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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttgtcggagtaattaaccattttgtgctgccagatttatatttgcttcatgaggaatacttcctttgatcagaacatataggtttgttctagttcaactttattttggttatatatcgctaaaattgctcctttttctttatagGCTGCTGTTGAGGAAGGTATTGTTGTTGGTGGAGGATGCACCCTTTTGCGGCTTGCAGCTAAAGTCGATGCCATCAAGGATACACTGGAGAACGATGAGC

Basic information

species Zea mays
transcript GRMZM2G095252_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G095252_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os06g02380.1 (Oryza sativa), 3'ss of exon 10
gtaagt-tgtcggagtaattaaccattttgtgctgccagatttatatttgcttcatgaggaatacttcctttgatcagaacatataggtttgttctagttcaactttattttggttatatatcgctaaaattgctcctttttctttatagGCTGCTGTTGAGGAAGGTATTGTTGTTGGTGGAGGATGCACCCTTTTGCGGCTTGCAGCTAAAGTCGATGCCATCAAGGATACACTGGAGAACGATGAGC
|| ||| ||| |   ||| |  |  |    |      ||||| || |||||||| | ||||| |     |  | |       |      |   |  |  ||||| || || ||| | |  |||  ||||     |||| ||| |    ||||||||||||||||||||||||||||||||||||| ||||| ||| || | || ||||||| ||| || ||||||||||| |  |||||||| |||||||
gttagtctgttgttataactg-ctttgagatagaaatagattaatgtttgcttcttaaggaagaaaaattaaggtagtttgttgctcactgagttgatatcaacgttcttctggctttggatctttaaaccgcttcctctttgtc---agGCTGCTGTTGAGGAAGGTATTGTTGTTGGTGGAGGGTGCACTCTTCTGAGACTGGCAGCTAGAGTTGACGCCATCAAGGACAACCTGGAGAATGATGAGC

upper sequence: GRMZM2G095252_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA08G18760.1 (Glycine max), 3'ss of exon 9
gtaagttgtcggagtaattaaccattttgtgctgccagatttatatttgcttcatgaggaatacttcctttgatcagaacatataggtttgttctagttcaactttattttggttatatatcgctaaaattgctcctttttctttatagGCTGCTGTTGAGGAAGGTATTGTTGTTGGTGGAGGATGCACCCTTTTGCGGCTTGCAGCTAAAGTCGATGCCATCAAGGATACACTGGAGAACGATGAGC
                                                          |  | |||   ||   || |   | ||| ||| ||             ||| ||  | ||    ||||| | |     | ||   ||  |||| ||||| ||||||||||||||||||||||| || ||||| ||| || | |||||| | || || ||||| ||||||||||  || || || |||||  
----------------------------------------------------------gtgtccttttctttcccaaagtttttagattttttggg----------attctgtctgtaa---gctaatagt----ttgttgactttcagGCAGCTGTAGAGGAAGGTATTGTTGTTGGTGGTGGTTGCACTCTTCTGAGACTTGCATCAAAGGTGGATGCAATCAAGGATAGCCTTGATAATGATGAAG

upper sequence: GRMZM2G095252_T02 (Zea mays), 3'ss of exon 4
lower sequence: AT3G13470.1 (Arabidopsis thaliana), 3'ss of exon 10
gtaagttgtcggagtaattaaccattttgtgctgccagatttatatttgcttcatgaggaatacttcctttgatcagaacatataggtttgttctagttcaactttattttggttatatatcgctaaaattgctcctttttctttatagGCTGCTGTTGAGGAAGGTATTGTTGTTGGTGGAGGATGCACCCTTTTGCGGCTTGCAGCTAAAGTCGATGCCATCAAGGATACACTGGAGAACGATGAGC
                                                              | || ||||   |||  |  || || || |    ||       || |   || |||| |   | | ||  |  | ||   |||  ||||||||||||||||||||||||| |||||||| || ||||| ||  | ||||||||| | || |||||||||||||||||||| || || || |||||  
-----------------------------------------------------------gtgattttctttatccag--ctgatggggttata--ggtatcgtgctactcatgt-atatcttaattatatgacctcattgagttt-cagGCTGCTGTTGAGGAAGGTATTGTCGTTGGTGGTGGTTGCACTCTGCTCCGGCTTGCATCAAAGGTCGATGCCATCAAGGATACCCTTGAAAATGATGAAG

upper sequence: GRMZM2G095252_T02 (Zea mays), 3'ss of exon 4
lower sequence: AT1G55490.1 (Arabidopsis thaliana), 3'ss of exon 10
gtaagttgtcggagtaattaaccattttgtgctgccagatttatatttgcttcatgaggaatacttcctttgatcagaacatataggtttgttctagttcaactttattttggttatatatcgctaaaattgctcctttttctttatagGCTGCTGTTGAGGAAGGTATTGTTGTTGGTGGAGGATGCACCCTTTTGCGGCTTGCAGCTAAAGTCGATGCCATCAAGGATACACTGGAGAACGATGAGC
                                                             |  ||   |   || ||   |  ||    ||  || ||       ||  | || |  |||  ||||    | |  |  |||||   |||| ||||| ||||||||||||||||||||||| || ||||| ||  | || |||||  | || || |||||||| || |  || || || || |||||  
------------------------------------------------------------gtgattttgtatttctgaggcttgagaagcgtgttatttg-----catactcgtgaactataactaatcaggattttaattcttc--agGCCGCTGTCGAGGAAGGTATTGTTGTTGGTGGTGGTTGCACTCTGCTTCGTCTTGCTTCCAAGGTTGATGCCATTAAAGCCACGCTTGATAATGATGAAG

upper sequence: GRMZM2G095252_T02 (Zea mays), 3'ss of exon 4
lower sequence: AT5G56500.2 (Arabidopsis thaliana), 3'ss of exon 10
gtaagttgtcggagtaattaaccattttgtgctgccagatttatatttgcttcatgaggaatacttcctttgatcagaacatataggtttgttctagttcaactttattttggttatatatcgctaaaattgctcctttttctttatagGCTGCTGTTGAGGAAGGTATTGTTGTTGGTGGAGGATGCACCCTTTTGCGGCTTGCAGCTAAAGTCGATGCCATCAAGGATACACTGGAGAACGATGAGC
                                                         | || |    || | | || |     | |   ||||    | ||       | ||||     |  |   || ||| |     || |   ||||||||||| || ||||||||||||||||| |||||||| || ||  |  | |||||| | ||||| || || || || || || || |  ||||||||  
---------------------------------------------------------gtaacatcatctctaagcaaagagccttgaaatgtttccatcca-------tatggt-----agagactaagttgttggaccttttaattagGCTGCTGTGGAAGAAGGTATTGTTGTTGGCGGAGGATGTACTCTGCTAAGACTTGCATCGAAAGTGGACGCTATTAAAGAGACTCTAGCAAACGATGAAG

upper sequence: GRMZM2G095252_T02 (Zea mays), 3'ss of exon 4
lower sequence: Vv09s0002g03930.t01 (Vitis vinifera), 3'ss of exon 9
gtaagttgtcggagtaattaaccattttgtgctgccagatttatatttgcttcatgaggaatacttcctttgatcagaacatataggtttgttctagttcaactttattttggttatatatcgctaaaattgctcctttttctttatagGCTGCTGTTGAGGAAGGTATTGTTGTTGGTGGAGGATGCACCCTTTTGCGGCTTGCAGCTAAAGTCGATGCCATCAAGGATACACTGGAGAACGATGAGC
          | | |  ||||  |       |   || ||||| |  | ||          |   ||| ||  |     ||      |||| ||| |    | || | ||  | | ||  | | | ||| |  ||  | || ||   |||| || ||||||||||||||||| |||||||| || |||||  | ||||| || ||||| ||||| ||||| ||||| || || || || |  |||||||
----------gtactgtttaattaaacatgaccatca-atttagaaatactctgc------tttctccatttgttgcctcactgccctttgctcttgc---atttaagttaaggtgtaactggttcaaaattttcaatattgtt---agGCAGCCGTTGAGGAAGGTATTGTGGTTGGTGGCGGGTGCACATTGTTGCGTCTAGCAGCAAAAGTTGATGCTATCAAAGACACTCTTGATAGTGATGAGC

upper sequence: GRMZM2G095252_T02 (Zea mays), 3'ss of exon 4
lower sequence: EFJ32217 (Selaginella moellendorffii), 3'ss of exon 9
gtaagttgtcggagtaattaaccattttgtgctgccagatttatatttgcttcatgaggaatacttcctttgatcagaacatataggtttgttctagttcaactttattttggttatatatcgctaaaattgctcctttttctttatagGCTGCTGTTGAGGAAGGTATTGTTGTTGGTGGAGGATGCACCCTTTTGCGGCTTGCAGCTAAAGTCGATGCCATCAAGGATACACTGGAGAACGATGAGC
                                                                                                ||   |      | | || |    |   |        ||||   | ||   ||||||||||||||||||| || ||||||||||||||     | |||||| ||||  |    ||||| |||||||||||||| || || || ||| | ||||
------------------------------------------------------------------------------------------------gtaatataccggtcttgtcacccgttttttctgcaattcctcgcttttcgcagGCTGCTGTTGAGGAAGGCATCGTTGTTGGTGGAGGCACAGCTCTTTTGAGGCTGTCGAAGAAAGTGGATGCCATCAAGGAAACGCTTGAAAACCAGGAGC

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|32837509|gb|CD977187.1|CD977187
EST:     AACTAAAAGAGAAGAAGTTAAGAGTTGAGGATGCCCTAAATGCAACCAAG                         GCTGCTGTTGAGGAAGGTATTGTTGTTGGTGGAGGATGCACCCTTTTGCGG
genomic: AACTAAAAGAGAAGAAGTTAAGAGTTGAGGATGCCCTAAATGCAACCAAGgtaagttgtc ... ttctttatagGCTGCTGTTGAGGAAGGTATTGTTGTTGGTGGAGGATGCACCCTTTTGCGG
EST: gi|32932965|gb|CF037777.1|CF037777
EST:     AACTAAAAGAGGAGAAGTTAAGAGTTGAGGATGCCCTAAATGCAACCAAG                         GCTGCTGTTGAGGAAGGTATTGTTGTTGGTGGAGGATGCACCCTTTTGCGG
genomic: AACTAAAAGAGAAGAAGTTAAGAGTTGAGGATGCCCTAAATGCAACCAAGgtaagttgtc ... ttctttatagGCTGCTGTTGAGGAAGGTATTGTTGTTGGTGGAGGATGCACCCTTTTGCGG
EST: gi|33092673|gb|CF052667.1|CF052667
EST:     AACTAAAAGAGAAGAAGTTAAGAGTTGAGGATGCCCTAAATGCAACCAAG                         GCTGCTGTTGAGGAAGGTATTGTTGTTGGTGGAGGATGCACCCTTTTGCGG
genomic: AACTAAAAGAGAAGAAGTTAAGAGTTGAGGATGCCCTAAATGCAACCAAGgtaagttgtc ... ttctttatagGCTGCTGTTGAGGAAGGTATTGTTGTTGGTGGAGGATGCACCCTTTTGCGG
EST: gi|32934171|gb|CF038983.1|CF038983
EST:     AACTAAAAGAGAAGAAGTTAAGAGTTGAGGATGCCCTAAATGCAACCAAA                         GCTGCTGTTGAGGAAGGTATTGTTGTTGGTGGAGGATGCACCCTTTTGCGG
genomic: AACTAAAAGAGAAGAAGTTAAGAGTTGAGGATGCCCTAAATGCAACCAAGgtaagttgtc ... ttctttatagGCTGCTGTTGAGGAAGGTATTGTTGTTGGTGGAGGATGCACCCTTTTGCGG
EST: gi|32931699|gb|CF036511.1|CF036511
EST:     AACTAAAAGAGAAGAAGTTAAGAGTTGAGGATGCCCTAAATGCAACCAAG                         GCTGCTGTTGAGGAAGGTATTGTTGTTGGTGGAGGATGCACCCTTTTGCGG
genomic: AACTAAAAGAGAAGAAGTTAAGAGTTGAGGATGCCCTAAATGCAACCAAGgtaagttgtc ... ttctttatagGCTGCTGTTGAGGAAGGTATTGTTGTTGGTGGAGGATGCACCCTTTTGCGG
EST: gi|32935108|gb|CF039920.1|CF039920
EST:     AACTAAAAGAGAAGAAGTTAAGAGTTGAGGATGCCCTAAATGCAACCAAG                         GCTGCTGTTGAGGAAGGTATTGTTGTTGGTGGAGGATGCACCCTTTTGCGG
genomic: AACTAAAAGAGAAGAAGTTAAGAGTTGAGGATGCCCTAAATGCAACCAAGgtaagttgtc ... ttctttatagGCTGCTGTTGAGGAAGGTATTGTTGTTGGTGGAGGATGCACCCTTTTGCGG
EST: gi|32931097|gb|CF035909.1|CF035909
EST:     AACTAAAAGAGAAGAAGTTAAGAGTTGAGGATGCCCTAAATGCAACCAAG                         GCTGCTGTTGAGGAAGGTATTGTTGTTGGTGGAGGATGCACCCTTTTGCGG
genomic: AACTAAAAGAGAAGAAGTTAAGAGTTGAGGATGCCCTAAATGCAACCAAGgtaagttgtc ... ttctttatagGCTGCTGTTGAGGAAGGTATTGTTGTTGGTGGAGGATGCACCCTTTTGCGG
EST: gi|32836365|gb|CD976043.1|CD976043
EST:     AACTAAAAGAGAAGAAGTTAAGAGTTGAGGATGCCCTAAATGCAACCAAG                         GCTGCTGTTGAGGAAGGTATTGTTGTTGGTGGAGGATGCACCCTTTTGCGG
genomic: AACTAAAAGAGAAGAAGTTAAGAGTTGAGGATGCCCTAAATGCAACCAAGgtaagttgtc ... ttctttatagGCTGCTGTTGAGGAAGGTATTGTTGTTGGTGGAGGATGCACCCTTTTGCGG
EST: gi|32935122|gb|CF039934.1|CF039934
EST:     AACTAAAAGAGAAGAAGTTAAGAGTTGAGGATGCCCTAAATGCAACCAAG                         GCTGCTGTTGAGGAAGGTATTGTTGTTGGTGGAGGATGCACCCTTTTGCGG
genomic: AACTAAAAGAGAAGAAGTTAAGAGTTGAGGATGCCCTAAATGCAACCAAGgtaagttgtc ... ttctttatagGCTGCTGTTGAGGAAGGTATTGTTGTTGGTGGAGGATGCACCCTTTTGCGG
EST: gi|32838764|gb|CD978445.1|CD978445
EST:     AACTAAAAGAGAAGAAGTTAAGAGTTGAGGATGCCCTAAATGCAACCAAG                         GCTGCTGTTGAGGAAGGTATTGTTGTTGGTGGAGGATGCACCCTTTTGCGG
genomic: AACTAAAAGAGAAGAAGTTAAGAGTTGAGGATGCCCTAAATGCAACCAAGgtaagttgtc ... ttctttatagGCTGCTGTTGAGGAAGGTATTGTTGTTGGTGGAGGATGCACCCTTTTGCGG
EST: gi|211173892|gb|FL341459.1|FL341459
EST:     AACTAAAAGAGAAGAAGTTAARAGTTGAGGATGCCCTAAATGCAACCAAG                         GCTGCTGTTGAGGAAGGTATTG
genomic: AACTAAAAGAGAAGAAGTTAAGAGTTGAGGATGCCCTAAATGCAACCAAGgtaagttgtc ... ttctttatagGCTGCTGTTGAGGAAGGTATTG
EST: gi|32930569|gb|CF035381.1|CF035381
EST:     AACTAAAAGAGAAGAAGTTAAGAGTTGAGGATGCCCTAAATGCAACCAAG                         GCTGCTGTTGAGGAAGGTATTGTTGTTGGTGGAGGATGCACCCTTTTGCGG
genomic: AACTAAAAGAGAAGAAGTTAAGAGTTGAGGATGCCCTAAATGCAACCAAGgtaagttgtc ... ttctttatagGCTGCTGTTGAGGAAGGTATTGTTGTTGGTGGAGGATGCACCCTTTTGCGG
EST: gi|33097092|gb|CF057052.1|CF057052
EST:     AACTAAAAGAGAAGAAGTTAAGAGTTGAGGATGCCCTAAATGCAACCAAG                         GCTGCTGTTGAGGAAGGTATTGTTGTTGGTGGAGGATGCACCCTTTTGCGG
genomic: AACTAAAAGAGAAGAAGTTAAGAGTTGAGGATGCCCTAAATGCAACCAAGgtaagttgtc ... ttctttatagGCTGCTGTTGAGGAAGGTATTGTTGTTGGTGGAGGATGCACCCTTTTGCGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagttcaactttattttggttatatatcgctaaaattgctcctttttctttatagGCTGCTGTTGAGGAAGGTATTGTTGTTGGTGGAGGATGCACCCTTTTGCGGCTTGCAGCTAAAGTCGATGCCATCAAGGATACACTGGAGAACGATGAGC
                           cgctaaa  putative branch site (score: 3)
                                   ttgctcctttttcttt  CT-rich tract
      aactttattttggtta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttgtcggagtaattaaccattttgtgctgccagatttatatttgcttcatgaggaatacttcctttgatcagaacatataggtttgttctagttcaactttattttggttatatatcgctaaaattgctcctttttctttatagGCTGCTGTTGAGGAAGGTATTGTTGTTGGTGGAGGATGCACCCTTTTGCGGCTTGCAGCTAAAGTCGATGCCATCAAGGATACACTGGAGAACGATGAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA