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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cattttctaaataccagacattgcaaatctggcaaccacgctttttctatgttactgcaggtgggtctgattaactatttaaatttattgattatcatagATACTCTTTGAACATATGGGATGTTGGAGGACAGAAGACAATCAGGTCTTACTGGAGAAACTACTTTGAGCAGACTGATGGATTAGTTTGGGTTGTTGAT

Basic information

species Zea mays
transcript GRMZM2G154890_T03
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G154890_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g22140.1 (Oryza sativa), 3'ss of exon 3
cattttctaaataccagacattgcaaatctggcaaccacgctttttctatgttactgcaggt--gggtctgattaactatttaaatttattgattatcatagATACTCTTTGAACATATGGGATGTTGGAGGACAGAAGACAATCAGGTCTTACTGGAGAAACTACTTTGAGCAGACTGATGGATTAGTTTGGGTTGTTGAT
  |  ||     | ||| ||   ||     ||||       |   | | | ||||| ||||   |    | || ||  || |   |||  | ||| |   || ||||| ||||||||||||||| | || ||||||||||| ||| | ||||||||||| || ||||||||||| ||||||||| |||||||||| ||||||
actgatcattgcatcagccaaaaca--ctaggcatagcaattccatttgtattacttcagggtggaaattaatgaataatgtttgttttgtcattgtggcagGTACTCATTGAACATATGGGATATCGGTGGACAGAAGACTATCCGATCTTACTGGAGGAATTACTTTGAGCAAACTGATGGACTAGTTTGGGTGGTTGAT

upper sequence: GRMZM2G154890_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA11G07330.1 (Glycine max), 3'ss of exon 2
cattttctaaataccagacattgcaaatctggcaaccacgctttttctatgttactgcaggtgggtctgattaactatttaaatttattgattatcatagATACTCTTTGAACATATGGGATGTTGGAGGACAGAAGACAATCAGGTCTTACTGGAGAAACTACTTTGAGCAGACTGATGGATTAGTTTGGGTTGTTGAT
       ||| |  ||    |  |||  |   ||   |   |    |||  || ||    ||   | |  || |   |||    |  ||||   |  ||| ||  |  | || |||||||||||||| || ||||| ||||| || |||||||||||||||||||||||||| || ||||| || |||||||| ||||| 
------gtaattctcacttttcacaacccaatcacatagcttgaaactagtttgct---tgttattttacttgatggttt---ctctttgacattgttagGTATACCCTAAATATATGGGATGTTGGGGGCCAGAAAACAATAAGATCTTACTGGAGAAACTACTTTGAGCAAACAGATGGTTTGGTTTGGGTGGTTGAC

upper sequence: GRMZM2G154890_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA01G38270.1 (Glycine max), 3'ss of exon 2
cattttctaaataccagacattgcaaatctggcaaccacgctttttcta-tgttactgcaggtg-ggtctgattaactatttaaatttattgattatcatagATACTCTTTGAACATATGGGATGTTGGAGGACAGAAGACAATCAGGTCTTACTGGAGAAACTACTTTGAGCAGACTGATGGATTAGTTTGGGTTGTTGAT
           ||     || |    | |   ||| |||  | |      | | | |    | |  || |||  || |||||   | |  | ||| |  ||| ||  || | || |||||||||||||| || ||||| ||||| || |||||||||||||||||||||||||| || ||||| || |||||||| ||||| 
----------gtaattttcacttttcaccactcaatcacattataatagctatcattatgtgcgtagtgtga--aattatttgcttcttattattgt--tagGTATACTCTAAATATATGGGATGTTGGGGGGCAGAAAACAATAAGATCTTACTGGAGAAACTACTTTGAGCAAACAGATGGTTTGGTTTGGGTGGTTGAC

upper sequence: GRMZM2G154890_T03 (Zea mays), 3'ss of exon 3
lower sequence: AT2G18390.1 (Arabidopsis thaliana), 3'ss of exon 2
-----------------cattttctaaataccagacattgcaaatctggcaaccacgctttttctatgttactgcaggtgggtctgattaactatttaaatttattgattatcatagATACTCTTTGAACATATGGGATGTTGGAGGACAGAAGACAATCAGGTCTTACTGGAGAAACTACTTTGAGCAGACTGATGGATTAGTTTGGGTTGTTGAT
                    | |   | |  |      | || |  |||         ||  || |   |  |  |||      |||| |  |  |      || ||  | |  ||| ||  |  | || |||||||||||||| || || ||||| || || || || ||||| || |||||||||||||||||||| || |||||||| ||||||
gtaaagctctatttctctgctcttgtagtttcgtgttcttcagagttggtttaggaatttcatcgaacatgttataggcaa---tgatgagtttgtggtgaataatgtgtgt-gtagGTATACGCTAAATATATGGGATGTTGGTGGGCAAAAGACTATAAGATCGTATTGGAGGAATTACTTTGAGCAGACTGATGGTTTGGTTTGGGTGGTTGAT

upper sequence: GRMZM2G154890_T03 (Zea mays), 3'ss of exon 3
lower sequence: Vv04s0023g01820.t01 (Vitis vinifera), 3'ss of exon 3
cattttctaaataccagacattgcaaatctggcaaccacgctttttctatgtt-actgcaggtgggtctgattaact---atttaaatttatt--gattatcatagATACTCTTTGAACATATGGGATGTTGGAGGACAGAAGACAATCAGGTCTTACTGGAGAAACTACTTTGAGCAGACTGATGGATTAGTTTGGGTTGTTGAT
    ||  || |   |  | ||  | || ||      | | ||| |   | || | ||    | ||  |||    ||   |||  | |||  |  || | | | || ||  || | || |||||||||||||| || || |  || || || |||||||||||||||||||| || || |||||||| || || ||||| ||||||
----ttacaactgatatgc-ttatagat-tgatcctgaggttttatacctatttattgggcattgggttgagacgctgaaattccattttggtatgaatctgacagGTATACTCTTAATATATGGGATGTTGGGGGCCAAAGAACCATAAGATCTTACTGGAGAAACTACTTCGAACAAACTGATGGTTTGGTATGGGTCGTTGAT

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|34391377|gb|CF384605.1|CF384605
EST:     GTCATTAGCCCAACCCTTGGATTCAACATCAAGACCATCAAGTACCACAA                         ATACTCTTTGAACATATGGGATGTTGGAGGACAGAAGACAATCAGGTCTTA
genomic: ATCATTAGCCCAACCCTTGGATTCAACATCAAGACCATCAAGTACCACAAgtatgttccc ... attatcatagATACTCTTTGAACATATGGGATGTTGGAGGACAGAAGACAATCAGGTCTTA
EST: gi|91874746|gb|EB404703.1|EB404703
EST:     ATCATTAGCCCAACCCTTGGATTCAACATCAAGACCATCAAGTACCACAA                         ATACTCTTTGAACATATGGGATGTTGGAGGACAGAAGACAATCAGGTCTTA
genomic: ATCATTAGCCCAACCCTTGGATTCAACATCAAGACCATCAAGTACCACAAgtatgttccc ... attatcatagATACTCTTTGAACATATGGGATGTTGGAGGACAGAAGACAATCAGGTCTTA
EST: gi|89755818|gb|DY686096.1|DY686096
EST:     TCATTAGCCCAACCCCTTGGATTCAACATCAAGACCATCAAGTACCACAA                         ATACTCTTTGAACATATGGGATGGTGGGAGGACAGAAGACAATCAGGTCTT
genomic: TCATTAGCCCAACCC-TTGGATTCAACATCAAGACCATCAAGTACCACAAgtatgttccc ... attatcatagATACTCTTTGAACATATGGGATGTTGG-AGGACAGAAGACAATCAGGTCTT
EST: gi|78112616|gb|DV531010.1|DV531010
EST:     ATCATTAGCCCAACCCTTGGATTCAACATCAAGACCATCAAGTACCACAA                         ATACTCTTTGAACATATGGGATGTTGGAGGACAGAAGACAATCAGGTCTTA
genomic: ATCATTAGCCCAACCCTTGGATTCAACATCAAGACCATCAAGTACCACAAgtatgttccc ... attatcatagATACTCTTTGAACATATGGGATGTTGGAGGACAGAAGACAATCAGGTCTTA
EST: gi|60358498|gb|DN225471.1|DN225471
EST:     ATCATTAGCCCAACCCTTGGATTCAACATCAAGACCATCAAGTACCACAA                         ATACTCTTTGAACATATGGGATGTTGGAGGACAGAAGACAATCAGGTCTTA
genomic: ATCATTAGCCCAACCCTTGGATTCAACATCAAGACCATCAAGTACCACAAgtatgttccc ... attatcatagATACTCTTTGAACATATGGGATGTTGGAGGACAGAAGACAATCAGGTCTTA
EST: gi|60345034|gb|DN212007.1|DN212007
EST:     ATCATTAGCCCAACCCTTGGATTCAACATCAAGACCATCAAGTACCACAA                         ATACTCTTTGAACATATGGGATGTTGGAGGACAGAAGACAATCAGGTCTTA
genomic: ATCATTAGCCCAACCCTTGGATTCAACATCAAGACCATCAAGTACCACAAgtatgttccc ... attatcatagATACTCTTTGAACATATGGGATGTTGGAGGACAGAAGACAATCAGGTCTTA
EST: gi|76016498|gb|DT943668.1|DT943668
EST:     ATCATTAGCCCAACCCTTGGATTCAACATCAAGACCATCAAGTACCACAA                         ATACTCTTTGAACATATGGGATGTTGGAGGACAGAAGACAATCAGGTCTTA
genomic: ATCATTAGCCCAACCCTTGGATTCAACATCAAGACCATCAAGTACCACAAgtatgttccc ... attatcatagATACTCTTTGAACATATGGGATGTTGGAGGACAGAAGACAATCAGGTCTTA
EST: gi|78114767|gb|DV533155.1|DV533155
EST:     ATCATTAGCCCAACCCTTGGATTCAACATCAAGACCATCAAGTACCACAA                         ATACTCTTTGAACATATGGGATGTTGGAGGACAGAAGACAATCAGGTCTTA
genomic: ATCATTAGCCCAACCCTTGGATTCAACATCAAGACCATCAAGTACCACAAgtatgttccc ... attatcatagATACTCTTTGAACATATGGGATGTTGGAGGACAGAAGACAATCAGGTCTTA
EST: gi|5932640|gb|AW057001.1|AW057001
EST:     GTCATTAGCCCAACCCTTGGATTCAACATCAAGACCATCAAGTACCACAA                         ATACTCTTTGAACATATGGGATGTTGGAGGACAGAAGACAATCAGGTCTTA
genomic: ATCATTAGCCCAACCCTTGGATTCAACATCAAGACCATCAAGTACCACAAgtatgttccc ... attatcatagATACTCTTTGAACATATGGGATGTTGGAGGACAGAAGACAATCAGGTCTTA
EST: gi|91874745|gb|EB404702.1|EB404702
EST:     CAACATCAAGACCATCAAGTACCACAA                         ATACTCTTTGAACATATGGGATGTTGGAGGACAGAAGACAATCAGGTCTTA
genomic: CAACATCAAGACCATCAAGTACCACAAgtatgttccc ... attatcatagATACTCTTTGAACATATGGGATGTTGGAGGACAGAAGACAATCAGGTCTTA
EST: gi|60337602|gb|DN204575.1|DN204575
EST:     GTCATTAGCCCAACCCTTGGATTCAACATCAAGACCATCAAGTACCACAA                         ATACTCTTTGAACATATGGGATGTTGGAGGACAGAAGACAATCAGGTCTTA
genomic: ATCATTAGCCCAACCCTTGGATTCAACATCAAGACCATCAAGTACCACAAgtatgttccc ... attatcatagATACTCTTTGAACATATGGGATGTTGGAGGACAGAAGACAATCAGGTCTTA
EST: gi|60345576|gb|DN212549.1|DN212549
EST:     ATCATTAGCCCAACCCTTGGATTCAACATCAAGACCATCAAGTACCACAA                         ATACTCTTTGAACATATGGGATGTTGGAGGACAGAAGACAATCAGGTCTTA
genomic: ATCATTAGCCCAACCCTTGGATTCAACATCAAGACCATCAAGTACCACAAgtatgttccc ... attatcatagATACTCTTTGAACATATGGGATGTTGGAGGACAGAAGACAATCAGGTCTTA
EST: gi|78114766|gb|DV533154.1|DV533154
EST:     ATCATTAGCCCAACCCTTGGATTCAACATCAAGACCATCAAGTACCACAA                         ATACTCTTTGAACATATGGGATGTTGGAGGACAGAAGACAATCAGGTCTTA
genomic: ATCATTAGCCCAACCCTTGGATTCAACATCAAGACCATCAAGTACCACAAgtatgttccc ... attatcatagATACTCTTTGAACATATGGGATGTTGGAGGACAGAAGACAATCAGGTCTTA
EST: gi|50335743|gb|CO530869.1|CO530869
EST:     ATCATTAGCCCAACCCTTGGATTCAACATCAAGACCATCAAGTACCACAA                         ATACTCTTTGAACATATGGGATGTTGGAGGACAGAAGACAATCAGGTCTTA
genomic: ATCATTAGCCCAACCCTTGGATTCAACATCAAGACCATCAAGTACCACAAgtatgttccc ... attatcatagATACTCTTTGAACATATGGGATGTTGGAGGACAGAAGACAATCAGGTCTTA
EST: gi|60336929|gb|DN203902.1|DN203902
EST:     GCCCAACCCTTGGATTCAACATCAAGACCATCAAGTACCACAA                         ATACTCTTTGAACATATGGGATGTTGGAGGACAGAAGACAATCAGGTCTTA
genomic: GCCCAACCCTTGGATTCAACATCAAGACCATCAAGTACCACAAgtatgttccc ... attatcatagATACTCTTTGAACATATGGGATGTTGGAGGACAGAAGACAATCAGGTCTTA
EST: gi|76016499|gb|DT943669.1|DT943669
EST:     ATCATTAGCCCAACCCTTGGATTCAACATCAAGACCATCAAGTACCACAA                         ATACTCTTTGAACATATGGGATGTTGGAGGACAGAAGACAATCAGGTCTTA
genomic: ATCATTAGCCCAACCCTTGGATTCAACATCAAGACCATCAAGTACCACAAgtatgttccc ... attatcatagATACTCTTTGAACATATGGGATGTTGGAGGACAGAAGACAATCAGGTCTTA
EST: gi|19351517|gb|BM896049.1|BM896049
EST:     CCCAACCCTTGGATTCAACATCAAGACCATCAAGTACCACAA                         ATACTCTTTGAACATATGGGATGTTGGAGGACAGAAGACAATCAGGTCTTA
genomic: CCCAACCCTTGGATTCAACATCAAGACCATCAAGTACCACAAgtatgttccc ... attatcatagATACTCTTTGAACATATGGGATGTTGGAGGACAGAAGACAATCAGGTCTTA
EST: gi|86469538|gb|DY235908.1|DY235908
EST:     ATCATTAGCCCAACCCTTGGATTCAACATCAAGACCATCAAGTACCACAA                         ATACTCTTTGAACATATGGGATGTTGGAGGACAGAAGACAATCAGGTCTTA
genomic: ATCATTAGCCCAACCCTTGGATTCAACATCAAGACCATCAAGTACCACAAgtatgttccc ... attatcatagATACTCTTTGAACATATGGGATGTTGGAGGACAGAAGACAATCAGGTCTTA
EST: gi|60339777|gb|DN206750.1|DN206750
EST:     CCATCAAGTACCACAA                         ATACTCTTTGAACATATGGGATGTTGGAGGACAGAAGACAATCAGGTCTTA
genomic: CCATCAAGTACCACAAgtatgttccc ... attatcatagATACTCTTTGAACATATGGGATGTTGGAGGACAGAAGACAATCAGGTCTTA
EST: gi|76286526|gb|DV026094.1|DV026094
EST:     ATCATTAGCCCAACCCTTGGATTCAACATCAAGACCATCAAGTACCACAA                         ATACTCTTTGAACATATGGGATGTTGGAGGACAGAAGACAATCAGGTCTTA
genomic: ATCATTAGCCCAACCCTTGGATTCAACATCAAGACCATCAAGTACCACAAgtatgttccc ... attatcatagATACTCTTTGAACATATGGGATGTTGGAGGACAGAAGACAATCAGGTCTTA
EST: gi|71318962|gb|DR796230.1|DR796230
EST:     TAGCCCAACCCTTGGATTCAACATCAAGACCATCAAGTACCACAA                         ATACTCTTTGAACATATGGGATGTTGGAGGACAGAAGACAATCAGTTCTTA
genomic: TAGCCCAACCCTTGGATTCAACATCAAGACCATCAAGTACCACAAgtatgttccc ... attatcatagATACTCTTTGAACATATGGGATGTTGGAGGACAGAAGACAATCAGGTCTTA
EST: gi|78112615|gb|DV531009.1|DV531009
EST:     ATCATTAGCCCAACCCTTGGATTCAACATCAAGACCATCAAGTACCACAA                         ATACTCTTTGAACATATGGGATGTTGGAGGACAGAAGACAATCAGGTCTTA
genomic: ATCATTAGCCCAACCCTTGGATTCAACATCAAGACCATCAAGTACCACAAgtatgttccc ... attatcatagATACTCTTTGAACATATGGGATGTTGGAGGACAGAAGACAATCAGGTCTTA
EST: gi|74239326|gb|DT647240.1|DT647240
EST:     ATCATTAGCCCAACCCTTGGATTCAACATCAAGACCATCAAGTACCACAA                         ATACTCTTTGAACATATGGGATGTTGGAGGACAGAAGACAATCAGGTCTTA
genomic: ATCATTAGCCCAACCCTTGGATTCAACATCAAGACCATCAAGTACCACAAgtatgttccc ... attatcatagATACTCTTTGAACATATGGGATGTTGGAGGACAGAAGACAATCAGGTCTTA
EST: gi|71318964|gb|DR796231.1|DR796231
EST:     ATCATTAGCCCAACCCTTGGATTCAACATCAAGACCATCAAGTACCACAA                         ATACTCTTTGAACATATGGGATGTTGGAGGACAGAAGACAATCA
genomic: ATCATTAGCCCAACCCTTGGATTCAACATCAAGACCATCAAGTACCACAAgtatgttccc ... attatcatagATACTCTTTGAACATATGGGATGTTGGAGGACAGAAGACAATCA
EST: gi|78082479|gb|DV510891.1|DV510891
EST:     ATCATTAGCCCAACCCTTGGATTCAACATCAAGACCATCAAGTACCACAA                         ATACTCTTTGAACATATGGGATGTTGGAGGACAGAAGACAATCAGGTCTTA
genomic: ATCATTAGCCCAACCCTTGGATTCAACATCAAGACCATCAAGTACCACAAgtatgttccc ... attatcatagATACTCTTTGAACATATGGGATGTTGGAGGACAGAAGACAATCAGGTCTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctatgttactgcaggtgggtctgattaactatttaaatttattgattatcatagATACTCTTTGAACATATGGGATGTTGGAGGACAGAAGACAATCAGGTCTTACTGGAGAAACTACTTTGAGCAGACTGATGGATTAGTTTGGGTTGTTGAT
                    tctgattaactattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cattttctaaataccagacattgcaaatctggcaaccacgctttttctatgttactgcaggtgggtctgattaactatttaaatttattgattatcatagATACTCTTTGAACATATGGGATGTTGGAGGACAGAAGACAATCAGGTCTTACTGGAGAAACTACTTTGAGCAGACTGATGGATTAGTTTGGGTTGTTGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA