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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatgacacatcccattgtttatcttctttccttatttgctcattcacatgaacctgataaaaccatatacattttttcttgaacaaaaacaatatactattggaacattaaaaaccttataatgtagctatctctttaacctatccagaacttatactcatactgacttgtccatttctttttcagCTTGAAAGGTTAAGTGACATACAAAGTCAACCTGAGTCACAGCTGAAGTTCATTATAGAGGCATGGTTACAG

Basic information

species Zea mays
transcript GRMZM2G006428_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G006428_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os04g41470.2 (Oryza sativa), 3'ss of exon 11
gtatatgacacatcccattgtttatcttctttccttatttgctcattcacatgaacctgataaaaccatatacattttttcttgaacaaaaacaatatactattggaacattaaaaaccttataatgtagctatctctttaacctatccagaacttatactcatactgac-ttgtccatttctttttcagCTTGAAAGGTTAAGTGACATACAAAGTCAACCTGAGTCACAGCTGAAGTTCATTATAGAGGCATGGTTACAG----------------------------
|||||| |   ||   ||  ||||| ||  |  ||  |||   |  |    |  | |  ||   |||  | |           | ||  || | || |    ||     |||||  |  |||||||  |||||   ||  | ||| |||||||| ||| || | |  ||| ||  | | |  ||||||||||||||| ||||||||| |||||||| ||||| ||||||||||| |||||||| |||||||| |||||||||                            
gtatataa---atatgatactttatatttatctctcctttatcctctt---tatatccaatttcacccaaaa-----------gtactgaagccatgttaggttcatgtattaatcat-ttataatacagcta---ctccagcctgtccagaacatatgctaacagcgacattcacaaatcatttttcagCTTGAAAAGTTAAGTGATATACAAAGCCAACCAGAGTCACAGCTCAAGTTCATCATAGAGGCTTGGTTACAGGTTAGTTTTCATTGCCAAGTTTAGTTCT

upper sequence: GRMZM2G006428_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os04g41470.1 (Oryza sativa), 3'ss of exon 11
gtatatgacacatcccattgtttatcttctttccttatttgctcattcacatgaacctgataaaaccatatacattttttcttgaacaaaaacaatatactattggaacattaaaaaccttataatgtagctatctctttaacctatccagaacttatactcatactgac-ttgtccatttctttttcagCTTGAAAGGTTAAGTGACATACAAAGTCAACCTGAGTCACAGCTGAAGTTCATTATAGAGGCATGGTTACAG
|||||| |   ||   ||  ||||| ||  |  ||  |||   |  |    |  | |  ||   |||  | |           | ||  || | || |    ||     |||||  |  |||||||  |||||   ||  | ||| |||||||| ||| || | |  ||| ||  | | |  ||||||||||||||| ||||||||| |||||||| ||||| ||||||||||| |||||||| |||||||| |||||||||
gtatataa---atatgatactttatatttatctctcctttatcctctt---tatatccaatttcacccaaaa-----------gtactgaagccatgttaggttcatgtattaatcat-ttataatacagcta---ctccagcctgtccagaacatatgctaacagcgacattcacaaatcatttttcagCTTGAAAAGTTAAGTGATATACAAAGCCAACCAGAGTCACAGCTCAAGTTCATCATAGAGGCTTGGTTACAG

upper sequence: GRMZM2G006428_T01 (Zea mays), 3'ss of exon 11
lower sequence: AT1G65430.1 (Arabidopsis thaliana), 3'ss of exon 11
gtatatgacacatcccattgtttatcttctttccttatttgctcattcacatgaacctgataaaaccatatacattttttcttgaacaaaaacaatatactattggaacattaaaaaccttataatgtagctatctctttaacctatc-cagaacttatactcatactgacttgt---ccatttctttttcagCTTGAAAGGTTAAGTGACATACAAAGTCAACCTGAGTCACAGCTGAAGTTCATTATAGAGGCATGGTTACAG
                                                                                             | | | |||||    |||   | |||| |   |      || | | |  | |||  |||   |     |||      ||| |   | ||    ||  ||| |||| | | | |||||||||||  |||| ||||| ||||| ||||||||||||||||| ||||||||||||
-------------------------------------------------------------------------------------------tgatttttctattttggcat--gagacctcaactttcgatgatttttcttgcttattacagtgttgggtttcactaaagcttttgttctatggacttcgcagATTGAGAAGCTCAGTGACATACAGTGTCAGCCTGAATCACAACTGAAGTTCATTATAGAAGCATGGTTACAG

upper sequence: GRMZM2G006428_T01 (Zea mays), 3'ss of exon 11
lower sequence: PP1S114_2V6.1 (Physcomitrella patens), 3'ss of exon 10
------------gtatatgacacatcccattgtttatctt---ctttccttatttgctcattcacatgaacctgat----aaaaccatatacattttttcttgaacaaaaacaatatactattggaacattaaaaaccttataatgtagctatctctttaacctatccagaacttatactcatactgact-tgtccatttctttttcagCTTGAAAGGTTAAGTGACATACAAAGTCAACCTGAGTCACAGCTGAAGTTCATTATAGAGGCATGGTTACAG
            | || || |||||       | |   ||    |||||| | ||   |||     || ||||  |    |  | | ||    | | |   |  | | |    || | |  |||     |    |   ||  ||| |   |   | || |  |||    |||        |  ||   |           | | | ||| |||||| ||||||||||| |||| ||||||||| ||| |||||||||||                      
gtaagtggtgcagaatctg-cacattttcccatctgaattaggttttcctcagttcgccatgggattgcacctattgtttaggatcttaactctctctcaatttaaagacgtgatctgcgtttgtgttttcttgacttttgaaatctcctttgtttttcagTCTAGGGCGAAGGCGCTTGCGGACCTTCAACAAATGCAGCCTGTGCAGATTGAAAAGTTAAGTGACAAACAATGTCAACCTGTGTCGCAGCTGAAGTTTG--------------------

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|211198902|gb|FL376281.1|FL376281
EST:     TCGAGGCAAAAGGCACTGGGGGACCTTCAAAGCCTACAGAACGACAAG                         CTTGAAAGGTTAAGTGACATACAAAGTCAACCCGAGTCACAGCTGAAGTTC
genomic: TCGAGGCAAAAGGCACTGGGGGACCTTCAAAGCCTACAGAACGACAAGgtatatgaca ... tctttttcagCTTGAAAGGTTAAGTGACATACAAAGTCAACCTGAGTCACAGCTGAAGTTC
EST: gi|211292139|gb|FL375498.1|FL375498
EST:     TCGAGGCAAAAGGCACTGGNGGGACCTTCAAAGCCTACAGAACGACAAG                         CTTGAAAGGTTAAGTGACATACAAAGTCAACCTGAGTCACAGCTGAAGTTC
genomic: TCGAGGCAAAAGGCACTGG-GGGACCTTCAAAGCCTACAGAACGACAAGgtatatgaca ... tctttttcagCTTGAAAGGTTAAGTGACATACAAAGTCAACCTGAGTCACAGCTGAAGTTC
EST: gi|22521335|gb|BU080146.1|BU080146
EST:     TCGAGGCAAAAGGCACTGGGGGACCTTCAAAGCCTACAGAATGACAAG                         CTTGAAAGGTTAAGTGACATACAAAGTCAACCTGAGTCACAGCTGAAGTTC
genomic: TCGAGGCAAAAGGCACTGGGGGACCTTCAAAGCCTACAGAACGACAAGgtatatgaca ... tctttttcagCTTGAAAGGTTAAGTGACATACAAAGTCAACCTGAGTCACAGCTGAAGTTC
EST: gi|78080365|gb|DV508777.1|DV508777
EST:     TCGAGGCAAAAGGCACTGGGGGACCTTCAAAGCCTACAGAACGACAAG                         CTTGAAAGGTTAAGTGACATACAAAGTCAACCTGAGTCACAGCTGAAGTTC
genomic: TCGAGGCAAAAGGCACTGGGGGACCTTCAAAGCCTACAGAACGACAAGgtatatgaca ... tctttttcagCTTGAAAGGTTAAGTGACATACAAAGTCAACCTGAGTCACAGCTGAAGTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctttaacctatccagaacttatactcatactgacttgtccatttctttttcagCTTGAAAGGTTAAGTGACATACAAAGTCAACCTGAGTCACAGCTGAAGTTCATTATAGAGGCATGGTTACAG
                             tactgac  putative branch site (score: 1)
                                   cttgtccatttctttt  CT-rich tract
                                          atttcttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatatgacacatcccattgtttatcttctttccttatttgctcattcacatgaacctgataaaaccatatacattttttcttgaacaaaaacaatatactattggaacattaaaaaccttataatgtagctatctctttaacctatccagaacttatactcatactgacttgtccatttctttttcagCTTGAAAGGTTAAGTGACATACAAAGTCAACCTGAGTCACAGCTGAAGTTCATTATAGAGGCATGGTTACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG