  || ||   ||  |  |||| || ||||||||||| ||| ||||||||||||| |||||||| ||||| ||||| |||||||||||||| || |   | ||| |  | || ||||| |
gagtagacaccgacactgagtagattcatgattttgaaacgtcatcaatctaatgtaacgattgctcaagtc-ttaactacttgact--tacaa---tgtgtgtagGTTTATCATCCAAATATAGATCTGGAAGGCAATGTGTGTCTGAATATTCTTCGTGAGGATTGGAAGCCTGTGCTGAGTGTAAACTCTATCATATATGGTC

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|32801453|gb|CD953689.1|CD953689
EST:     TGTCCCCATCTTATCCTCATGATCCTCCGAAGGTCAAATGCAAGACCAAG                         GTGTACCATCCAAATATTGATCTGGAAGGCAATGTCTGTCTGAACATTCTG
genomic: TGTCCCCATCTTATCCTCATGATCCTCCGAAGGTCAAATGCAAGACCAAGgtataaggca ... atgcattcagGTGTACCATCCAAATATTGATTTGGAAGGCAATGTCTGTCTGAACATTCTG
EST: gi|8516672|gb|BE123397.1|BE123397
EST:     TGTCCCCATCTTATCCTCATGATCCTCCGAAGGTCAAATGCAAGACCAAG                         GTGTACCATCCAAATATTGATTTGGAAGGCAATGTCTGTCTGAACATTCTG
genomic: TGTCCCCATCTTATCCTCATGATCCTCCGAAGGTCAAATGCAAGACCAAGgtataaggca ... atgcattcagGTGTACCATCCAAATATTGATTTGGAAGGCAATGTCTGTCTGAACATTCTG
EST: gi|9028438|gb|BE238583.1|BE238583
EST:     TGTCCCCATCTTATCCTCATGATCCTCCGAAGGTCAAATGCAAGACCAAG                         GTGTACCATCCAAATATTGATTTGGAAGGCAATGTCTGTCTGAACATTCTG
genomic: TGTCCCCATCTTATCCTCATGATCCTCCGAAGGTCAAATGCAAGACCAAGgtataaggca ... atgcattcagGTGTACCATCCAAATATTGATTTGGAAGGCAATGTCTGTCTGAACATTCTG
EST: gi|32915063|gb|CF019875.1|CF019875
EST:     TGTCCCCATCTTATCCTCATGATCCTCCGAAGGTCAAATGCAAGACCAAG                         GTGTACCATCCAAATATTGATTTGGAAGGCAATGTCTGTCTGAACATTCTG
genomic: TGTCCCCATCTTATCCTCATGATCCTCCGAAGGTCAAATGCAAGACCAAGgtataaggca ... atgcattcagGTGTACCATCCAAATATTGATTTGGAAGGCAATGTCTGTCTGAACATTCTG
EST: gi|211291785|gb|FL131028.1|FL131028
EST:     TGTCCCCATCTTATCCTCATGATCCTCCGAAGGTCAAATGCAAGACCAAG                         GTGTACCATCCAAATATTGATTTGGAAGGCAATGTCTGTCTGAACATTCTG
genomic: TGTCCCCATCTTATCCTCATGATCCTCCGAAGGTCAAATGCAAGACCAAGgtataaggca ... atgcattcagGTGTACCATCCAAATATTGATTTGGAAGGCAATGTCTGTCTGAACATTCTG
EST: gi|78077789|gb|DV506218.1|DV506218
EST:     TGTCCCCATCTTATCCTCATGATCCTCCGAAGGTCAAATGCAAGACCAAG                         GTGTACCATCCAAATATTGATTTGGAAGGCAATGTCTGTCTGAACATTCTG
genomic: TGTCCCCATCTTATCCTCATGATCCTCCGAAGGTCAAATGCAAGACCAAGgtataaggca ... atgcattcagGTGTACCATCCAAATATTGATTTGGAAGGCAATGTCTGTCTGAACATTCTG
EST: gi|211320075|gb|FL327296.1|FL327296
EST:     TGTCCCCATCTTATCCTCATGATCCTCCGAAGGTCAAATGCAAGACCAAG                         GTGTACCATCCAAATATTGATTTGGAAGGCAATGTCTGTCTGAACATTCTG
genomic: TGTCCCCATCTTATCCTCATGATCCTCCGAAGGTCAAATGCAAGACCAAGgtataaggca ... atgcattcagGTGTACCATCCAAATATTGATTTGGAAGGCAATGTCTGTCTGAACATTCTG
EST: gi|211153912|gb|FL325451.1|FL325451
EST:     TGTCCCCATCTTATCCTCATGATCCTCCGAAGGTCAAATGCAAGACCAAG                         GTGTACCATCCAAATATTGATTTGGAAGGCAATGTCTGTCTGAACATTCTG
genomic: TGTCCCCATCTTATCCTCATGATCCTCCGAAGGTCAAATGCAAGACCAAGgtataaggca ... atgcattcagGTGTACCATCCAAATATTGATTTGGAAGGCAATGTCTGTCTGAACATTCTG
EST: gi|50326390|gb|CO521516.1|CO521516
EST:     TGTCCCCATCTTATCCTCATGATCCTCCGAAGGTCAAATGCAAGACCAAG                         GTGTACCATCCAAATATTGATTTGGAAGGCAATGTCTGTCTGAACATTCTG
genomic: TGTCCCCATCTTATCCTCATGATCCTCCGAAGGTCAAATGCAAGACCAAGgtataaggca ... atgcattcagGTGTACCATCCAAATATTGATTTGGAAGGCAATGTCTGTCTGAACATTCTG
EST: gi|211407585|gb|FL360124.1|FL360124
EST:     TGTCCCCATCTTATCCTCATGATCCTCCGAAGGTCAAATGCAAGACCAAG                         GTGTACCATCCAAATATTGATTTGGAAGGCAATGTCTGTCTGAACATTCTG
genomic: TGTCCCCATCTTATCCTCATGATCCTCCGAAGGTCAAATGCAAGACCAAGgtataaggca ... atgcattcagGTGTACCATCCAAATATTGATTTGGAAGGCAATGTCTGTCTGAACATTCTG
EST: gi|211291786|gb|FL131029.1|FL131029
EST:     TGTCCCCATCTTATCCTCATGATCCTCCGAAG-TCAAATGCAAGACCAAG                         GTGTACCATCCAAATATTGATTTGGAAGGCAATGTCTGTCTGAACATTCTG
genomic: TGTCCCCATCTTATCCTCATGATCCTCCGAAGGTCAAATGCAAGACCAAGgtataaggca ... atgcattcagGTGTACCATCCAAATATTGATTTGGAAGGCAATGTCTGTCTGAACATTCTG
EST: gi|78077788|gb|DV506217.1|DV506217
EST:     TGTCCCCATCTTATCCTCATGATCCTCCGAAGGTCAAATGCAAGACCAAG                         GTGTACCATCCAAATATTGATTTGGAAGGCAATGTCTGTCTGAACATTCTG
genomic: TGTCCCCATCTTATCCTCATGATCCTCCGAAGGTCAAATGCAAGACCAAGgtataaggca ... atgcattcagGTGTACCATCCAAATATTGATTTGGAAGGCAATGTCTGTCTGAACATTCTG
EST: gi|91875000|gb|EB404957.1|EB404957
EST:     TGTCCCCATCTTATCCTCATGATCCTCCGAAGGTCAAATGCAAGACCAAG                         GTGTACCATCCAAATATTGATTTGGAAGGCAATGTCTGTCTGAACATTCTG
genomic: TGTCCCCATCTTATCCTCATGATCCTCCGAAGGTCAAATGCAAGACCAAGgtataaggca ... atgcattcagGTGTACCATCCAAATATTGATTTGGAAGGCAATGTCTGTCTGAACATTCTG
EST: gi|211291784|gb|FL131027.1|FL131027
EST:     TGTCCCCATCTTATCCTCATGATCCTCCGAAG-TCAAATGCAAGACCAAG                         GTGTACCATCCAAATATTGATTTGGAAGGCAATGTCTGTCTGAACATTCTG
genomic: TGTCCCCATCTTATCCTCATGATCCTCCGAAGGTCAAATGCAAGACCAAGgtataaggca ... atgcattcagGTGTACCATCCAAATATTGATTTGGAAGGCAATGTCTGTCTGAACATTCTG
EST: gi|8516280|gb|BE123007.1|BE123007
EST:     TGTCCCCATCTTATCCTCATGATCCTCCGAAGGTCAAATGCAAGACCAAG                         GTGTACCATCCAAATATTGATTTGGAAGGCAATGTCTGTCTGAACATTCTG
genomic: TGTCCCCATCTTATCCTCATGATCCTCCGAAGGTCAAATGCAAGACCAAGgtataaggca ... atgcattcagGTGTACCATCCAAATATTGATTTGGAAGGCAATGTCTGTCTGAACATTCTG
EST: gi|19770077|gb|BQ034798.1|BQ034798
EST:     TGTCCCCATCTTATCCTCATGATCCTCCGAAGGTCAAATGCAAGACCAAG                         GTGTACCATCCAAATATTGATCTGGAAGGCAATGTCTGTCTGAACATTCTG
genomic: TGTCCCCATCTTATCCTCATGATCCTCCGAAGGTCAAATGCAAGACCAAGgtataaggca ... atgcattcagGTGTACCATCCAAATATTGATTTGGAAGGCAATGTCTGTCTGAACATTCTG
EST: gi|71442439|gb|DR823489.1|DR823489
EST:     TGTCCCCATCTTATCCTCATGATCCTCCGAAGGTCAAATGCAAGACCAAG                         GTGTACCATCCAAATATTGATCTGGAAGGCAATGTCTGTCTGAACATTCTG
genomic: TGTCCCCATCTTATCCTCATGATCCTCCGAAGGTCAAATGCAAGACCAAGgtataaggca ... atgcattcagGTGTACCATCCAAATATTGATTTGGAAGGCAATGTCTGTCTGAACATTCTG
EST: gi|211090799|gb|FL312054.1|FL312054
EST:     TGTCCCCATCTTATCCTCATGATCCTCCGAAGGTCAAATGCAAGACCAAG                         GTGTACCATCCAAATATTGATTTGGAAGGCAATGTCTGTCTGAACATTCTG
genomic: TGTCCCCATCTTATCCTCATGATCCTCCGAAGGTCAAATGCAAGACCAAGgtataaggca ... atgcattcagGTGTACCATCCAAATATTGATTTGGAAGGCAATGTCTGTCTGAACATTCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattacatttcttctaaagtgattaaatacttagctgttataaacatgcattcagGTGTACCATCCAAATATTGATTTGGAAGGCAATGTCTGTCTGAACATTCTGCGTGAAGATTGGAAGCCTGTTCTCAACATCAACACCGTTATTTATGGCC
           ttctaaa  putative branch site (score: 2)
              taaagtgattaaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtataaggcagtattctttacatctatggttctttctgattatccactaaattacatttcttctaaagtgattaaatacttagctgttataaacatgcattcagGTGTACCATCCAAATATTGATTTGGAAGGCAATGTCTGTCTGAACATTCTGCGTGAAGATTGGAAGCCTGTTCTCAACATCAACACCGTTATTTATGGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG