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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttggttatttctccatgtgttgtgctattattcccgaatgagttgaactgtttctcacctagtgaaaaaactattatctcactggattcttgttgcagTGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTCCCACCAAAAATTGACCCAAGTGTTACCATGATGACTGTGGAGGAAAAGCCAGATGTGACGTAC

Basic information

species Zea mays
transcript GRMZM2G110185_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G110185_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os06g09290.2 (Oryza sativa), 3'ss of exon 5
---------ttttggttatttctccatgtgttgtgctattattcccgaatgagttgaactgtttctcacctagtgaaaaaactattatctcactggattcttgttgcagTGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTCCCACCAAAAATTGACCCAAGTGTTACCATGATGACTGTGGAGGAAAAGCCAGATGTGACGTAC
         | ||| ||   | | ||  ||| ||| |  | |||  |||  | ||  | | |   |    | ||      | | || |||||     |   |  | ||| |||||||| ||||||||||| |||||||| ||| | |||||||| ||||| || || |||||||||||||||||||| ||||| ||||||||||| |||
ttccacatatgttgtttgcat-tgcacttgt-gtgatgctgttcttgaagtaattatattatcaattggattgt------attgtt-tctcatcctgtgtatcatacagAGTTGATCGAAACAAGTACCAAATTCAAATTCCTTTGCCACCAAAGATTGATCCCAGCGTTACCATGATGACTGTGGAAGAAAAACCAGATGTGACTTAC

upper sequence: GRMZM2G110185_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA16G01810.1 (Glycine max), 3'ss of exon 5
--ttttggttatttctccatgtgttgtgctattattcccg--aatgagttgaactgtttct-cacctagtgaaaaaactattatctcactggattcttgttgcagTGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTCCCACCAAAAATTGACCCAAGTGTTACCATGATGACTGTGGAGGAAAAGCCAGATGTGACGTAC
   | |    | |     || || ||    | ||||      ||  ||  ||||  |||   ||  | ||         |||    |      || |  |||||| |||||| | ||||| || |||||||| || ||| | || || |||||||| |||||||| ||||||||||| || || || |||||||||||||| || 
gtatgtttccaataagtaatttgatgcaagaatatttatagaaagaagaggaaccctttgggcatgttgtctgcttgtaatttgaccttcattttatcattgcagGGTTGATAGAAACAAATATCAGATTCAGATTCCTTTGCCTCCGAAAATTGATCCAAGTGTAACCATGATGACGGTTGAAGAGAAGCCAGATGTGACATAT

upper sequence: GRMZM2G110185_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA03G42370.2 (Glycine max), 3'ss of exon 5
-----ttttggttatttctccatg-tgttgtgctattattcccgaatgagttgaactgtttctcacctagtgaaaaaacta-ttatctcactggattc-------ttgttgcagTGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTCCCACCAAAAATTGACCCAAGTGTTACCATGATGACTGTGGAGGAAAAGCCAGATGTGACGTAC
     ||    | | |      || ||||    ||||        | |||  |||  | |  ||   |  |       ||  || ||| |||| | |        |  || ||| |||||| | ||||| || ||||||||||| || || || |||||||||||||||||||||||||||||||| || || || ||||| |||||||| || 
gtatgttccaatcagtaacttttgatgttaaaatattccatgttga-gagaagaaggggtattctagtgttatgttgtctgcttgtctgactgaacttcattccatcatttcagGGTTGATAGAAACAAATATCAGATTCAAATTCCACTGCCTCCAAAAATTGACCCAAGTGTTACCATGATGACAGTTGAAGAGAAGCCTGATGTGACATAT

upper sequence: GRMZM2G110185_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA19G45140.1 (Glycine max), 3'ss of exon 5
-----ttttggttatttctccatg-tgttgtgctattattcccgaatgagttgaactgtttctcacctagtgaaaaaacta-ttatctcactggattc-------ttgttgcagTGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTCCCACCAAAAATTGACCCAAGTGTTACCATGATGACTGTGGAGGAAAAGCCAGATGTGACGTAC
     ||    | | |      || ||||    ||||        | |||  |||  | |  ||   |  |       ||  || ||| |||| | |        |  || ||| |||||| | ||||| || ||||||||||| || || || |||||||||||||| ||||||||||||||||| || || || ||||| |||||||| || 
gtatgttccaatcagtaacttttgatgttaaaatattccatgttga-gagaagaaggggtattctagtgttatgctgtctgcttgtctgactgaacttcattgcatcatttcagGGTTGATAGAAACAAATATCAGATTCAAATTCCACTGCCTCCAAAAATTGACCCTAGTGTTACCATGATGACAGTTGAAGAGAAGCCTGATGTGACATAT

upper sequence: GRMZM2G110185_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA07G05220.1 (Glycine max), 3'ss of exon 5
----------ttttggttatttctccatgtgttgtgctattattcccgaatgagttgaactgtttctcacctagtgaaaaaactattatctcact---ggattcttgttgcagTGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTCCCACCAAAAATTGACCCAAGTGTTACCATGATGACTGTGGAGGAAAAGCCAGATGTGACGTAC
            |  || ||||     |    |||   |  ||     ||  ||  ||||| | |  | | |  || |       || | | ||       || |  |||||| |||||| | || || || |||||||| || ||| | || ||||||||||| |||||||| |||||||||||||| || || ||||||||||| || || 
gtatgcctccaataagtaatttgatgctagaatgtataaccatag--aaagaagaggaactctatggc-cttgttgtatgcttgtttgtttgaccttcattttatcattgcagGGTTGATAGAAATAAATATCAGATTCAGATTCCTTTGCCTCCAAAAATTGATCCAAGTGTGACCATGATGACTGTTGAAGAGAAGCCAGATGTAACATAT

upper sequence: GRMZM2G110185_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv09s0002g00170.t01 (Vitis vinifera), 3'ss of exon 5
ttttggttatttctccatgtgttgtgctattattcccgaatgagttgaactgtttctcacctagtgaaaaaactattatctcactggattcttg---ttgcagTGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTCCCACCAAAAATTGACCCAAGTGTTACCATGATGACTGTGGAGGAAAAGCCAGATGTGACGTAC
   ||  | |     |||||  |     || |||   |  ||     ||   ||  |    || ||         || ||||||     |  ||   |||||| |||||||| || || || ||||||||||| ||  | || ||||| ||||| |||||||| ||||||||||| || || || || || |||||||| || 
-gatgcctttaaaggcatgtacttcctcataatttttg--tggtgaaaaaatttatttgtttaatgtgttcttgtttgtctcaccaacatgctgccattgcagGGTTGATCGAAATAAATATCAGATTCAAATTCCCTTGCCCCCAAAGATTGATCCAAGTGTAACCATGATGACAGTAGAAGAGAAACCGGATGTGACATAT

upper sequence: GRMZM2G110185_T01 (Zea mays), 3'ss of exon 5
lower sequence: PP1S152_13V6.2 (Physcomitrella patens), 3'ss of exon 5
-----------------------------------------------------------------------ttttggttatttctccatgt----gttgtgctattattcccgaatgagttgaactgtttctcacctagtgaaaaaactattatctcactggattcttgttgcagTGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTCCCACCAAAAATTGACCCAAGTGTTACCATGATGACTGTGGAGGAAAAGCCAGATGTGACGTAC
                                                                       | |    ||| ||||  |||    |||||| ||    |      |  ||  |   | |   |  ||      ||   |||||  | |    || | ||| |||| || || || ||||||||||| || || || || || ||||| || |||||||| ||||| || |||||||| || || |||||||||||||| ||||||
gtatgtcgtcctgatttttcgttttgtcatatgggtgcgctatttttgttaaattaggattttgatacatctctcaactatatctctttgttaacgttgtggtaactgttttagctaggtaaagtggatgtgcttctt-----aactttattagtt-ataatatacctgt-gcagGGTAGACCGAAACAAGTACCAAATCCAGATTCCGCTGCCACCTAAGATTGACCCGAGTGTCACTATGATGACAGTAGAAGAAAAGCCAGATGTTACGTAC

upper sequence: GRMZM2G110185_T01 (Zea mays), 3'ss of exon 5
lower sequence: PP1S49_256V6.1 (Physcomitrella patens), 3'ss of exon 5
--------------------------------------------------------------------------------------ttttggttatttctccatgtgttgtgctattattcccgaatgagttga-actgtttctcacctagt-----gaaaaaactattatctcactggattcttgt-------tgcagTGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTCCCACCAAAAATTGACCCAAGTGTTACCATGATGACTGTGGAGGAAAAGCCAGATGTGACGTAC
                                                                                        |   || | |   | |  ||| | ||    |  |  |   ||  ||   || ||   | || ||     |    |  | ||| ||   | | |  |  |       ||||| || ||| | |||||||| || || || || ||  | || || || |||||||| || ||||| |||||||| |||||||||||||||||||| || |||
gtacgttttcttaacttctcgttctactttatactcggttcctgagtgagctgtattgatcatgtgaagataggtctctagttgggcctcacttgtctggacgttcgttttactgcagtatcgaaggaaggagatgatgattaaaagctggtattttgttcgagatgttaactttttcggtcataatatacatgtgcagGGTAGATAGAAACAAGTATCAAATCCAGATTCCATTGCCTCCTAAGATTGACCCCAGCGTTACAATGATGACAGTGGAGGAAAAGCCAGATGTCACCTAC

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|149015235|gb|EE045022.2|EE045022
EST:     TTGGGAGATAAGGTCTCTCCAACTGATATCGAGGAAGGGATGAGGGTTGG                         TGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTCCCACCAAAAATTGA
genomic: TTGGGAGATAAGGTCTCTCCAACTGATATCGAGGAAGGGATGAGGGTTGGgtatggcatc ... cttgttgcagTGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTCCCACCAAAAATTGA
EST: gi|211399668|gb|FL004442.1|FL004442
EST:     TTGGGAGATAAGGTCTCTCCAACTGATATCGAGGAAGGGATGAGGGTTGG                         TGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTTCCACCAAAAATTGA
genomic: TTGGGAGATAAGGTCTCTCCAACTGATATCGAGGAAGGGATGAGGGTTGGgtatggcatc ... cttgttgcagTGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTCCCACCAAAAATTGA
EST: gi|149015481|gb|EE045355.2|EE045355
EST:     TTGGGAGATAAGGTCTCTCCAACTGATATCGAGGAAGGGATGAGGGTTGG                         TGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTCCCACCAAAAATTGA
genomic: TTGGGAGATAAGGTCTCTCCAACTGATATCGAGGAAGGGATGAGGGTTGGgtatggcatc ... cttgttgcagTGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTCCCACCAAAAATTGA
EST: gi|211285323|gb|FL004422.1|FL004422
EST:     TTGGGAGATAAGGTCTCTCCAACTGATATCGAGGAAGGGATGAGGGTTGG                         TGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTTCCACCAAAAATTGA
genomic: TTGGGAGATAAGGTCTCTCCAACTGATATCGAGGAAGGGATGAGGGTTGGgtatggcatc ... cttgttgcagTGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTCCCACCAAAAATTGA
EST: gi|211283517|gb|FL004412.1|FL004412
EST:     TTGGGAGATAAGGTCTCTCCAACTGATATCGAGGAAGGGATGAGGGTTGG                         TGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTCCCACCAAAAATTGA
genomic: TTGGGAGATAAGGTCTCTCCAACTGATATCGAGGAAGGGATGAGGGTTGGgtatggcatc ... cttgttgcagTGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTCCCACCAAAAATTGA
EST: gi|149087114|gb|EE176653.2|EE176653
EST:     TTGGGAGATAAGGTCTCTCCAACTGATATCGAGGAAGGGATGAGGGTTGG                         TGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTCCCACCAAAAATTGA
genomic: TTGGGAGATAAGGTCTCTCCAACTGATATCGAGGAAGGGATGAGGGTTGGgtatggcatc ... cttgttgcagTGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTCCCACCAAAAATTGA
EST: gi|211285334|gb|FL004433.1|FL004433
EST:     TTGGGAGATAAGGTCTCTCCAACTGATATCGAGGAAGGGATGAGGGTTGG                         TGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTTCCACCAAAAATTGA
genomic: TTGGGAGATAAGGTCTCTCCAACTGATATCGAGGAAGGGATGAGGGTTGGgtatggcatc ... cttgttgcagTGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTCCCACCAAAAATTGA
EST: gi|30087195|gb|CB885403.1|CB885403
EST:     TTGGGAGATAAGGTCTCTCCAACTGATATCGAGGAAGGGATGAGGGTTGG                         TGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTCCCACCAAAAATTGA
genomic: TTGGGAGATAAGGTCTCTCCAACTGATATCGAGGAAGGGATGAGGGTTGGgtatggcatc ... cttgttgcagTGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTCCCACCAAAAATTGA
EST: gi|19437016|gb|BM953426.1|BM953426
EST:     TTGGGAGATAAGGTCTCTCCAACTGATATCGAGGAAGGGATGAGGGTTGG                         TGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTTCCACCAAAAATTGA
genomic: TTGGGAGATAAGGTCTCTCCAACTGATATCGAGGAAGGGATGAGGGTTGGgtatggcatc ... cttgttgcagTGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTCCCACCAAAAATTGA
EST: gi|211283515|gb|FL004410.1|FL004410
EST:     TTGGGAGATAAGGTCTCTCCAACTGATATCGAGGAAGGGATGAGGGTTGG                         TGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTTCCACCAAAAATTGA
genomic: TTGGGAGATAAGGTCTCTCCAACTGATATCGAGGAAGGGATGAGGGTTGGgtatggcatc ... cttgttgcagTGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTCCCACCAAAAATTGA
EST: gi|211283510|gb|FL004405.1|FL004405
EST:     TTGGGAGATAAGGTCTCTCCAACTGATATCGAGGAAGGGATGAGGGTTGG                         TGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTTCCACCAAAAATTGA
genomic: TTGGGAGATAAGGTCTCTCCAACTGATATCGAGGAAGGGATGAGGGTTGGgtatggcatc ... cttgttgcagTGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTCCCACCAAAAATTGA
EST: gi|67028224|gb|CO456973.1|CO456973
EST:     TTGGGAGATAAGGTCTCTCCAACTGATATCGAGGAAGGGATGAGGGTTGG                         TGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTTCCACCAAAAATTGA
genomic: TTGGGAGATAAGGTCTCTCCAACTGATATCGAGGAAGGGATGAGGGTTGGgtatggcatc ... cttgttgcagTGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTCCCACCAAAAATTGA
EST: gi|78085799|gb|DV514192.1|DV514192
EST:     TTGGGAGATAAGGTCTCTCCAACTGATATCGAGGAAGGGATGAGGGTTGG                         TGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTCCCACCAAAAATTGA
genomic: TTGGGAGATAAGGTCTCTCCAACTGATATCGAGGAAGGGATGAGGGTTGGgtatggcatc ... cttgttgcagTGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTCCCACCAAAAATTGA
EST: gi|19436438|gb|BM952848.1|BM952848
EST:     TTGGGAGATAAGGTCTCTCCAACTGATATCGAGGAAGGGATGAGGGTTGG                         TGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTTCCACCAAAAATTGA
genomic: TTGGGAGATAAGGTCTCTCCAACTGATATCGAGGAAGGGATGAGGGTTGGgtatggcatc ... cttgttgcagTGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTCCCACCAAAAATTGA
EST: gi|211285332|gb|FL004431.1|FL004431
EST:     TTGGGAGATAAGGTCTCTCCAACTGATATCGAGGAAGGGATGAGGGTTGG                         TGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTTCCACCAAAAATTGA
genomic: TTGGGAGATAAGGTCTCTCCAACTGATATCGAGGAAGGGATGAGGGTTGGgtatggcatc ... cttgttgcagTGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTCCCACCAAAAATTGA
EST: gi|28930845|gb|CB334206.1|CB334206
EST:     TTGGGAGATAAGGTCTCTCCAACTGATATCGAGGAAGGGATGAGGGTTGG                         TGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTCCCACCAAAAATTGA
genomic: TTGGGAGATAAGGTCTCTCCAACTGATATCGAGGAAGGGATGAGGGTTGGgtatggcatc ... cttgttgcagTGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTCCCACCAAAAATTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaactgtttctcacctagtgaaaaaactattatctcactggattcttgttgcagTGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTCCCACCAAAAATTGACCCAAGTGTTACCATGATGACTGTGGAGGAAAAGCCAGATGTGACGTAC
                                           ttcttgtt  CT-rich tract
                   tgaaaaaactattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttggttatttctccatgtgttgtgctattattcccgaatgagttgaactgtttctcacctagtgaaaaaactattatctcactggattcttgttgcagTGTTGATCGCAACAAGTACCAGATTCAAATCCCTCTCCCACCAAAAATTGACCCAAGTGTTACCATGATGACTGTGGAGGAAAAGCCAGATGTGACGTAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
ttttggt
- - - - - - ctccatg
- - - - - - - - - - - tgtgcta
- - - - - - - - - - - - - - - - - - - - - - -tgaactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cactgga