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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagactaaatttaagcttaagatagagataaaatacgagtcatggacttgttttcaattgtttccaaaggtctaatgttttccgtttgcccttccaccagGATTTATGGGTGCCATGATATCCAACCTTGCATTTGTTTTCCGCAACATCTTCTCGAAGAGGGGCATGAAGGGGAAGTCCGTCAGTGGCATGAATTACTA

Basic information

species Zea mays
transcript GRMZM2G180720_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G180720_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os08g08840.2 (Oryza sativa), 3'ss of exon 3
tagactaaatttaagcttaagatagagataaaatacg---agtcatggacttgttttcaattgtttccaaaggt-ctaatgttttccgtttgcccttccaccagGATTTATGGGTGCCATGATATCCAACCTTGCATTTGTTTTCCGCAACATCTTCTCGAAGAGGGGCATGAAGGGGAAGTCCGTCAGTGGCATGAATTACTA
   | |   |  |    |  | |   | | |  |  |   || || || ||| |  |    | ||||    | |  |||   ||   ||||  |||   ||||||||| ||||||||||||||||| |||||||||||||||||||||||||||||||| |||||||||||||||||||| || ||||||||||||||||||||
---attgtttccagtggtctggtcttgctcaggttagctcaggca-ggtcttctcctgttctctttctcttgatgttaacagttgttgtttctcctcataccagGATTCATGGGTGCCATGATATCAAACCTTGCATTTGTTTTCCGCAACATCTTCTCAAAGAGGGGCATGAAGGGGAAATCTGTCAGTGGCATGAATTACTA

upper sequence: GRMZM2G180720_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA18G12080.1 (Glycine max), 3'ss of exon 3
---tagactaaatttaagcttaagatagagataaaatacgagtcatggacttgttttcaattgt--ttccaaaggtctaatgttttccgtttgcccttccaccagGATTTATGGGTGCCATGATATCCAACCTTGCATTTGTTTTCCGCAACATCTTCTCGAAGAGGGGCATGAAGGGGAAGTCCGTCAGTGGCATGAATTACTA
     |     ||||| | ||  ||| | | |  ||      ||    | || |  ||   ||   |  |     | |||| |  |    ||    ||    |||| |||||||| || |||||||| ||  | |||||||| ||||| || ||||| || || | |||||||||||| ||||| |||||||| |||||||||| 
gtaatggtgtcatttatggtt--gattgtgctggaactaatttctcataattatagtcctctgcactctcctgactttaatttcattgactt--ttttttttcaGGTTTTATGGGAGCTATGATATCGAATTTGGCATTTGTATTCCGTAATATCTTTTCCAAAAAGGGCATGAAGGGAAAGTCTGTCAGTGGAATGAATTACT-

upper sequence: GRMZM2G180720_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA02G25290.1 (Glycine max), 3'ss of exon 3
tagactaaatttaagcttaagatagagataaaatacgagtcatggacttgttttcaattgtttccaaaggtctaatgtt--ttccgtttgcccttcca-ccagGATTTATGGGTGCCATGATATCCAACCTTGCATTTGTTTTCCGCAACATCTTCTCGAAGAGGGGCATGAAGGGGAAGTCCGTCAGTGGCATGAATTACTA
   || ||    |||  | |  ||     | |||   |    |   | |  ||  | |  | | ||     || |  ||  |  | |   |  ||    ||||| |||||||| ||||||||||| ||  | |||||||| ||||| || ||||| ||||| | |||||||||||| ||||| || ||||| |||||||||||
---accaagcgcaagtgtgatttacttgcataatggtatcatttctcataattatagtcctctgcactctcctgactttaatgtcatcgacttttttttccagGTTTTATGGGGGCCATGATATCGAATTTGGCATTTGTATTCCGTAATATCTTTTCGAAAAAGGGCATGAAGGGAAAGTCTGTTAGTGGAATGAATTACTA

upper sequence: GRMZM2G180720_T02 (Zea mays), 3'ss of exon 3
lower sequence: AT4G03950.1 (Arabidopsis thaliana), 3'ss of exon 4
----tagactaaatttaagct-taagatagagataaaatacgagtcatggacttgttttcaattgtttccaaaggtctaatgttttccgtttgcccttccaccagGATTTATGGGTGCCATGATATCCAACCTTGCATTTGTTTTCCGCAACATCTTCTCGAAGAGGGGCATGAAGGGGAAGTCCGTCAGTGGCATGAATTACTA
    |  || | ||   |    ||   ||   |   ||| | | |||  ||  |||||| |  ||||   | |   |   |||||   |   |   |     |||| |||||||| || |||||||| ||  | || ||||| || || ||||| ||||| |||| ||| |||||||||||||| || ||||  |||||||||||
gtacttaacaacatcctattgataccttaagaagctaatgcaattcaatgaaatgttttgagatgttgatata---cgggtgtttcttgggggtttt-----cagGGTTTATGGGGGCAATGATATCGAATTTGGCGTTTGTGTTTCGTAACATATTCTCAAAGAAGGGAATGAAGGGGAAGTCAGTGAGTGTGATGAATTACTA

upper sequence: GRMZM2G180720_T02 (Zea mays), 3'ss of exon 3
lower sequence: AT5G54800.1 (Arabidopsis thaliana), 3'ss of exon 2
--------tagactaaatttaagcttaagata----gagataaaatacgagtca-----tggacttgttttcaattgtttccaaaggtctaatgttttccgtttgcccttccaccagGATTTATGGGTGCCATGATATCCAACCTTGCATTTGTTTTCCGCAACATCTTCTCGAAGAGGGGCATGAAGGGGAAGTCCGTCAGTGGCATGAATTACTA
        ||   | |  |||    | |||||    ||| |  |||  |  |       || | | | |||  ||  ||      ||  | |  | | | | |  |        |||| || ||||| || ||||| || ||| | || || || ||||| |||||||||||||||| ||| |||||||| ||||| || || || ||||| |||||
gtaacatatatcttcatcttatttgttagatacattgaggtgtaattgggattgagatttgaaatggctttgcatgtttgattttggcttcaaatctgctgctc-cttacttttcagGTTTCATGGGAGCTATGATTTCGAACTTGGCTTTCGTGTTCCGTAACATCTTCTCGAAGAAGGGAATGAAGGGAAAGTCTGTGAGCGGGATGAACTACTA

upper sequence: GRMZM2G180720_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv19s0177g00300.t01 (Vitis vinifera), 3'ss of exon 2
tagactaaatttaagcttaagatagagataaaatacgagtcatggacttgt-tttcaattgtttccaaaggtctaa--tgttttccgtttgcccttcc----accagGATTTATGGGTGCCATGATATCCAACCTTGCATTTGTTTTCCGCAACATCTTCTCGAAGAGGGGCATGAAGGGGAAGTCCGTCAGTGGCATGAATTACTA
       | |||  ||  |||| |             ||  ||| | || |  | | ||| |      ||| || |  ||   |  ||  |  |||      | |||| |||||||| |||||||| || ||||| || |||||||| |||||||| || || ||||| ||||||||||||||||| || ||||| ||||| |||||
-------attttttgcaaaagacattttgggggggttaggaatgtaattttactcctattttccttttagggctgacctgaacttggtaggtgcttgtctgtatcagGTTTTATGGGAGCCATGATTTCGAACCTGGCTTTTGTTTTTCGCAACATATTTTCAAAGAGAGGCATGAAGGGGAAGTCTGTTAGTGGAATGAACTACTA

upper sequence: GRMZM2G180720_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv10s0116g00760.t01 (Vitis vinifera), 3'ss of exon 2
----------tagactaa-atttaagcttaagatagaga----taaaatacgagtcatg--gacttgttttcaat--tgtttccaaagg---tctaatgttttccgtttgcccttcca----ccagGATTTATGGGTGCCATGATATCCAACCTTGCATTTGTTTTCCGCAACATCTTCTCGAAGAGGGGCATGAAGGGGAAGTCCGTCAGTGGCATGAATTACTA
          | || ||| ||| ||| || | || ||       ||||| |   | ||   ||  || |    ||  | ||||  | ||   | | | ||| |   ||||   | | |    | ||| |||||||| || ||||| || || || |||||||| ||||| ||||| ||||| ||||| || |||||||||||||| ||  | || ||||| |||||
gtgagaaggattgattaatattaaagattgaaattgatggtctcaaaattctcttgattttgatgtgatgatcatgatatttcttatgggtttttcaagttctgaatttgtgttgctatgttctagGGTTTATGGGGGCTATGATTTCAAATCTGGCATTTGTGTTCCGGAACATATTCTCAAAGAGAGGGATGAAGGGGAAGTCTGTTGGGGGAATGAACTACTA

upper sequence: GRMZM2G180720_T02 (Zea mays), 3'ss of exon 3
lower sequence: PP1S143_174V6.1 (Physcomitrella patens), 3'ss of exon 2
--------------------------tagactaaatttaagcttaagatagagataaaatacgagtcatggacttgttttc-------------aattgtttccaaaggtctaatgttttccgtttgcccttccaccagGATTTATGGGTGCCATGATATCCAACCTTGCATTTGTTTTCCGCAACATCTTCTCGAAGAGGGGCATGAAG---GGGAAGTCCGTCAGTGGCATGAATTACTA
                          |  |  ||  |   |  |    |   |||||  |   ||  ||| |  ||||||              | ||| |   |||||   |||  | |   |       |    |||||||| |||| |||||||| || ||| |||| || || ||||| |||||||||||||||| ||| ||||     || |||  |||  |||||||||| ||   
gtattgtactgttagtattgcgtttgttcaacaaggtcgcgtgtttattctggataatctgaaagggatgcaggtgtttttggacccaataaggagttgatggtaaagggtgaatcatctgattactttggtatggcagGATTTGTGGGAGCCATGATTTCGAACGTTGCGTTCGTCTTCCGTAACATCTTCTCGAAGAAGGGGATGACAACCGGCAAGAGCGTTGGTGGCATGAACTA---

upper sequence: GRMZM2G180720_T02 (Zea mays), 3'ss of exon 3
lower sequence: PP1S70_177V6.1 (Physcomitrella patens), 3'ss of exon 3
-------------------------------tagactaaatttaagcttaagatagagataaaatacgagtcatg---gacttgttttcaattgtttccaaaggtctaatgttttccgtttgcccttccaccagGATTTATGGGTGCCATGATATCCAACCTTGCATTTGTTTTCCGCAACATCTTCTCGAAGAGGGGCATGAA---GGGGAAGTCCGTCAGTGGCATGAATTACTA
                                |||| |  | |        ||| ||  |   ||    ||| |    || ||   |  | |   |   ||||    |||  | |      |    |    |||||||| |||| |||||| | || ||  |||| ||||| |||||||||||||||||||| | ||| ||||    ||| |||   ||  |||| ||||| ||   
gtgctgttcagtttgacttgcgtcggtcaaagagaccagttgtttttggtggatggaattggtatgaatgtcttatatgattttcatgaagtaagtggtaaagtgtgaatcgtctgacggggttggtgtggcagGATTTGTGGGGGCCATGGTTTCGAATATTGCGTTTGTGTTCCGCAACATCTTCTCGAAAAAGGGAATGACAACGGGCAAGAGTGTTGGTGGGATGAACTA---

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|76908644|gb|DV163027.1|DV163027
EST:     TGGTGGTTGTGCTCTAGCTGCTGTCACAGAGCTGAACTTTAATATGGTTG                         GATTTATGGGTGCCATGATATCCAACCTTGCATTTGTTTTCCGCAACATCT
genomic: TGGTGGTTGTGCTCTAGCTGCTGTCACAGAGCTGAACTTTAATATGGTTGgtaagtaaaa ... cttccaccagGATTTATGGGTGCCATGATATCCAACCTTGCATTTGTTTTCCGCAACATCT
EST: gi|67042737|gb|CO468992.1|CO468992
EST:     TGGTGGTTGTGCTCTAGCTGCTGTCACAGAGCTGAACTTTAATATGGTTG                         GATTTATGGGTGCCATGATATCCAACCTTGCATTTGTTTTCCGCAACATCT
genomic: TGGTGGTTGTGCTCTAGCTGCTGTCACAGAGCTGAACTTTAATATGGTTGgtaagtaaaa ... cttccaccagGATTTATGGGTGCCATGATATCCAACCTTGCATTTGTTTTCCGCAACATCT
EST: gi|60396004|gb|DN228874.1|DN228874
EST:     CTGCTGTCACAGAGCTGAACTTTAATATGGTTG                         GATTTATGGGTGCCATGATATCCAACCTTGCATTTGTTTTCCGCAACATCT
genomic: CTGCTGTCACAGAGCTGAACTTTAATATGGTTGgtaagtaaaa ... cttccaccagGATTTATGGGTGCCATGATATCCAACCTTGCATTTGTTTTCCGCAACATCT
EST: gi|60345607|gb|DN212580.1|DN212580
EST:     GGTGGTTGTGCTCTAGCTGCTGTCACAGAGCTGAACTTTAATATGGTTG                         GATTTATGGGTGCCATGATATCCAACCTTGCATTTGTTTTCCGCAACATCT
genomic: GGTGGTTGTGCTCTAGCTGCTGTCACAGAGCTGAACTTTAATATGGTTGgtaagtaaaa ... cttccaccagGATTTATGGGTGCCATGATATCCAACCTTGCATTTGTTTTCCGCAACATCT
EST: gi|71440959|gb|DR822009.1|DR822009
EST:     AGAGCTGAACTTTAATATGGTTG                         GATTTATGGGTGCCATGATATCCAACCTTGCATTTGTTTTCCGCAACATCT
genomic: AGAGCTGAACTTTAATATGGTTGgtaagtaaaa ... cttccaccagGATTTATGGGTGCCATGATATCCAACCTTGCATTTGTTTTCCGCAACATCT
EST: gi|211127527|gb|FL066343.1|FL066343
EST:     TGGTGGTTGTGCTCTAGCTGCTGTCACAGAGCTGAACTTTAATATGGTTG                         GATTTATGGGTGCCATGATATCCAACCTTGCATTTGTTTTCCGCAACATCT
genomic: TGGTGGTTGTGCTCTAGCTGCTGTCACAGAGCTGAACTTTAATATGGTTGgtaagtaaaa ... cttccaccagGATTTATGGGTGCCATGATATCCAACCTTGCATTTGTTTTCCGCAACATCT
EST: gi|211127528|gb|FL066344.1|FL066344
EST:     TGGTGGTTGTGCTCTAGCTGCTGTCACAGAGCTGAACTTTAATATGGTTG                         GATTTATGGGTGCCATGATATCCAACCTTGCATTTGTTTTCCGCAACATCT
genomic: TGGTGGTTGTGCTCTAGCTGCTGTCACAGAGCTGAACTTTAATATGGTTGgtaagtaaaa ... cttccaccagGATTTATGGGTGCCATGATATCCAACCTTGCATTTGTTTTCCGCAACATCT
EST: gi|211029602|gb|FL384590.1|FL384590
EST:     TGGTGGTTGTGCTCTAGCTGCTGTCACAGAGCTGAACTTTAATATGGTTG                         GATTTATGGGTGCCATGATATCCAACCTTGCATTTGTTTTCCGCAACATCT
genomic: TGGTGGTTGTGCTCTAGCTGCTGTCACAGAGCTGAACTTTAATATGGTTGgtaagtaaaa ... cttccaccagGATTTATGGGTGCCATGATATCCAACCTTGCATTTGTTTTCCGCAACATCT
EST: gi|33771219|gb|CF273398.1|CF273398
EST:     TGGTGGTTGNGCTCTAGCTGCTGNCACAGAGCTGAACTTTAATATGGNTG                         GATTTATGGGTGCCATGATATCCAACCTTGCATTTGTTTTCCGCAACATCT
genomic: TGGTGGTTGTGCTCTAGCTGCTGTCACAGAGCTGAACTTTAATATGGTTGgtaagtaaaa ... cttccaccagGATTTATGGGTGCCATGATATCCAACCTTGCATTTGTTTTCCGCAACATCT
EST: gi|211128448|gb|FL066345.1|FL066345
EST:     TGGTGGTTGTGCTCTAGCTGCTGTCACAGAGCTGAACTTTAATATGGTTG                         GATTTATGGGTGCCATGATATCCAACCTTGCATTTGTTTTCCGCAACATCT
genomic: TGGTGGTTGTGCTCTAGCTGCTGTCACAGAGCTGAACTTTAATATGGTTGgtaagtaaaa ... cttccaccagGATTTATGGGTGCCATGATATCCAACCTTGCATTTGTTTTCCGCAACATCT
EST: gi|67042492|gb|CO468747.1|CO468747
EST:     TGGTGGTTGTGCTCTAGCTGCTGTCACAGAGCTGAACTTTAATATGGTTG                         GATTTATGGGTGCCATGATATCCAACCTTGCATTTGTTTTCCGCAACATCT
genomic: TGGTGGTTGTGCTCTAGCTGCTGTCACAGAGCTGAACTTTAATATGGTTGgtaagtaaaa ... cttccaccagGATTTATGGGTGCCATGATATCCAACCTTGCATTTGTTTTCCGCAACATCT
EST: gi|67040435|gb|CO466690.1|CO466690
EST:     TGGTGGTTGTGCTCTAGCTGCTGTCACAGAGCTGAACTTTAATATGGTTG                         GATTTATGGGTGCCATGATATCCAACCTTGCATTTGTTTTCCGCAACATCT
genomic: TGGTGGTTGTGCTCTAGCTGCTGTCACAGAGCTGAACTTTAATATGGTTGgtaagtaaaa ... cttccaccagGATTTATGGGTGCCATGATATCCAACCTTGCATTTGTTTTCCGCAACATCT
EST: gi|211039688|gb|FL176199.1|FL176199
EST:     TGGTGGTTGTGCTCTAGCTGCTGTCACAGAGCTGAACTTTAATATGGTTG                         GATTTATGGGTGCCATGATATCCAACCTTGCATTTGTTTTCCGCAACATCT
genomic: TGGTGGTTGTGCTCTAGCTGCTGTCACAGAGCTGAACTTTAATATGGTTGgtaagtaaaa ... cttccaccagGATTTATGGGTGCCATGATATCCAACCTTGCATTTGTTTTCCGCAACATCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttgttttcaattgtttccaaaggtctaatgttttccgtttgcccttccaccagGATTTATGGGTGCCATGATATCCAACCTTGCATTTGTTTTCCGCAACATCTTCTCGAAGAGGGGCATGAAGGGGAAGTCCGTCAGTGGCATGAATTACTA
                        gtctaat  putative branch site (score: 3)
                                ttttccgtttgccctt  CT-rich tract
     ttttcaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagactaaatttaagcttaagatagagataaaatacgagtcatggacttgttttcaattgtttccaaaggtctaatgttttccgtttgcccttccaccagGATTTATGGGTGCCATGATATCCAACCTTGCATTTGTTTTCCGCAACATCTTCTCGAAGAGGGGCATGAAGGGGAAGTCCGTCAGTGGCATGAATTACTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG