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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcgcagttaataaatcaggtcggttcactttaaaggtgccacactcagcaatgtggagaaccatacattgttaaatgatctttttttgtctattctcagGTGTGATAGCGATTGTTGTGGCAAATCCAACTGATCTTGTCAAAGTTAGGTTGCAAGCTGATGGAAAAGCTAACACTATCAAGAGGAGTTATTCTGGAGC

Basic information

species Zea mays
transcript GRMZM5G852877_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G852877_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g74640.3 (Oryza sativa), 3'ss of exon 3
----------------------------------------------------------------------------atcgcagttaataaatcaggtcg-gttcactttaaaggtgcca--cactca--------gcaatgtggagaacca--tacattgttaaatga--tctttttttgtctattctcagGTGTGATAGCGATTGTTGTGGCAAATCCAACTGATCTTGTCAAAGTTAGGTTGCAAGCTGATGGAAAAGCTAACACTATCAAGAGGAGTTATTCTGGAGC
                                                                            ||   |   |   || ||| |    | ||  ||  | |||  |   ||| |        ||| | || | ||  |  || | | ||| || |  |    || | | |||||  |||||| ||||| ||||||||||||||||||||||||||||||||||| || ||||||||||||||||| || | |||| ||||||||   |||||||||||
gtgggtacttttccctatccgtttctctttgctgcactttctcaataatttgtcacatattaaattgcttttgctaattaaatgcagccaaccagtttacatccaaatttcatgtgttaaggacttaaggtaggtgcactatgcacaagtaaatatactcttatattaattaccgttctatatattcatagGTGTCATAGCAATTGTTGTGGCAAATCCAACTGATCTTGTCAAAGTGAGATTGCAAGCTGATGGAAAGGCCACCACTGTCAAGAGGCACTATTCTGGAGC

upper sequence: GRMZM5G852877_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA07G17380.1 (Glycine max), 3'ss of exon 2
------------------------------------------------------------------------------------------atcgcagttaataaatcaggtcggttcactttaaaggtgccacactcagcaatgtggagaaccatacattg--ttaaatgatctttttttgtctattctcagGTGTGATAGCGATTGTTGTGGCAAATCCAACTGATCTTGTCAAAGTTAGGTTGCAAGCTGATGGAAAAGCTAACACTATCAAG---AGGAGTTATTCTGGAGC
                                                                                           ||    |   |  | ||       |   | | |||    |    |   || | || | |||  | |||||    |  ||| ||| | || || |    ||||||  || || ||||  ||||||||||||||||||||||| ||||||||  | ||||| || ||||||       ||  |  |   | | | || |||||   
gtaaagcccaattctggacattgtattgtagtgatggttttttctatatgccaatatgtgaatttgtttcctaatgtgcggagtgtgaacttcttgctagctggagcatacgttatttttgtcaagaattcttgat--acattatgcaaaactctgcattgagccacttgaacttgtgttatcaa----cagGTGCTATGGCAATTGCAGTGGCAAATCCAACTGATCTTGTGAAAGTTAGACTTCAAGCAGAAGGAAAATTGCCTCCTGGCGTGCCCAAGCGCTACTCTGG---

upper sequence: GRMZM5G852877_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA08G45130.1 (Glycine max), 3'ss of exon 3
atcgcagttaataaatcaggtcggttcactt-taaaggtgccacactcagca--atgtggagaaccatacattgttaaatgatctttttttgtctattctcagGTGTGATAGCGATTGTTGTGGCAAATCCAACTGATCTTGTCAAAGTTAGGTTGCAAGCTGATGGAAAA--GCTAACACTATCAAG-AGGAGTTATTCTGGAGC
      || |  || | ||       ||    || |  ||  |   |  | |  ||||        |    |  || | | |  |||||  |  | |  | |||||   | || ||     | || |||||||||||||| |||||||||||| | |||||||| ||  ||  || |||      |   | | ||||||||||   
-caaaggtgaggaagttagcattccccatggatatatatgt-atgttttgtattatgttatttgttaatagtcattgactcacttttttgagcttgtgat-agGTGCTTTGGCAATCACAATTGCTAATCCAACTGATCTAGTCAAAGTTAGGCTTCAAGCTGAAGGTCAATTGCCAACTGGGGTACCTAAGCGTTATTCTGG---

upper sequence: GRMZM5G852877_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA03G14780.1 (Glycine max), 3'ss of exon 3
---------------------------------------------------------------atcgcagttaataaatcaggtcggttcactttaaag------gtgccacactcagc--aatgtggagaaccatacattgttaaatgatctttt---tttgtctattct-cagGTGTGATAGCGATTGTTGTGGCAAATCCAACTGATCTTGTCAAAGTTAGGTTGCAAGCTGATGGAAAAG---CTAACACTATCAAGAGGAGTTATTCTGGAGC
                                                                |   | |  ||  || |  |   ||  |||    |      |||  |  |  | |  |||    |   | |||  |   | |   |    ||   |||||||  ||  ||||||   | || ||||  |||||||||||||| |||||||||||||||||  | |||||||| ||||||    ||     | |    ||| | || |||||   
gtaaatctcaatgctggaaattgtgggaataatttgtatatgtgtgctattatatgagtttcttttctaatctatggattatttactttttcttaggggcatcttgtgttattcctatctaaatactcatcgcaataactcaatcacgaactcgttcaatttgtcttgtcaacagGTGCTTTTGCAATTGCAGTGGCAAATCCAACCGATCTTGTCAAAGTTAGACTTCAAGCTGAAGGAAAATTACCTCCTGGTGTTCCCAGGCGCTACTCTGG---

upper sequence: GRMZM5G852877_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA01G27120.1 (Glycine max), 3'ss of exon 2
---------------------------------------------------------------atcgcagttaataaatcaggtcggttcactttaaagg------tgccacactcagc--aatgtggagaaccatacattgttaaatgatctttt---tttgtctattct-cagGTGTGATAGCGATTGTTGTGGCAAATCCAACTGATCTTGTCAAAGTTAGGTTGCAAGCTGATGGAAAAG---CTAACACTATCAAGAGGAGTTATTCTGGAGC
                                                                |     |  ||  || |  |   ||  |||   |||      |   |  | || |  |||    |   | |||  |   | |   |    |    |||||||  ||  ||||||   | || ||||  ||||||||||||||||||||||||||||||||  | ||||| || ||||||    ||     | |    ||| | || |||||   
gtaaatctcaatgctggaaactgtgggaatattttgtatatatattctattctatgagtttcttttctcatctatggattatttactttttcttaggaggatcttgtattattcccatctaaatactcattgcaataactcaatcataaactcctcgaatttgtcttgtcaacagGTGCTTTTGCAATTGCAGTGGCAAATCCAACTGATCTTGTCAAAGTTAGACTTCAAGCAGAAGGAAAATTACCTCCTGGTGTTCCCAGGCGGTACTCTGG---

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|89762468|gb|DY690033.1|DY690033
EST:     TGTGGGTGATGTCAGTTTACTAAGCAAGATCCTTGCTGCACTTACCACAG                         GTGTGATAGCGATTGTTGTGGCAAATCCAACTGATCTTGTCAAAGTTAGGT
genomic: TGTGGGTGATGTCAGTTTACTAAGCAAGATCCTTGCTGCACTTACCACAGgttggtacat ... ctattctcagGTGTGATAGCGATTGTTGTGGCAAATCCAACTGATCTTGTCAAAGTTAGGT
EST: gi|78084604|gb|DV512997.1|DV512997
EST:     TGTGGGTGATGTCAGTTTACTAAGCAAGATCCTTGCTGCACTTACCACAG                         GTGTGATAGCGATTGTTGTGGCAAATCCAACTGATCTTGTCAAAGTTAGGT
genomic: TGTGGGTGATGTCAGTTTACTAAGCAAGATCCTTGCTGCACTTACCACAGgttggtacat ... ctattctcagGTGTGATAGCGATTGTTGTGGCAAATCCAACTGATCTTGTCAAAGTTAGGT
EST: gi|84980856|gb|DW531205.1|DW531205
EST:     TGTGGGTGATGTCAGTTTACTAAGCAAGATCCTTGCTGCGCTTACCACAG                         GTGTGATAGCGATTGTTGTGGCAAATCCAACTGATCTTGTCAAAGTTAGGT
genomic: TGTGGGTGATGTCAGTTTACTAAGCAAGATCCTTGCTGCACTTACCACAGgttggtacat ... ctattctcagGTGTGATAGCGATTGTTGTGGCAAATCCAACTGATCTTGTCAAAGTTAGGT
EST: gi|32788041|gb|CD940277.1|CD940277
EST:     GATCCTTGCTGCACTTACCACAG                         GTGTGATAGCGATTGTTGTGGCAAATCCAACTGATCTTGTCAAAGTTAGGT
genomic: GATCCTTGCTGCACTTACCACAGgttggtacat ... ctattctcagGTGTGATAGCGATTGTTGTGGCAAATCCAACTGATCTTGTCAAAGTTAGGT
EST: gi|93017382|gb|EB642902.1|EB642902
EST:     TGTGGGTGATGTCAGTTTACTAAGCAAGATCCTTGCTGCACTTACCACAG                         GTGTGATAGCGATTGTTGTGGCAAATCCAACTGATCTTGTCAAAGTTAGGT
genomic: TGTGGGTGATGTCAGTTTACTAAGCAAGATCCTTGCTGCACTTACCACAGgttggtacat ... ctattctcagGTGTGATAGCGATTGTTGTGGCAAATCCAACTGATCTTGTCAAAGTTAGGT
EST: gi|60354253|gb|DN221226.1|DN221226
EST:     TGTGGGTGATGTCAGTTTACTAAGCAAGATCCTTGCTGCACTTACCACAG                         GTGTGATAGCGATTGTTGTGGCAAATCCAACTGATCTTGTCAAAGTTAGGT
genomic: TGTGGGTGATGTCAGTTTACTAAGCAAGATCCTTGCTGCACTTACCACAGgttggtacat ... ctattctcagGTGTGATAGCGATTGTTGTGGCAAATCCAACTGATCTTGTCAAAGTTAGGT
EST: gi|60401298|gb|DN234105.1|DN234105
EST:     TGTGGGTGATGTCAGTTTACTAAGCAAGATCCTTGCTGCACTTACCACAG                         GTGTGATAGCGATTGTTGTGGCAAATCCAACTGATCTTGTCAAAGTTAGGT
genomic: TGTGGGTGATGTCAGTTTACTAAGCAAGATCCTTGCTGCACTTACCACAGgttggtacat ... ctattctcagGTGTGATAGCGATTGTTGTGGCAAATCCAACTGATCTTGTCAAAGTTAGGT
EST: gi|32803924|gb|CD956160.1|CD956160
EST:     GATCCTTGCTGCACTTACCACAG                         GTGTGATAGCGATTGTTGTGGCAAATCCAACTGATCTTGTCAAAGTTGGGT
genomic: GATCCTTGCTGCACTTACCACAGgttggtacat ... ctattctcagGTGTGATAGCGATTGTTGTGGCAAATCCAACTGATCTTGTCAAAGTTAGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcagcaatgtggagaaccatacattgttaaatgatctttttttgtctattctcagGTGTGATAGCGATTGTTGTGGCAAATCCAACTGATCTTGTCAAAGTTAGGTTGCAAGCTGATGGAAAAGCTAACACTATCAAGAGGAGTTATTCTGGAGC
                                  tctttttttgtctatt  CT-rich tract
                      attgttaaatgatctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atcgcagttaataaatcaggtcggttcactttaaaggtgccacactcagcaatgtggagaaccatacattgttaaatgatctttttttgtctattctcagGTGTGATAGCGATTGTTGTGGCAAATCCAACTGATCTTGTCAAAGTTAGGTTGCAAGCTGATGGAAAAGCTAACACTATCAAGAGGAGTTATTCTGGAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG