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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccaatatgttcttaaaggttttatgaggattactaaaaataaatgtttcactttgcctgcaaattcatgtgtgatgatatctctctgatgctactactagGTTTCAATGTCGAGAAAGTTCAATACAAGAATGTGATGTTTACTGTTTGGGATGTTGGTGGCCAAGAAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAA

Basic information

species Zea mays
transcript GRMZM2G106795_T03
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G106795_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g47110.1 (Oryza sativa), 3'ss of exon 2
ccaatatgttcttaaaggttttatgaggattact---aaaaataaatgtttcactttgcctgcaaattcatgtgtgatgatatctctctgatgctactactagGTTTCAATGTCGAGAAAGTTCAATACAAGAATGTGATGTTTACTGTTTGGGATGTTGGTGGCCAAGAAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAA
   ||||  || | | || |||    || ||| |   ||||    |  | |||||||||  | | | | ||   || |  |  || | || || ||| || ||| |||||||| |||||||| || |||||||| ||||||||||| || |||||||| ||||||||||| |||||||||||  |||||||||| ||||||||
--gatattatcatcatggcttttatggggttatttgaaaaatctgacatctcactttgctgggacactgattgatgcttctgcctttgtgctg-taccaccagGGTTCAATGTTGAGAAAGTACAGTACAAGAACGTGATGTTTACAGTATGGGATGTCGGTGGCCAAGAGAAGTTGAGGCCTCTGTGGAGGCATTACTTCAA

upper sequence: GRMZM2G106795_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA11G01380.2 (Glycine max), 3'ss of exon 3
ccaatatgttcttaaaggttttatgaggattactaaaaataaatgtttcactttgcctgcaaatt---catgtgtgatgatatctctctgatgctactactagGTTTCAATGTCGAGAAAGTTCAATACAAGAATGTGATGTTTACTGTTTGGGATGTTGGTGGCCAAGAAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAA
   |  |||   ||  |  || |   || ||  ||    |     |   | |  | || || |||     | | || | |||  | | |  |||  ||   |||||||||||| ||||||||||| || || ||||| || || || |||||||||||||| || ||||| ||  | |||||  | ||||||||||| || ||
attaagtgtctatatggtattgacctggcttgttagttttgg-cctgcaaatgagtctacatattgtttctctatgtttataaatttatattgc--cttgcagGTTTCAATGTGGAGAAAGTTCAGTATAAAAATGTTATTTTCACAGTTTGGGATGTTGGAGGACAAGAGAAACTAAGGCCACTTTGGAGGCACTATTTTAA

upper sequence: GRMZM2G106795_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA01G43910.2 (Glycine max), 3'ss of exon 3
ccaatatgttcttaaaggttttatgaggattactaaaaata---aatgtttcactttgcctgcaaattcatgtgtgatgatatctctctgatgctactactagGTTTCAATGTCGAGAAAGTTCAATACAAGAATGTGATGTTTACTGTTTGGGATGTTGGTGGCCAAGAAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAA
     ||||   ||  |  ||   |  | ||  ||    |    |     | | | | | |  |  ||  | |  | |  ||  | | |  |||  ||   |||||||||||| ||||||||||| || |||||||| || || || || ||||||||||| || ||||| ||  | |||||  | ||||||||||||||  |
gttgaatgtctatatggtattggcgccgcttgttagttttggccagcaaatgagtctacata-atgtttctctaggtttttaaatttatattgc--cttgcagGTTTCAATGTGGAGAAAGTTCAGTATAAGAATGTTATTTTCACAGTCTGGGATGTTGGAGGACAAGAGAAACTAAGGCCACTTTGGAGGCACTACTTTGA

upper sequence: GRMZM2G106795_T03 (Zea mays), 3'ss of exon 2
lower sequence: AT3G03120.1 (Arabidopsis thaliana), 3'ss of exon 2
ccaatatgttcttaaaggttttatgaggattactaaaaataaatgtt-tcactttgcctgcaaattcatgtgtgatgatatctctctgatgctactactagGTTTCAATGTCGAGAAAGTTCAATACAAGAATGTGATGTTTACTGTTTGGGATGTTGGTGGCCAAGAAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAA
      |       |  | |  |  |   ||| |     |   | || ||| ||  | | |||   |  || |  |||    | |    | ||   || |||||||||||| ||||||||||| ||||||||||| || || || ||||||||||||||||||||||| ||| ||||||||||||||||||| ||||||||
-----gtaggtcagattgctcaagcatttttattttttttgcgttttctcatttatcttacaa---cgggtttactgaggattttaaatttcttacac-agGTTTCAATGTTGAGAAAGTTCAGTACAAGAATGTCATCTTCACAGTTTGGGATGTTGGTGGCCAAGAGAAGCTGAGGCCCTTGTGGAGGCATTACTTCAA

upper sequence: GRMZM2G106795_T03 (Zea mays), 3'ss of exon 2
lower sequence: AT5G17060.1 (Arabidopsis thaliana), 3'ss of exon 2
ccaatatgttcttaaaggttttatgaggattactaaaaataaatgtttcactttgcctgcaaattcatgtgtgatgatatctct--ctgatgctactactagGTTTCAATGTCGAGAAAGTTCAATACAAGAATGTGATGTTTACTGTTTGGGATGTTGGTGGCCAAGAAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAA
    | ||   ||| |  |||    | ||||| |        || || |  || |         | |||| || ||| |  |    || ||| ||||   ||| |||||||| ||||||||||| ||||||||||||||||| || ||||||||||||||||||||||| ||  |||| ||  | |||||||| ||||||||
ttcttgtgacattatacttttatctatgattattgttctgtcattttccttttggttgtttggattatgtctgctgacaatttaaacttatgttact--cagGATTCAATGTTGAGAAAGTTCAGTACAAGAATGTGATGTTCACAGTTTGGGATGTTGGTGGCCAAGAGAAACTGAGACCTCTTTGGAGGCATTACTTCAA

upper sequence: GRMZM2G106795_T03 (Zea mays), 3'ss of exon 2
lower sequence: Vv16s0039g02240.t01 (Vitis vinifera), 3'ss of exon 2
ccaatatgttcttaaaggttttatgaggattactaaaaata--aatgtttcactttgc-ctgcaaattcatgtgtgatgatatctctctgatgctactactagGTTTCAATGTCGAGAAAGTTCAATACAAGAATGTGATGTTTACTGTTTGGGATGTTGGTGGCCAAGAAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAA
  || |  |  | | |   |  |||     |||||   ||    |||| ||   | |  || || ||| || |    ||||   | |||| |  ||    ||||||||||||| ||||||||||| || ||||| |||||||| || || |||||||| ||||| ||||| ||  | |||||  | |||||||| ||||| ||
-taacagttgatcatattgtacatgtattatactatggatgttgatgtgtcgaatggagcttcagattgattttaattgatcattttctggtaatat--atagGTTTCAATGTGGAGAAAGTTCAGTATAAGAACGTGATGTTCACAGTGTGGGATGTAGGTGGACAAGAGAAACTCAGGCCACTCTGGAGGCATTACTTTAA

upper sequence: GRMZM2G106795_T03 (Zea mays), 3'ss of exon 2
lower sequence: PP1S37_304V6.1 (Physcomitrella patens), 3'ss of exon 2
-----------------------------------------------------------------------------ccaatatgttcttaaaggttttatgaggatt----actaaaaataaatgtttcactttgcctgcaaattcatgtgtgatgatatctctctgatgctactactagGTTTCAATGTCGAGAAAGTTCAATACAAGAATGTGATGTTTACTGTTTGGGATGTTGGTGGCCAAGAAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAA
                                                                             |   | | || |  || |||  |   | |||     | ||    |  ||  |   ||||   | ||  ||   ||  |   ||  | |   || | | |   ||| |||||||| |||||||||||||||||||||||   |||||| || ||||| ||||| |||||||| || ||| | ||  ||||| |||| ||||||||
gtaatttgacttatcacttgtagtcaatccttcatttttttggtagtgcgcctcttcgtttctgagtatagatggcactgttgttttatacaatgttgcaaccgtatttcctgccaagtgcatgtgagtgtttttgagggtaacatctgttgctaaattacattttccattcaattttcagGGTTCAATGTAGAGAAAGTTCAATACAAGAATGTTGAGTTTACAGTGTGGGACGTTGGAGGCCAAGAGAAATTGCGACCTCTGTGGCGGCATTACTTCAA

upper sequence: GRMZM2G106795_T03 (Zea mays), 3'ss of exon 2
lower sequence: PP1S47_298V6.1 (Physcomitrella patens), 3'ss of exon 2
--------------------------------------------------------------------ccaatatgttc------ttaaaggttttatga-----ggattactaaaaat-aaatgtt--tcactttgcctgcaaat---tcatgtgtgatgatatctctctgatgctactactagGTTTCAATGTCGAGAAAGTTCAATACAAGAATGTGATGTTTACTGTTTGGGATGTTGGTGGCCAAGAAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAA
                                                                       || | ||       || | ||| || ||      | |||| |     |  | || |  | | ||||| | | |     |||| ||| | | | |     | |||| |     ||| |||||||| ||||||||||| |||||||| ||   |||||| || ||||||||||| || ||||| || ||| ||||  ||||| |||| || |||||
gtagcttgacttaacacttccagttgatccttttgtatttgaaagagcccctcttcgtttctgcttatttgatgtatttgcttatttgacggtgttttgtttgatgtattattctgtgtcgagtgctggtgaatttgctttcgaggatgtcatttgttaagttgttgtggttatgcaatattcagGGTTCAATGTGGAGAAAGTTCAGTACAAGAACGTCGAGTTTACAGTGTGGGATGTTGGAGGTCAAGAGAAATTGCGGCCTCTGTGGCGGCATTATTTCAA

upper sequence: GRMZM2G106795_T03 (Zea mays), 3'ss of exon 2
lower sequence: EFJ24533 (Selaginella moellendorffii), 3'ss of exon 2
ccaatatgttcttaaaggttttatgaggattactaaaaataaatgtttcactttgcctgcaaattcatgtgtgatgatatctctctgatgctactactagGTTTCAATGTCGAGAAAGTTCAATACAAGAATGTGATGTTTACTGTTTGGGATGTTGGTGGCCAAGAAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAA
            |||   |||| |  || || ||     |  || ||   |||      | | |||  |  |||||  |   ||          | ||||| || || || ||||| || || |||||||||||| |||| || || ||||||||||||||||| || ||| | || ||  | |||| ||||||||| | 
-----------gtaatccttttttctggttt-cttggctttcatcttgaccttcttgctcgatttctcgactgatgtgaatcct----------tgctagGATTTAACGTGGAGAAGGTCCAGTACAAGAATGTGGTGTTCACGGTGTGGGATGTTGGTGGCCAGGAGAAGCTAAGACCGCTCTGGAAGCACTACTTTAG

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|211091310|gb|FL335551.1|FL335551
EST:     CTTGTACAAGCTGCAAATCGGGGAGGTTTTGTCGACTGTTCCCACGATTG                         GTTTCAATGTCGAGAAAGTTCAATACAAGAATGTGATGTTTACTGTTTGGG
genomic: CTTGTACAAGCTGCAAATCGGGGAGGTTTTGTCGACTGTTCCCACGATTGgtaggctatc ... ctactactagGTTTCAATGTCGAGAAAGTTCAATACAAGAATGTGATGTTTACTGTTTGGG
EST: gi|74241061|gb|DT648975.1|DT648975
EST:     CTTGTACAAGCTGCAAATCGGGGAGGTTTTGTCGACTGTTCCCACGATTG                         GTTTCAATGTCGAGAAAGTTCAATACAAGAATGTGATGTTTACTGTTTGGG
genomic: CTTGTACAAGCTGCAAATCGGGGAGGTTTTGTCGACTGTTCCCACGATTGgtaggctatc ... ctactactagGTTTCAATGTCGAGAAAGTTCAATACAAGAATGTGATGTTTACTGTTTGGG
EST: gi|101398288|gb|EB821017.1|EB821017
EST:     CTTGTACAAGCTGCAAATCGGGGAGGTTTTGTCGACTGTTCCCACGATTG                         GTTTCAATGTCGAGAAAGTTCAATACAAGAATGTGATGTTTACTGTTTGGG
genomic: CTTGTACAAGCTGCAAATCGGGGAGGTTTTGTCGACTGTTCCCACGATTGgtaggctatc ... ctactactagGTTTCAATGTCGAGAAAGTTCAATACAAGAATGTGATGTTTACTGTTTGGG
EST: gi|211076278|gb|FL377992.1|FL377992
EST:     CTTGTACAAGCTGCAAATCGGGGAGGTTTTGTCGACTGTTCCCACGATTG                         GTTTCAATGTCGAGAAAGTTCAATACAAGAATGTGATGTTTACTGTTTGGG
genomic: CTTGTACAAGCTGCAAATCGGGGAGGTTTTGTCGACTGTTCCCACGATTGgtaggctatc ... ctactactagGTTTCAATGTCGAGAAAGTTCAATACAAGAATGTGATGTTTACTGTTTGGG
EST: gi|211066463|gb|FL305323.1|FL305323
EST:     CTTGTACAAGCTGCAAATCGGGGAGGTTTTGTCGACTGTTCCCACGATTG                         GTTTCAATGTCGAGAAAGTTCAATACAAGAATGTGATGTTTACTGTTTGGG
genomic: CTTGTACAAGCTGCAAATCGGGGAGGTTTTGTCGACTGTTCCCACGATTGgtaggctatc ... ctactactagGTTTCAATGTCGAGAAAGTTCAATACAAGAATGTGATGTTTACTGTTTGGG
EST: gi|211069201|gb|FL305331.1|FL305331
EST:     CTTGTACAAGCTGCAAATCGGGGAGGTTTTGTCGACTGTTCCCACGATTG                         GTTTCAATGTCGAGAAAGTTCAATACAAGAATGTGATGTTTACTGTTTGGG
genomic: CTTGTACAAGCTGCAAATCGGGGAGGTTTTGTCGACTGTTCCCACGATTGgtaggctatc ... ctactactagGTTTCAATGTCGAGAAAGTTCAATACAAGAATGTGATGTTTACTGTTTGGG
EST: gi|211497259|gb|FL426008.1|FL426008
EST:     CTTGTACAAGCTGCAAATCGGGGAGGTTTTGTCGACTGTTCCCACGATTG                         GTTTCAATGTCGAGAAAGTTCAATACAAGAATGTGATGTTTACTGTTTGGG
genomic: CTTGTACAAGCTGCAAATCGGGGAGGTTTTGTCGACTGTTCCCACGATTGgtaggctatc ... ctactactagGTTTCAATGTCGAGAAAGTTCAATACAAGAATGTGATGTTTACTGTTTGGG
EST: gi|211066466|gb|FL305326.1|FL305326
EST:     CTTGTACAAGCTGCAAATCGGGGAGGTTTTGTCGACTGTTCCCACGATTG                         GTTTCAATGTCGAGAAAGTTCAATACAAGAATGTGATGTTTACTGTTTGGG
genomic: CTTGTACAAGCTGCAAATCGGGGAGGTTTTGTCGACTGTTCCCACGATTGgtaggctatc ... ctactactagGTTTCAATGTCGAGAAAGTTCAATACAAGAATGTGATGTTTACTGTTTGGG
EST: gi|211066464|gb|FL305324.1|FL305324
EST:     CTTGTACAAGCTGCAAATCGGGGAGGTTTTGTCGACTGTTCCCACGATTG                         GTTTCAATGTCGAGAAAGTTCAATACAAGAATGTGATGTTTACTGTTTGGG
genomic: CTTGTACAAGCTGCAAATCGGGGAGGTTTTGTCGACTGTTCCCACGATTGgtaggctatc ... ctactactagGTTTCAATGTCGAGAAAGTTCAATACAAGAATGTGATGTTTACTGTTTGGG
EST: gi|211069203|gb|FL305333.1|FL305333
EST:     CTTGTASAAGCTGCAAAYCGGGGAGGTTTTGTCGACTGTTCCCACGATTG                         GTTTCAATGTCGAGAAAGTTCAATAYAAGAATGTGATGTTTACTGTTTGGG
genomic: CTTGTACAAGCTGCAAATCGGGGAGGTTTTGTCGACTGTTCCCACGATTGgtaggctatc ... ctactactagGTTTCAATGTCGAGAAAGTTCAATACAAGAATGTGATGTTTACTGTTTGGG
EST: gi|211066470|gb|FL305330.1|FL305330
EST:     CTTGTACAAGCTGCAAATCGGGGAGGTTTTGTCGACTGTTCCCACGATTG                         GTTTCAATGTCGAGAAAGTTCAATACAAGAATGTGATGTTTACTGTTTGGG
genomic: CTTGTACAAGCTGCAAATCGGGGAGGTTTTGTCGACTGTTCCCACGATTGgtaggctatc ... ctactactagGTTTCAATGTCGAGAAAGTTCAATACAAGAATGTGATGTTTACTGTTTGGG
EST: gi|211066462|gb|FL305322.1|FL305322
EST:     CTTGTACAAGCTGCAAATCGGGGAGGTTTTGTCGACTGTTCCCACGATTG                         GTTTCAATGTCGAGAAAGTTCAATACAAGAATGTGATGTTTACTGTTTGGG
genomic: CTTGTACAAGCTGCAAATCGGGGAGGTTTTGTCGACTGTTCCCACGATTGgtaggctatc ... ctactactagGTTTCAATGTCGAGAAAGTTCAATACAAGAATGTGATGTTTACTGTTTGGG
EST: gi|211066467|gb|FL305327.1|FL305327
EST:     CTTGTACAAGCTGCAAATCGGGGAGGTTTTGTCGACTGTTCCCACGATTG                         GTTTCAATGTCGAGAAAGTTCAATACAAGAATGTGATGTTTACTGTTTGGG
genomic: CTTGTACAAGCTGCAAATCGGGGAGGTTTTGTCGACTGTTCCCACGATTGgtaggctatc ... ctactactagGTTTCAATGTCGAGAAAGTTCAATACAAGAATGTGATGTTTACTGTTTGGG
EST: gi|211069202|gb|FL305332.1|FL305332
EST:     CTTGTACAAGCTGCAAATCGGGGAGGTTTTGTCGACTGTTCCCACGATTG                         GTTTCAATGTCGAGAAAGTTCAATACAAGAATGTGATGTTTACTGTTTGGG
genomic: CTTGTACAAGCTGCAAATCGGGGAGGTTTTGTCGACTGTTCCCACGATTGgtaggctatc ... ctactactagGTTTCAATGTCGAGAAAGTTCAATACAAGAATGTGATGTTTACTGTTTGGG
EST: gi|211066468|gb|FL305328.1|FL305328
EST:     CTTGTACAAGCTGCAAATCGGGGAGGTTTTGTCGACTGTTCCCACGATTG                         GTTTCAATGTCGAGAAAGTTCAATACAAGAATGTGATGTTTACTGTTTGGG
genomic: CTTGTACAAGCTGCAAATCGGGGAGGTTTTGTCGACTGTTCCCACGATTGgtaggctatc ... ctactactagGTTTCAATGTCGAGAAAGTTCAATACAAGAATGTGATGTTTACTGTTTGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcactttgcctgcaaattcatgtgtgatgatatctctctgatgctactactagGTTTCAATGTCGAGAAAGTTCAATACAAGAATGTGATGTTTACTGTTTGGGATGTTGGTGGCCAAGAAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAA
                                     ctctgat  putative branch site (score: 4)
               aaattcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccaatatgttcttaaaggttttatgaggattactaaaaataaatgtttcactttgcctgcaaattcatgtgtgatgatatctctctgatgctactactagGTTTCAATGTCGAGAAAGTTCAATACAAGAATGTGATGTTTACTGTTTGGGATGTTGGTGGCCAAGAAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - aaaaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - gcctgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - attcatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tctgatg