Skip to another splice site:
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaataagcttgcttttttcccgtgttgctacgacaccaaacgccatgcatttctttaaactttggtgtactaaaaaaaagctcgtcgtacgtctgctcgttctctttgcatccagTGCTGGGAAACCATGACTACAGGGGTGACGCGCTCGCGCAGCTGAGCCCGGTCCTGCGGAAGATCGACAGCCGGTTCATTTGCATCAAATCATTCGTCGT

Basic information

species Zea mays
transcript GRMZM2G152477_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G152477_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g13540.1 (Oryza sativa), 3'ss of exon 2
gtaataagcttgcttttt-tcccgtgttgctacgacaccaaacgccatgcatttctttaaactttggtgtactaaaaaaaagctcgt-cgtacgtctgctcgttctctttgcatccagTGCTGGGAAACCATGACTACAGGGGTGACGCGCTCGCGCAGCTGAGCCCGGTCCTGCGGAAGATCGACAGCCGGTTCATTTGCATCAAATCATTCGTCGT
||||      ||||| || || | | |  |  | | | ||    ||| | |   || | |       | | |||| |      | |  |||         | |   | || | | ||||||||||||| ||||||||||||||||| | ||| || ||||| ||||| ||| |||| |||||||||   || ||||||||||| |  || ||| | ||
gtaagctttctgcttcttgtcacttatgtcaccaataacatttaccaagtacccctgtta--cgaaatatgctaatatgttatttgaacgtgtactaaaacatgaacatttc-ttcagTGCTGGGAAATCATGACTACAGGGGTGATGTGCTAGCACAGCTTAGCCCAGTCTTGCGAAAGATCGACCAGCGATTCATTTGCATGAGGTCGTTCATTGT
















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|101397948|gb|EB820851.1|EB820851
EST:     TTTCACCGATATCTACACGGCGAAGAGCCTGCAGAAGCCGTGGTACCTGG                         TGCTGGGAAACCATGACTACAGGGGTGACGCGCTCGCGCAGCTGAGCCCGG
genomic: TTTCACCGATATCTACACGGCGAAGAGCCTGCAGAAGCCGTGGTACCTGGgtaataagct ... ttgcatccagTGCTGGGAAACCATGACTACAGGGGTGACGCGCTCGCGCAGCTGAGCCCGG
EST: gi|149107111|gb|EE189001.2|EE189001
EST:     TTTCACCGATATCTACACGGCGAAGAGCCTGCAGAAGCCGTGGTACCTGG                         TGCTGGGAAACCATGACTACAGGGGTGACGCGCTCGCGCAGCTGAGCCCGG
genomic: TTTCACCGATATCTACACGGCGAAGAGCCTGCAGAAGCCGTGGTACCTGGgtaataagct ... ttgcatccagTGCTGGGAAACCATGACTACAGGGGTGACGCGCTCGCGCAGCTGAGCCCGG
EST: gi|50335510|gb|CO530636.1|CO530636
EST:     TTTCACCGATATCTACACGGCGAAGAGCCTGCAGAAGCCGTGGTACCTGG                         TGCTGGGAAACCATGACTACAGGGGTGACGCGCTCGCGCAGCTGAGCCCGG
genomic: TTTCACCGATATCTACACGGCGAAGAGCCTGCAGAAGCCGTGGTACCTGGgtaataagct ... ttgcatccagTGCTGGGAAACCATGACTACAGGGGTGACGCGCTCGCGCAGCTGAGCCCGG
EST: gi|71767234|gb|DR965171.1|DR965171
EST:     TTTCACCGATATCTACACGGCGAAGAGCCTGCAGAAGCCGTGGTACCTGG                         TGCTGGGAAACCATGACTACAGGGGTGACGCGCTCGCGCAGCTGAGCCCGG
genomic: TTTCACCGATATCTACACGGCGAAGAGCCTGCAGAAGCCGTGGTACCTGGgtaataagct ... ttgcatccagTGCTGGGAAACCATGACTACAGGGGTGACGCGCTCGCGCAGCTGAGCCCGG
EST: gi|148973087|gb|EE024151.2|EE024151
EST:     TTTCACCGATATCTACACGGCGAAGAGCCTGCAGAAGCCGTGGTACCTGG                         TGCTGGGAAACCATGACTACAGGGGTGACGCGCTCGCGCAGCTGAGCCCGG
genomic: TTTCACCGATATCTACACGGCGAAGAGCCTGCAGAAGCCGTGGTACCTGGgtaataagct ... ttgcatccagTGCTGGGAAACCATGACTACAGGGGTGACGCGCTCGCGCAGCTGAGCCCGG
EST: gi|149072306|gb|EE160571.2|EE160571
EST:     TTTCACCGATATCTACACGGCGAAGAGCCTGCAGAAGCCGTGGTACCTGG                         TGCTGGGAAACCATGACTACAGGGGTGACGCGCTCGCGCAGCTGAGCCCGG
genomic: TTTCACCGATATCTACACGGCGAAGAGCCTGCAGAAGCCGTGGTACCTGGgtaataagct ... ttgcatccagTGCTGGGAAACCATGACTACAGGGGTGACGCGCTCGCGCAGCTGAGCCCGG
EST: gi|76289549|gb|DV029117.1|DV029117
EST:     TTTCACCGATATCTACACGGCGAAGAGCCTGCAGAAGCCGTGGTACCTGG                         TGCTGGGAAACCATGACTACAGGGGTGACGCGCTCGCGCAGCTGAGCCCGG
genomic: TTTCACCGATATCTACACGGCGAAGAGCCTGCAGAAGCCGTGGTACCTGGgtaataagct ... ttgcatccagTGCTGGGAAACCATGACTACAGGGGTGACGCGCTCGCGCAGCTGAGCCCGG
EST: gi|89247687|gb|DY619473.1|DY619473
EST:     TTTCACCGATATCTACACGGCGAAGAGCCTGCAGAAGCCGTGGTACCTGG                         TGCTGGGAAACCATGACTACAGGGGTGACGCGCTCGCGCAGCTGAGCCCGG
genomic: TTTCACCGATATCTACACGGCGAAGAGCCTGCAGAAGCCGTGGTACCTGGgtaataagct ... ttgcatccagTGCTGGGAAACCATGACTACAGGGGTGACGCGCTCGCGCAGCTGAGCCCGG
EST: gi|78087669|gb|DV516062.1|DV516062
EST:     TTTCACCGATATCTACACGGCGAAGAGCCTGCAGAAGCCGTGGTACCTGG                         TGCTGGGAAACCATGACTACAGGGGTGACGCGCTCGCGCAGCTGAGCCCGG
genomic: TTTCACCGATATCTACACGGCGAAGAGCCTGCAGAAGCCGTGGTACCTGGgtaataagct ... ttgcatccagTGCTGGGAAACCATGACTACAGGGGTGACGCGCTCGCGCAGCTGAGCCCGG
EST: gi|74239383|gb|DT647297.1|DT647297
EST:     TTTCACCGATATCTACACGGCGAAGAGCCTGCAGAAGCCGTGGTACCTGG                         TGCTGGGAAACCATGACTACAGGGGTGACGCGCTCGCGCAGCTGAGCCCGG
genomic: TTTCACCGATATCTACACGGCGAAGAGCCTGCAGAAGCCGTGGTACCTGGgtaataagct ... ttgcatccagTGCTGGGAAACCATGACTACAGGGGTGACGCGCTCGCGCAGCTGAGCCCGG
EST: gi|37426126|gb|CF650813.1|CF650813
EST:     TTTCACCGATATCTACACGGCGAAGAGCCTGCAGAAGCCGTGGTACCTGG                         TGCTGGGAAACCATGACTACAGGGGTGACGCGCTCGCGCAGCTGAGCCCGG
genomic: TTTCACCGATATCTACACGGCGAAGAGCCTGCAGAAGCCGTGGTACCTGGgtaataagct ... ttgcatccagTGCTGGGAAACCATGACTACAGGGGTGACGCGCTCGCGCAGCTGAGCCCGG
EST: gi|71432358|gb|DR813408.1|DR813408
EST:     TTTCACCGATATCTACACGGCGAAGAGCCTGCAGAAGCCGTGGTACCTGG                         TGCTGGGAAACCATGACTACAGGGGTGACGCGCTCGCGCAGCTGAGCCCGG
genomic: TTTCACCGATATCTACACGGCGAAGAGCCTGCAGAAGCCGTGGTACCTGGgtaataagct ... ttgcatccagTGCTGGGAAACCATGACTACAGGGGTGACGCGCTCGCGCAGCTGAGCCCGG
EST: gi|76012119|gb|DT939289.1|DT939289
EST:     TTTCACCGATATCTACACGGCGAAGAGCCTGCAGAAGCCGTGGTACCTGG                         TGCTGGGAAACCATGACTACAGGGGTGACGCGCTCGCGCAGCTGAGCCCGG
genomic: TTTCACCGATATCTACACGGCGAAGAGCCTGCAGAAGCCGTGGTACCTGGgtaataagct ... ttgcatccagTGCTGGGAAACCATGACTACAGGGGTGACGCGCTCGCGCAGCTGAGCCCGG
EST: gi|20299974|gb|BQ162917.1|BQ162917
EST:     TTTCACCGATATCTACACGGCGAAGAGCCTGCAGAAGCCGTGGTACCTGG                         TGCTGGGAAACCATGACTACAGGGGTGACGCGCTCGCGCAGCTGAGCCCGG
genomic: TTTCACCGATATCTACACGGCGAAGAGCCTGCAGAAGCCGTGGTACCTGGgtaataagct ... ttgcatccagTGCTGGGAAACCATGACTACAGGGGTGACGCGCTCGCGCAGCTGAGCCCGG
EST: gi|148943407|gb|EC888466.2|EC888466
EST:     TTTCACCGATATCTACACGGCGAAGAGCCTGCAGAAGCCGTGGTACCTGG                         TGCTGGGAAACCATGACTACAGGGGTGACGCGCTCGCGCAGCTGAGCCCGG
genomic: TTTCACCGATATCTACACGGCGAAGAGCCTGCAGAAGCCGTGGTACCTGGgtaataagct ... ttgcatccagTGCTGGGAAACCATGACTACAGGGGTGACGCGCTCGCGCAGCTGAGCCCGG
EST: gi|148966046|gb|EE016980.2|EE016980
EST:     TTTCACCGATATCTACACGGCGAAGAGCCTGCAGAAGCCGTGGTACCTGG                         TGCTGGGAAACCATGACTACAGGGGTGACGCGCTCGCGCAGCTGAGCCCGG
genomic: TTTCACCGATATCTACACGGCGAAGAGCCTGCAGAAGCCGTGGTACCTGGgtaataagct ... ttgcatccagTGCTGGGAAACCATGACTACAGGGGTGACGCGCTCGCGCAGCTGAGCCCGG
EST: gi|71767917|gb|DR965854.1|DR965854
EST:     TTTCACCGATATCTACACGGCGAAGAGCCTGCAGAAGCCGTGGTACCTGG                         TGCTGGGAAACCATGACTACAGGGGTGACGCGCTCGCGCAGCTGAGCCCGG
genomic: TTTCACCGATATCTACACGGCGAAGAGCCTGCAGAAGCCGTGGTACCTGGgtaataagct ... ttgcatccagTGCTGGGAAACCATGACTACAGGGGTGACGCGCTCGCGCAGCTGAGCCCGG
EST: gi|78118175|gb|DV536562.1|DV536562
EST:     TTTCACCGATATCTACACGGCGAAGAGCCTGCAGAAGCCGTGGTACCTGG                         TGCTGGGAA-CCATGACTACAGGGGTG
genomic: TTTCACCGATATCTACACGGCGAAGAGCCTGCAGAAGCCGTGGTACCTGGgtaataagct ... ttgcatccagTGCTGGGAAACCATGACTACAGGGGTG
EST: gi|76012840|gb|DT940010.1|DT940010
EST:     TTTCACCGATATCTACACGGCGAAGAGCCTGCAGAAGCCGTGGTACCTGG                         TGCTGGGAAACCATGACTACAGGGGTGACGCGCTCGCGCAGCTGAGCCCGG
genomic: TTTCACCGATATCTACACGGCGAAGAGCCTGCAGAAGCCGTGGTACCTGGgtaataagct ... ttgcatccagTGCTGGGAAACCATGACTACAGGGGTGACGCGCTCGCGCAGCTGAGCCCGG
EST: gi|19821796|gb|BQ047820.1|BQ047820
EST:     TTTCACCGATATCTACACGGCGAAGAGCCTGCAGAAGCCGTGGTACCTGG                         TGCTGGGAAACCATGACTACAGGGGTGACGCGCTCGCGCAGCTGAGCCCGG
genomic: TTTCACCGATATCTACACGGCGAAGAGCCTGCAGAAGCCGTGGTACCTGGgtaataagct ... ttgcatccagTGCTGGGAAACCATGACTACAGGGGTGACGCGCTCGCGCAGCTGAGCCCGG
EST: gi|76280616|gb|DV020184.1|DV020184
EST:     TTTCACCGATATCTACACGGCGAAGAGCCTGCAGAAGCCGTGGTACCTGG                         TGCTGGGAAACCATGACTACAGGGGTGACGCGCTCGCGCAGCTGAGCCCGG
genomic: TTTCACCGATATCTACACGGCGAAGAGCCTGCAGAAGCCGTGGTACCTGGgtaataagct ... ttgcatccagTGCTGGGAAACCATGACTACAGGGGTGACGCGCTCGCGCAGCTGAGCCCGG
EST: gi|78114011|gb|DV532400.1|DV532400
EST:     TTTCACCGATATCTACACGGCGAAGAGCCTGCAGAAGCCGTGGTACCTGG                         TGCTGGGAAACCATGACTACAGGGGTGACGCGCTCGCGCAGCTGAGCCCGG
genomic: TTTCACCGATATCTACACGGCGAAGAGCCTGCAGAAGCCGTGGTACCTGGgtaataagct ... ttgcatccagTGCTGGGAAACCATGACTACAGGGGTGACGCGCTCGCGCAGCTGAGCCCGG
EST: gi|149008292|gb|EE040441.2|EE040441
EST:     TTTCACCGATATCTACACGGCGAAGAGCCTGCAGAAGCCGTGGTACCTGG                         TGCTGGGAAACCATGACTACAGGGGTGACGCGCTCGCGCAGCTGAGCCCGG
genomic: TTTCACCGATATCTACACGGCGAAGAGCCTGCAGAAGCCGTGGTACCTGGgtaataagct ... ttgcatccagTGCTGGGAAACCATGACTACAGGGGTGACGCGCTCGCGCAGCTGAGCCCGG
EST: gi|78105515|gb|DV523933.1|DV523933
EST:     TTTCACCGATATCTACACGGCGAAGAGCCTGCAGAAGCCGTGGTACCTGG                         TGCTGGGAAACCATGACTACAGGGGTGACGCGCTCGCGCAGCTGAGCCCGG
genomic: TTTCACCGATATCTACACGGCGAAGAGCCTGCAGAAGCCGTGGTACCTGGgtaataagct ... ttgcatccagTGCTGGGAAACCATGACTACAGGGGTGACGCGCTCGCGCAGCTGAGCCCGG
EST: gi|74245680|gb|DT653594.1|DT653594
EST:     TTTCACCGATATCTACACGGCGAAGAGCCTGCAGAAGCCGTGGTACCTGG                         TGCTGGGAAACCATGACTACAGGGGTGACGCGCTCGCGCAGCTGAGCCCGG
genomic: TTTCACCGATATCTACACGGCGAAGAGCCTGCAGAAGCCGTGGTACCTGGgtaataagct ... ttgcatccagTGCTGGGAAACCATGACTACAGGGGTGACGCGCTCGCGCAGCTGAGCCCGG
EST: gi|71433301|gb|DR814351.1|DR814351
EST:     TTTCACCGATATCTACACGGCGAAGAGCCTGCAGAAGCCGTGGTACCTGG                         TGCTGGGAAACCATGACTACAGGGGTGACGCGCTCGCGCAGCTGAGCCCGG
genomic: TTTCACCGATATCTACACGGCGAAGAGCCTGCAGAAGCCGTGGTACCTGGgtaataagct ... ttgcatccagTGCTGGGAAACCATGACTACAGGGGTGACGCGCTCGCGCAGCTGAGCCCGG
EST: gi|149014265|gb|EE043835.2|EE043835
EST:     TTTCACCGATATCTACACGGCGAAGAGCCTGCAGAAGCCGTGGTACCTGG                         TGCTGGGAAACCATGACTACAGGGGTGACGCGCTCGCGCAGCTGAGCCCGG
genomic: TTTCACCGATATCTACACGGCGAAGAGCCTGCAGAAGCCGTGGTACCTGGgtaataagct ... ttgcatccagTGCTGGGAAACCATGACTACAGGGGTGACGCGCTCGCGCAGCTGAGCCCGG
EST: gi|149039483|gb|EE046624.2|EE046624
EST:     TTTCACCGATATCTACACGGCGAAGAGCCTGCAGAAGCCGTGGTACCTGG                         TGCTGGGAAACCATGACTACAGAGGTGACGCGCTCGCGCAGCTGAGCCCGG
genomic: TTTCACCGATATCTACACGGCGAAGAGCCTGCAGAAGCCGTGGTACCTGGgtaataagct ... ttgcatccagTGCTGGGAAACCATGACTACAGGGGTGACGCGCTCGCGCAGCTGAGCCCGG
EST: gi|211074959|gb|FL200236.1|FL200236
EST:     TTTCACCGATATCTACACGGCGAAGAGCCTGCAGAAGCCGTGGTAC-TGG                         TGCTGGGAAACCATGACTA
genomic: TTTCACCGATATCTACACGGCGAAGAGCCTGCAGAAGCCGTGGTACCTGGgtaataagct ... ttgcatccagTGCTGGGAAACCATGACTA
EST: gi|71430081|gb|DR811131.1|DR811131
EST:     TTTCACCGATATCTACACGGCGAAGAGCCTGCAGAAGCCGTGGTACCTGG                         TGCTGGGAAACCATGACTACAGGGGTGACGCGCTCGCGCAGCTGAGCCCGG
genomic: TTTCACCGATATCTACACGGCGAAGAGCCTGCAGAAGCCGTGGTACCTGGgtaataagct ... ttgcatccagTGCTGGGAAACCATGACTACAGGGGTGACGCGCTCGCGCAGCTGAGCCCGG
EST: gi|89758274|gb|DY687518.1|DY687518
EST:     TTTCACCGATATCTACACGGCGAAGAGCCTGCAGAAGCCGTGGTACCTGG                         TGCTGGGAAACCATGACTACAGGGGTGACGCGCTCGCGCAGCTGAGCCCGG
genomic: TTTCACCGATATCTACACGGCGAAGAGCCTGCAGAAGCCGTGGTACCTGGgtaataagct ... ttgcatccagTGCTGGGAAACCATGACTACAGGGGTGACGCGCTCGCGCAGCTGAGCCCGG
EST: gi|17970297|gb|BM277060.1|BM277060
EST:     TTTCACCGATATCTACACGGCGAAGAGCCTGCAGAAGCCGTGGTACCTGG                         TGCTGGGAAACCATGACTACAGGGGTGACGCGCTCGCGCAGCTGAGCCCGG
genomic: TTTCACCGATATCTACACGGCGAAGAGCCTGCAGAAGCCGTGGTACCTGGgtaataagct ... ttgcatccagTGCTGGGAAACCATGACTACAGGGGTGACGCGCTCGCGCAGCTGAGCCCGG
EST: gi|148986094|gb|EE029903.2|EE029903
EST:     TTTCACCGATATCTACACGGCGAAGAGCCTGCAGAAGCCGTGGTACCTGG                         TGCTGGGAAACCATGACTACAGGGGTGACGCGCTCGCGCAGCTGAGCCCGG
genomic: TTTCACCGATATCTACACGGCGAAGAGCCTGCAGAAGCCGTGGTACCTGGgtaataagct ... ttgcatccagTGCTGGGAAACCATGACTACAGGGGTGACGCGCTCGCGCAGCTGAGCCCGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttggtgtactaaaaaaaagctcgtcgtacgtctgctcgttctctttgcatccagTGCTGGGAAACCATGACTACAGGGGTGACGCGCTCGCGCAGCTGAGCCCGGTCCTGCGGAAGATCGACAGCCGGTTCATTTGCATCAAATCATTCGTCGT
       tactaaa  putative branch site (score: 1)
                               tctgctcgttctcttt  putative PPT
     tgtactaaaaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaataagcttgcttttttcccgtgttgctacgacaccaaacgccatgcatttctttaaactttggtgtactaaaaaaaagctcgtcgtacgtctgctcgttctctttgcatccagTGCTGGGAAACCATGACTACAGGGGTGACGCGCTCGCGCAGCTGAGCCCGGTCCTGCGGAAGATCGACAGCCGGTTCATTTGCATCAAATCATTCGTCGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA