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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcgttcttccttgctgacatttcttttgccatgatatttgtggatatttatgcaaaatgtcgattggttcacatattcctaactggccctgtttctgcagCATACAATATGTGCTATCTTCTATCGACACATGTATCCAGTATGGGGAAGATGCAGACGTGAAGGTCAGGGACTTCGAAGAAGACGAAGACTAACCACTG

Basic information

species Zea mays
transcript GRMZM2G131324_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G131324_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os03g50620.1 (Oryza sativa), 3'ss of exon 8
-tcgttcttccttgctgacatttcttttgccatgatatttgtggatatttatgcaaaatgtcgattggttcacatattcctaactggccctg-----tttctgcagCATACAATATGTGCTATCTTCTATCGACACATGTATCCAGTATGGGGAAGATGCAGACGTGAAGGTCAGGGACTTCGAAGAAGACGAAGACTAACCACTG
  | |     |  | |   |  | || || | ||| ||   ||    ||| | |    |||   |   ||  ||| |  ||||||| ||||      ||| | |||||| || |||||||| ||    |||||||  || ||||||||||||||||| ||||| |||||||| |||||||||||    || || |||||| || | 
aacttaacatcaagtttgtaaatgttctgtcttgagatacctg----tttgtaccgtgtgtttctc--ttttcatctctctaactgtcccttatttctttttccagCATTCAGTATGTGCTGTCGCACATCGACAACTGCATCCAGTATGGGGAAGACGCAGATGTGAAGGTTAGGGACTTCGATCCCGAGGAGGACTAATCATTT

upper sequence: GRMZM2G131324_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os03g21914.1 (Oryza sativa), 3'ss of exon 8
tcgttcttccttgctgacatttcttttgccatgatatttgtggatatttatgcaaaatgtcgattggttcacatattcctaactggccctg-----tttctgcagCATACAATATGTGCTATCTTCTATCGACACATGTATCCAGTATGGGGAAGATGCAGACGTGAAGGTCAGGGACTTCGAAGAAGACGAAGACTAACCACTG---
      |       | ||||    ||||  |   ||    |   | ||| | |    ||    |   ||  ||| |  |||||||||||||     ||| | |||||| || |||||||| ||    |||||||  || ||||||||||||| ||| ||||| |||||||| |||||||||||      ||| |||||| || |    
---aaataaaaacttaacatcaagtttgtaaatgtacagatacctgtttgtaccgtgtgctcctc--ttttcatctctctaactggccctgatttctttttccagCATTCAGTATGTGCTGTCGCACATCGACAACTGCATCCAGTATGGGGTAGACGCAGATGTGAAGGTTAGGGACTTCGATCC---CGAGGACTAATCATTTGAT
















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|22818869|gb|BU498959.1|BU498959
EST:     GATTACAGCATGGTTAATTTCATTCCACTTGATTTGAGAAAGGAAAGCAG                         CATACAATATGTGCTATCTTCTATCGACACATGTATCCAGTATGGGGAAGA
genomic: GATTACAGCATGGTTAATTTCATTCCACTTGATTTGAGAAAGGAAAGCAGgtgatttttt ... gtttctgcagCATACAATATGTGCTATCTTCTATCGACACATGTATCCAGTATGGGGAAGA
EST: gi|76293904|gb|DV033472.1|DV033472
EST:     GATTACAGCATGGTTAATTTCATTCCACTTGATTTGAGAAAGGAAAGCAG                         CATACAATATGTGCTATCTTCTATCGACACATGTATCCAGTATGGGGAAGA
genomic: GATTACAGCATGGTTAATTTCATTCCACTTGATTTGAGAAAGGAAAGCAGgtgatttttt ... gtttctgcagCATACAATATGTGCTATCTTCTATCGACACATGTATCCAGTATGGGGAAGA
EST: gi|76281817|gb|DV021385.1|DV021385
EST:     GATTACAGCATGGTTAATTTCATTCCACTTGATTTGAGAAAGGAAAGCAG                         CATACAATATGTGCTATCTTCTATCGACACATGTATCCAGTATGGGGAAGA
genomic: GATTACAGCATGGTTAATTTCATTCCACTTGATTTGAGAAAGGAAAGCAGgtgatttttt ... gtttctgcagCATACAATATGTGCTATCTTCTATCGACACATGTATCCAGTATGGGGAAGA
EST: gi|67031739|gb|CO460488.1|CO460488
EST:     ATTACAGCATGGTTAATTTCATTCCACTTTGATT-GAGAAAGGAA-GCAG                         CATACAATATGTGCTATCTTCTATCG
genomic: ATTACAGCATGGTTAATTTCATTCCACTT-GATTTGAGAAAGGAAAGCAGgtgatttttt ... gtttctgcagCATACAATATGTGCTATCTTCTATCG
EST: gi|71435200|gb|DR816250.1|DR816250
EST:     GATTACAGCATGGTTAATTTCATTCCACTTGATTTGAGAAAGGAAAGCAG                         CATACAATATGTGCTATCTTCTATCGACACATGTATCCAGTATGGGGAAGA
genomic: GATTACAGCATGGTTAATTTCATTCCACTTGATTTGAGAAAGGAAAGCAGgtgatttttt ... gtttctgcagCATACAATATGTGCTATCTTCTATCGACACATGTATCCAGTATGGGGAAGA
EST: gi|76016034|gb|DT943204.1|DT943204
EST:     GATTACAGCATGGTTAATTTCATTCCACTTGATTTGAGAAAGGAAAGCAG                         CATACAATATGTGCTATCTTCTATCGACACATGTATCCAGTATGGGGAAGA
genomic: GATTACAGCATGGTTAATTTCATTCCACTTGATTTGAGAAAGGAAAGCAGgtgatttttt ... gtttctgcagCATACAATATGTGCTATCTTCTATCGACACATGTATCCAGTATGGGGAAGA
EST: gi|71758032|gb|DR955969.1|DR955969
EST:     GATTACAGCATGGTTAATTTCATTCCACTTGATTTGAGAAAGGAAAGCAG                         CATACAATATGTGCTATCTTCTATCGACACATGTATCCAGTATGGGGAAGA
genomic: GATTACAGCATGGTTAATTTCATTCCACTTGATTTGAGAAAGGAAAGCAGgtgatttttt ... gtttctgcagCATACAATATGTGCTATCTTCTATCGACACATGTATCCAGTATGGGGAAGA
EST: gi|76010883|gb|DT938053.1|DT938053
EST:     GATTACAGCATGGTTAATTTCATTCCACTTGATTTGAGAAAGGAAAGCAG                         CATACAATATGTGCTATTTTCTATCGACACATGTATCCAGTATGGGGAAGA
genomic: GATTACAGCATGGTTAATTTCATTCCACTTGATTTGAGAAAGGAAAGCAGgtgatttttt ... gtttctgcagCATACAATATGTGCTATCTTCTATCGACACATGTATCCAGTATGGGGAAGA
EST: gi|148995051|gb|EE034364.2|EE034364
EST:     GATTACAGCATGGTTAATTTCATTCCCCTTGATTTGAGAAAGGAAAGCAG                         CATACAATATGTGCTATTTTTTATCGACACATGTATCCAGTATGGGGAAGA
genomic: GATTACAGCATGGTTAATTTCATTCCACTTGATTTGAGAAAGGAAAGCAGgtgatttttt ... gtttctgcagCATACAATATGTGCTATCTTCTATCGACACATGTATCCAGTATGGGGAAGA
EST: gi|24764738|gb|CA399901.1|CA399901
EST:     GATTACAGCATGGTTAATTTCATTCCACTTGATTTGAGAAAGGAAAGCAG                         CATACAATATGTGCTATCTTCTATCGACACATGTATCCAGTATGGGGAAGA
genomic: GATTACAGCATGGTTAATTTCATTCCACTTGATTTGAGAAAGGAAAGCAGgtgatttttt ... gtttctgcagCATACAATATGTGCTATCTTCTATCGACACATGTATCCAGTATGGGGAAGA
EST: gi|78113480|gb|DV531871.1|DV531871
EST:     GATTACAGCATGGTTAATTTCATTCCACTTGATTTGAGAAAGGAAAGCAG                         CATACAATATGTGCTATCTTCTATCGACACATGTATCCAGTATGGGGAAGA
genomic: GATTACAGCATGGTTAATTTCATTCCACTTGATTTGAGAAAGGAAAGCAGgtgatttttt ... gtttctgcagCATACAATATGTGCTATCTTCTATCGACACATGTATCCAGTATGGGGAAGA
EST: gi|71758174|gb|DR956111.1|DR956111
EST:     GATTACAGCATGGTTAATTTCATTCCACTTGATTTGAGAAAGGAAAGCAG                         CATACAATATGTGCTATCTTCTATCGACACATGTATCCAGTATGGGGAAGA
genomic: GATTACAGCATGGTTAATTTCATTCCACTTGATTTGAGAAAGGAAAGCAGgtgatttttt ... gtttctgcagCATACAATATGTGCTATCTTCTATCGACACATGTATCCAGTATGGGGAAGA
EST: gi|111197436|gb|EE295571.1|EE295571
EST:     GATTACAGCATGGTTAATTTCATTCCACTTGATTTGAGAAAGGAAAGCAG                         CATACAATATGTGCTATCTTCTATCGACACATGTATCCAGTATGGGGAAGA
genomic: GATTACAGCATGGTTAATTTCATTCCACTTGATTTGAGAAAGGAAAGCAGgtgatttttt ... gtttctgcagCATACAATATGTGCTATCTTCTATCGACACATGTATCCAGTATGGGGAAGA
EST: gi|211012560|gb|FL439511.1|FL439511
EST:     GATTACAGCATGGTTAATTTCATTCCACTTGATTTGAGAAAGGAAAGCAG                         CATACAATATGTGCTATCTTCTATCGACACATGTATCCAGTATGGGGAAGA
genomic: GATTACAGCATGGTTAATTTCATTCCACTTGATTTGAGAAAGGAAAGCAGgtgatttttt ... gtttctgcagCATACAATATGTGCTATCTTCTATCGACACATGTATCCAGTATGGGGAAGA
EST: gi|87156287|gb|DY401076.1|DY401076
EST:     GATTACAGCATGGTTAATTTCATTCCACTTGATTTGAGAAAGGAAAGCAG                         CATACAATATGTGCTATCTTCTATCGACACATGTATCCAGTATGGGGAAGA
genomic: GATTACAGCATGGTTAATTTCATTCCACTTGATTTGAGAAAGGAAAGCAGgtgatttttt ... gtttctgcagCATACAATATGTGCTATCTTCTATCGACACATGTATCCAGTATGGGGAAGA
EST: gi|60343210|gb|DN210183.1|DN210183
EST:     GATTACAGCATGGTTAATTTCATTCCACTTGATTTGAGAAAGGAAAGCAG                         CATACAATATGTGCTATCTTCTATCGACACATGTATCCAGTATGGGGAAGA
genomic: GATTACAGCATGGTTAATTTCATTCCACTTGATTTGAGAAAGGAAAGCAGgtgatttttt ... gtttctgcagCATACAATATGTGCTATCTTCTATCGACACATGTATCCAGTATGGGGAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttatgcaaaatgtcgattggttcacatattcctaactggccctgtttctgcagCATACAATATGTGCTATCTTCTATCGACACATGTATCCAGTATGGGGAAGATGCAGACGTGAAGGTCAGGGACTTCGAAGAAGACGAAGACTAACCACTG
                               tcctaac  putative branch site (score: 1)
                                         ccctgtttct  putative PPT
        aaaatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcgttcttccttgctgacatttcttttgccatgatatttgtggatatttatgcaaaatgtcgattggttcacatattcctaactggccctgtttctgcagCATACAATATGTGCTATCTTCTATCGACACATGTATCCAGTATGGGGAAGATGCAGACGTGAAGGTCAGGGACTTCGAAGAAGACGAAGACTAACCACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA