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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtttgtcatgcattctgttagctgtgtagcatttctgcatttttgttctctgcataatgctaaacgcttaaatttgcacataaccttttgtaccctgcagGACATCAAGTTTGCTGTTCATGCACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAG

Basic information

species Zea mays
transcript GRMZM2G145595_T01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G145595_T01 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 13
gtgagtttgtcatgcattctgttagctgtgtagcatttctgcatttttgttctctgcataatgctaaacgcttaaatttgcacataaccttttgtaccctgcagGACATCAAGTTTGCTGTTCATGCACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAG
                             |||        |||||||  || | |    ||||      | ||  |||||| ||   |  |||  | ||  ||||||||||||||||||||||||||||||||||| |||||||| ||||||||||| |||||||| |||||||||
-----------------------------gtaagtgacgagcatttt-attgtttatg-aatg------gattgcatttgctcaacgctgtttacatcccccagGACATCAAGTTTGCTGTTCATGCACACCCAACTTTGTCTGAGGTTCTGGATGAGCTCTTCAAAGCTGCCAAG

upper sequence: GRMZM2G145595_T01 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA17G03560.1 (Glycine max), 3'ss of exon 13
---------------------gtgagtttgtcatgcattctgttagctgtg-tagcatttctgcatttttgttctctgcataatgctaaacgcttaaatttgcacataaccttttgtaccctgcagGACATCAAGTTTGCTGTTCATGCACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAG
                      || ||    |  |||||  ||||    |  | |  |    |  |||   |  | |  ||  |||        |||||||   | |    | | ||||  |||||||||| || ||||| ||||||||||| ||||| ||||| || ||||| |||||||| |||||  | || |||
gtaagtttttctaccacatttatgtgtgcacctggcatttagttattaataatggtctcaaagtctttcactgttatttatcctgcctgtttggtaaatttcaccgt--tttgtggtacaatgcagGACATAAAATTTGCCGTTCATGCACATCCAACTTTGTCCGAGGTTCTTGATGAACTATTCAAATCAGCAAAG

upper sequence: GRMZM2G145595_T01 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA07G37050.1 (Glycine max), 3'ss of exon 13
-----------------gtgagtttgtcatg-cattctgttagctgtgtagcatttctgcatttttgttctc-tgcataatgctaaacgcttaaatttgcacataaccttttgtaccctgcagGACATCAAGTTTGCTGTTCATGCACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAG
                  |   | |||  || ||||  |||| ||    |   |  |    | ||   |||  |  ||  ||||       |||||||   | |    | | ||||  |||||||||| || ||||| ||||||||||| ||||| ||||| || ||||| |||||||| |||||  | || |||
gtaaatttttctaccacatttatgtgtattggcatttagtta-ctaataatagtcacaaagtcttcactcttatttatcctgcttgtttggtaaatttcaccgt--tttgtggtacaatgcagGACATAAAATTTGCAGTTCATGCACATCCAACTTTGTCCGAGGTTCTTGATGAACTATTCAAATCAGCAAAG

upper sequence: GRMZM2G145595_T01 (Zea mays), 3'ss of exon 13
lower sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 13
gtgagtttgtcatgcattctgttagctgtgtagcatttctgcatttttgttctctgcataatgctaaacgcttaaatttgcacataaccttttgtaccctg-------cagGACATCAAGTTTGCTGTTCATGCACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAG
                 ||||   ||    || | | ||| |  | ||| ||     |  |   || |   | |  |||     |     |||||    ||       |||||||| ||  |||||||||||||||| |||||  ||||||||||| | || ||||| || || || ||||||
----------------gtctggctgcaaactaacctctctccggtattgatc---ataggactttagattgtgagctttttttgtgtgtctttgtgtgatgataaatgcagGACATAAAACTTGCTGTTCATGCACATCCAACACTGTCTGAAGTTGTAGACGAACTGTTTAAAGCAGCCAAG

upper sequence: GRMZM2G145595_T01 (Zea mays), 3'ss of exon 13
lower sequence: Vv14s0060g01330.t01 (Vitis vinifera), 3'ss of exon 13
------------------------------------gtgagtttgtcatgc---attctgttagc-tgtgtagcat--ttctgcattttt-----------gttctctgcataatgctaaacgcttaaattt-gcacataaccttt---------tgtaccctgcagGACATCAAGTTTGCTGTTCATGCACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAG
                                    |  ||   || || |   || || ||  | | | | ||||  |||   || |||            |||     |||||| |      ||   ||     | | | ||||         || |||||||||||||| |||||||||||||||||||| ||||| ||||| || || || || |||||||||||  |||| |||
gttttttttttttttctccatttgcccatacaatttgcaagacagtaataccaaatcctctttacatctatggcatgattcattatgttttgactcataccattcaaaatataatggttgctattttccttccattcgtcatctttcacaacccgtgcaccctgcagGACATAAAGTTTGCTGTTCATGCACATCCAACCTTGTCCGAGGTGCTTGACGAACTCTTCAAATCTGCTAAG

upper sequence: GRMZM2G145595_T01 (Zea mays), 3'ss of exon 13
lower sequence: Vv05s0077g01210.t01 (Vitis vinifera), 3'ss of exon 13
-gtgagtttgtcatgcattctgttagctgtgtagcatttctgcatttttgttctctgcataatgctaaacgcttaaatttgcacataaccttttgtaccctgcagGACATCAAGTTTGCTGTTCATGCACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAG
    | |   |||| |  |  |||   | |  |   |    |       | |  ||   | ||| | |    ||  |  |     |    ||    ||| | |||||||| || |||||||||||||| || ||||| ||||| ||||| |||||||||||||| ||  | || |||
tcaaactcaatcat-ctcttggtttcttcttgaaagtgagggtggaaccggtagct-tgttatgatgagtattttgacatttcttt---tttggacaccttacagGACATAAAATTTGCTGTTCATGCGCATCCAACCTTGTCAGAAGTGCTGGATGAACTCTTTAAATCAGCTAAG

upper sequence: GRMZM2G145595_T01 (Zea mays), 3'ss of exon 13
lower sequence: Vv14s0060g01410.t01 (Vitis vinifera), 3'ss of exon 5
gtgagtttgtcatgcattctgttagctgtgtagcatttctgcatttttgttctctgcataatgctaaacgcttaaatttgcacataaccttttgtaccctgcagGACATCAAGTTTGCTGTTCATGCACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAG
 | |     | || |||| ||||   ||  | | |    |  |  | |  |   |||    | |    |  |     |  | || || || | | ||||||||||||||  ||||||||||||||||||| ||||| ||||| || || || ||  ||||||||||  |||| |||
-ttatggcatgattcattatgtt--ttgactcgtaccattcaaaatataatggttgctattttccttccattcgtcatctctcacaatctgt-gcaccctgcagGACATAGAGTTTGCTGTTCATGCACATCCAACCTTGTCCGAGGTGCTTGACAAACTCTTCAAATCTGCTAAG

upper sequence: GRMZM2G145595_T01 (Zea mays), 3'ss of exon 13
lower sequence: PP1S112_186V6.1 (Physcomitrella patens), 3'ss of exon 13
----------------------------------gtgagtttgtcatgcattctgttagctgtgtagcatttctgcatttttgttctctgcataatgctaaacgcttaaatttgcacataaccttttgtaccctgcagGACATCAAGTTTGCTGTTCATGCACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAG
                                  |        | | |  |  ||   |   ||  | | || |  | | | | | || | ||  |||  |   |||  |    | |||  |  | |||      ||||||||||| |||||||| ||||| || || || |||||||||||  |||| || ||||||||| | || |||
gtgagtgccaagtttcattttactagaattgtctgccgaaccttgacgtctaatggatgtgatgatgtagttgtcaagtctcgctatc-gaatgctgc-gatttcttctaacaacccattgc--tctgtctttgacagGACATCAAATTTGCTGTGCATGCCCATCCGACCTTGTCTGAAGTGTTGGACGAGCTCTTCAAGTCAGCGAAG

upper sequence: GRMZM2G145595_T01 (Zea mays), 3'ss of exon 13
lower sequence: PP1S35_94V6.1 (Physcomitrella patens), 3'ss of exon 13
-----------------------------------gtgagtttgtcatgcattctgttagctgtgtagcatttctgcatttttgttctctgcataatgcta---aacgct-taaatttgcaca-taaccttttgtaccct----gcagGACATCAAGTTTGCTGTTCATGCACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAG
                                    |||   | | |      | | |||     | | ||||    ||   | |||    | |  |||||   |  ||| |  |||   | |  |||   |||| |         ||||||||||||||||||||||||| || || || || ||||||||| |||| || || |||||||| || |||
gtgagtccatgaactcatttgattcacagttgctgctgaacctttta-attcccagctaggatccttg-atttaccaatcaatattcgtcacgtcttgctatcgattgctgtgtattcctaaaacaactggttgttcttcttgaatagGACATCAAGTTTGCTGTTCATGCCCATCCCACCTTATCTGAAGTTTTGGACGAGCTGTTCAAGGCAGCTAAG

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|211470347|gb|FL451278.1|FL451278
EST:     ATCTCATCCATGAGGCATCAAATGCCATTGCCCTTGGAACCCATGTGCAG                         GACATCAAGTTTGCTGTTCATGCACACCCAACGTTGTCTGAAGTTCTGGAT
genomic: ATCTCATCCATGAGGCATCAAATGCCATTGCCCTTGGAACCCATGTGCAGgtgagtttgt ... taccctgcagGACATCAAGTTTGCTGTTCATGCACACCCAACGTTGTCTGAAGTTCTGGAT
EST: gi|6672118|gb|AW282293.1|AW282293
EST:     ATCTCATCCATNAGGCATCAAATGCCATTGCCCTTGGAACCCATGTGCAG                         GACATCAAGTTTGCTGTTCATGCACACCCAACGTTGTCTGAAGTTCTGGAT
genomic: ATCTCATCCATGAGGCATCAAATGCCATTGCCCTTGGAACCCATGTGCAGgtgagtttgt ... taccctgcagGACATCAAGTTTGCTGTTCATGCACACCCAACGTTGTCTGAAGTTCTGGAT
EST: gi|20512800|gb|BQ279999.1|BQ279999
EST:     ATCTCATCCATGAGGCATCAAATGCCATTGCCCTTGGAACCCATGTGCAG                         GACATCAAGTTTGCTGTTCATGCACACCCAACGTTGTCTGAAGTTCTGGAT
genomic: ATCTCATCCATGAGGCATCAAATGCCATTGCCCTTGGAACCCATGTGCAGgtgagtttgt ... taccctgcagGACATCAAGTTTGCTGTTCATGCACACCCAACGTTGTCTGAAGTTCTGGAT
EST: gi|13249875|gb|BG360780.1|BG360780
EST:     ATCTCATCCATGAGGCATCAAATGCCATTGCCCTTGGAACCCATGTGCAG                         GACATCAAGTTTGCTGTTCATGCACACCCAACGTTGTCTGAAGTTCTGGAT
genomic: ATCTCATCCATGAGGCATCAAATGCCATTGCCCTTGGAACCCATGTGCAGgtgagtttgt ... taccctgcagGACATCAAGTTTGCTGTTCATGCACACCCAACGTTGTCTGAAGTTCTGGAT
EST: gi|211093993|gb|FL455618.1|FL455618
EST:     ATCTCATCCATGAGGCATCAAATGCCATTGCCCTTGGAACCCATGTGCAG                         GACATCAAGTTTGCTGTTCATGCACACCCAACGTTGTCTGAAGTTCTGGAT
genomic: ATCTCATCCATGAGGCATCAAATGCCATTGCCCTTGGAACCCATGTGCAGgtgagtttgt ... taccctgcagGACATCAAGTTTGCTGTTCATGCACACCCAACGTTGTCTGAAGTTCTGGAT
EST: gi|211470346|gb|FL451277.1|FL451277
EST:     ATCTCATCCATGAGGCATCAAATGCCATTGCCCTTGGAACCCATGTGCAG                         GACATCAAGTTTGCTGTTCATGCACACCCAACGTTGTCTGAAGTTCTGGAT
genomic: ATCTCATCCATGAGGCATCAAATGCCATTGCCCTTGGAACCCATGTGCAGgtgagtttgt ... taccctgcagGACATCAAGTTTGCTGTTCATGCACACCCAACGTTGTCTGAAGTTCTGGAT
EST: gi|16378429|gb|BI992442.1|BI992442
EST:     ATCTCATCCATGAGGCATCAAATGCCATTGCCCTTGGAACCCATGTGCAG                         GACATCAAGTTTGCTGTTCATGCACACCCAACGTTGTCTGAAGTTCTGGAT
genomic: ATCTCATCCATGAGGCATCAAATGCCATTGCCCTTGGAACCCATGTGCAGgtgagtttgt ... taccctgcagGACATCAAGTTTGCTGTTCATGCACACCCAACGTTGTCTGAAGTTCTGGAT
EST: gi|6865111|gb|AW360461.1|AW360461
EST:     TCTCATCCATGAGGCATCAAATGNCNTTTGCCCTTGGAACCCATGTGCAG                         GACATCAAGTTTGCTGTTCATGCACACCCAACGTTGTCTGAAGTTCTGGAT
genomic: TCTCATCCATGAGGCATCAAATG-CCATTGCCCTTGGAACCCATGTGCAGgtgagtttgt ... taccctgcagGACATCAAGTTTGCTGTTCATGCACACCCAACGTTGTCTGAAGTTCTGGAT
EST: gi|13249874|gb|BG360779.1|BG360779
EST:     ATCTCATCCATGAGGCATCAAATGCCATTGCCCTTGGAACCCATGTGCAG                         GACATCAAGTTTGCTGTTCATGCACACCCAACGTTGTCTGAAGTTCTGGAT
genomic: ATCTCATCCATGAGGCATCAAATGCCATTGCCCTTGGAACCCATGTGCAGgtgagtttgt ... taccctgcagGACATCAAGTTTGCTGTTCATGCACACCCAACGTTGTCTGAAGTTCTGGAT
EST: gi|32830615|gb|CD970293.1|CD970293
EST:     ATCTCATCCATGAGGCATCAAATGCCATTGCCCTTGGAACCCATGTGCAG                         GACATCAAGTTTGCTGTTCATGCACACCCAACGTTGTCTGAAGTTCTGGAT
genomic: ATCTCATCCATGAGGCATCAAATGCCATTGCCCTTGGAACCCATGTGCAGgtgagtttgt ... taccctgcagGACATCAAGTTTGCTGTTCATGCACACCCAACGTTGTCTGAAGTTCTGGAT
EST: gi|26456706|gb|CA828289.1|CA828289
EST:     ATCTCATCCATGAGGCATCAAATGCCATTGCCCTTGGAACCCATGTGCAG                         GACATCAAGTTTGCTGTTCATGCACACCCAACGTTGTCTGAAGTTCTGGAT
genomic: ATCTCATCCATGAGGCATCAAATGCCATTGCCCTTGGAACCCATGTGCAGgtgagtttgt ... taccctgcagGACATCAAGTTTGCTGTTCATGCACACCCAACGTTGTCTGAAGTTCTGGAT
EST: gi|20512799|gb|BQ279998.1|BQ279998
EST:     TTGCCCTTGGAACCCATGTGCAG                         GACATCAAGTTTGCTGTTCATGCACACCCAACGTTGTCTGAAGTTCTGGAT
genomic: TTGCCCTTGGAACCCATGTGCAGgtgagtttgt ... taccctgcagGACATCAAGTTTGCTGTTCATGCACACCCAACGTTGTCTGAAGTTCTGGAT
EST: gi|6563894|gb|AW231516.1|AW231516
EST:     ATCTCATCCATGAGGCATCAAATGCCATTGCCCTTGGAACCCATGTGCAG                         GACATCAAGTTTGCTGTTCATGCACACCCAACGTTGTCTGAAGTTCTGGAT
genomic: ATCTCATCCATGAGGCATCAAATGCCATTGCCCTTGGAACCCATGTGCAGgtgagtttgt ... taccctgcagGACATCAAGTTTGCTGTTCATGCACACCCAACGTTGTCTGAAGTTCTGGAT
EST: gi|32830552|gb|CD970230.1|CD970230
EST:     ATCTCATCCATGAGGCATCAAATGCCATTGCCCTTGGAACCCATGTGCAG                         GACATCAAGTTTGCTGTTCATGCACACCCAACGTTGTCTGAAGTTCTGGAT
genomic: ATCTCATCCATGAGGCATCAAATGCCATTGCCCTTGGAACCCATGTGCAGgtgagtttgt ... taccctgcagGACATCAAGTTTGCTGTTCATGCACACCCAACGTTGTCTGAAGTTCTGGAT
EST: gi|32831600|gb|CD971278.1|CD971278
EST:     ATCTCATCCATGAGGCATCAAATGCCATTGCCCTTGGAACCCATGTGCAG                         GACATCAAGTTTGCTGTTCATGCACACCCAACGTTGTCTGAAGTTCTGGAT
genomic: ATCTCATCCATGAGGCATCAAATGCCATTGCCCTTGGAACCCATGTGCAGgtgagtttgt ... taccctgcagGACATCAAGTTTGCTGTTCATGCACACCCAACGTTGTCTGAAGTTCTGGAT
EST: gi|37377273|gb|CF625226.1|CF625226
EST:     ATCTCATCCATGAGGCATCAAATGCCATTGCCCTTGGAACCCATGTGCAG                         GACATCAAGTTTGCTGTTCATGCACACCCAACGTTGTGTGAAGTTCTGGAT
genomic: ATCTCATCCATGAGGCATCAAATGCCATTGCCCTTGGAACCCATGTGCAGgtgagtttgt ... taccctgcagGACATCAAGTTTGCTGTTCATGCACACCCAACGTTGTCTGAAGTTCTGGAT
EST: gi|211093992|gb|FL455617.1|FL455617
EST:     ATCTCATCCATGAGGCATCAAATGCCATTGCCCTTGGAACCCATGTGCAG                         GACATCAAGTTTGCTGTTCATGCACACCCAACGTTGTCTGAAGTTCTGGAT
genomic: ATCTCATCCATGAGGCATCAAATGCCATTGCCCTTGGAACCCATGTGCAGgtgagtttgt ... taccctgcagGACATCAAGTTTGCTGTTCATGCACACCCAACGTTGTCTGAAGTTCTGGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctctgcataatgctaaacgcttaaatttgcacataaccttttgtaccctgcagGACATCAAGTTTGCTGTTCATGCACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAG
                                      ccttttgt  CT-rich tract
                      ttaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtttgtcatgcattctgttagctgtgtagcatttctgcatttttgttctctgcataatgctaaacgcttaaatttgcacataaccttttgtaccctgcagGACATCAAGTTTGCTGTTCATGCACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG