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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgtgaatgtatcgccgtttagtatgtgctcaggttgagcttgtatgtgtttttgcacctttttgtgctaactgcaatttgctattatttatgcacccagGATCTGTTAGATGCTCTGAATCAACTAGAGGTGGGACTCAAAGAAAACCTCAAGAAGTTGAGTTCCTTTGATAAGTACAAACAGCAAGTTCTTCTTGGTC

Basic information

species Zea mays
transcript GRMZM2G019999_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G019999_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os07g36470.1 (Oryza sativa), 3'ss of exon 5
atgtgaatgtatcgccgtttagtatgtgctcaggttga-gcttgtatgtgtttttgcacctttttgtgctaactgcaat-ttgctattatttatgcacccagGATCTGTTAGATGCTCTGAATCAACTAGAGGTGGGACTCAAAGAAAACCTCAAGAAGTTGAGTTCCTTTGATAAGTACAAACAGCAAGTTCTTCTTGGTC
|| |  |  |    | ||  | |||||       || |   |||    ||| |||   |  |||||  || ||  |  | ||  ||  |  |||||||||||||| | |||||||| |||||||| |||||  | ||||||||||| ||||| |||||||||||||| ||||| |||||||| || |||||||||||||| |
atctacacttga-actgtcaaatatgtttatttattcacatttgagcttgtctttat-ctcttttgaactgacaaccttctttttacaacctatgcacccagGATTTATTAGATGCGCTGAATCAGCTAGAAATAGGACTCAAAGACAACCTTAAGAAGTTGAGTTCATTTGAGAAGTACAAGCAACAAGTTCTTCTTGGCC
















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|149005181|gb|EE039721.2|EE039721
EST:     GATTGCCACAAATGGTACAAAACTTGAAAGCTCAAGCATGGACTGATGAG                         GATCTGTTAGATGCTCTGAATCAACTAGAGGTGGGACTCAAAGAAAACCTC
genomic: GATTGCCACAAATGGTACAAAACTTGAAAGCTCAAGCATGGACTGATGAGgtgaggagct ... atgcacccagGATCTGTTAGATGCTCTGAATCAACTAGAGGTGGGACTCAAAGAAAACCTC
EST: gi|78080157|gb|DV508569.1|DV508569
EST:     GATTGCCACAAATGGTACAAAACTTGAAAGCTCAAGCATGGACTGATGAG                         GATCTGTTAGATGCTCTGAATCAACTAGAGGTGGGACTCAAAGAAAACCTC
genomic: GATTGCCACAAATGGTACAAAACTTGAAAGCTCAAGCATGGACTGATGAGgtgaggagct ... atgcacccagGATCTGTTAGATGCTCTGAATCAACTAGAGGTGGGACTCAAAGAAAACCTC
EST: gi|5847348|gb|AW000427.1|AW000427
EST:     GATTGCCACAAATGGTACAAAACTTGAAAGCTCAAGCATGGACTGATGAG                         GATCTGTTAGATGCTCTGAATCAACTAGAGGTGGGACTCAAAGAAAACCTT
genomic: GATTGCCACAAATGGTACAAAACTTGAAAGCTCAAGCATGGACTGATGAGgtgaggagct ... atgcacccagGATCTGTTAGATGCTCTGAATCAACTAGAGGTGGGACTCAAAGAAAACCTC
EST: gi|60401227|gb|DN234034.1|DN234034
EST:     GATTGCCACAAATGGTACAAAACTTGAAAGCTCAAGCATGGACTGATGAG                         GATCTGTTAGATGCTCTGAATCAACTAGAGGTGGGACTCAAAGAAAACCTC
genomic: GATTGCCACAAATGGTACAAAACTTGAAAGCTCAAGCATGGACTGATGAGgtgaggagct ... atgcacccagGATCTGTTAGATGCTCTGAATCAACTAGAGGTGGGACTCAAAGAAAACCTC
EST: gi|32851781|gb|CD991462.1|CD991462
EST:     GGACTGATGAG                         GATCTGTGAGATGCTCTGAATCAACTAGAGGTGGGACTCAAAGAAAACCTC
genomic: GGACTGATGAGgtgaggagct ... atgcacccagGATCTGTTAGATGCTCTGAATCAACTAGAGGTGGGACTCAAAGAAAACCTC
EST: gi|149089827|gb|EE179105.2|EE179105
EST:     ATGGTACAAAACTTGAAAGCTCAAGCATGGACTGATGAG                         GATCTGTTAGATGCTCTGAATCAACTAGAGGTGGGACTCAAAGAAAACCTC
genomic: ATGGTACAAAACTTGAAAGCTCAAGCATGGACTGATGAGgtgaggagct ... atgcacccagGATCTGTTAGATGCTCTGAATCAACTAGAGGTGGGACTCAAAGAAAACCTC
EST: gi|6031414|gb|AW076316.1|AW076316
EST:     GATTGCCACAAATGGTACAAAACTTGAAAGCTCAAGCATGGACTGATGAG                         GATCTGTTAGATGCTCTGAATCAACTAGAGGTGGGACTCAAAGAAAACCTT
genomic: GATTGCCACAAATGGTACAAAACTTGAAAGCTCAAGCATGGACTGATGAGgtgaggagct ... atgcacccagGATCTGTTAGATGCTCTGAATCAACTAGAGGTGGGACTCAAAGAAAACCTC
EST: gi|148949226|gb|EC894668.2|EC894668
EST:     CTTGAAAGCTCAAGCATGGACTGATGAG                         GATTTGTTAGATGCTCTGAATCAACTAGAGGTGGGACTCAAAGAAAACCTC
genomic: CTTGAAAGCTCAAGCATGGACTGATGAGgtgaggagct ... atgcacccagGATCTGTTAGATGCTCTGAATCAACTAGAGGTGGGACTCAAAGAAAACCTC
EST: gi|5915146|gb|AW052787.1|AW052787
EST:     GATTGCCACAAATGGTACAAAACTTGAAAGCTCAAGCATGGACTGATGAG                         GATCTGTTAGATGCTCTGAATCAACTAGAGGTGGGACTCAAAGAAAACCTT
genomic: GATTGCCACAAATGGTACAAAACTTGAAAGCTCAAGCATGGACTGATGAGgtgaggagct ... atgcacccagGATCTGTTAGATGCTCTGAATCAACTAGAGGTGGGACTCAAAGAAAACCTC
EST: gi|5846782|gb|AI999865.1|AI999865
EST:     AAGCTCAAGCATGGACTGATGAG                         GATCTGTTAGATGCTCTGAATCAACTAGAGGTGGGACTCAAAGAAAACCTT
genomic: AAGCTCAAGCATGGACTGATGAGgtgaggagct ... atgcacccagGATCTGTTAGATGCTCTGAATCAACTAGAGGTGGGACTCAAAGAAAACCTC
EST: gi|76909294|gb|DV163314.1|DV163314
EST:     GATTGCCACAAATGGTACAAAACTTGAAAGCTCAAGCATGGACTGATGAG                         GATCTGTTAGATGCTCTGAATCAACTAGAGGTGGGACTCAAAGAAAACCTC
genomic: GATTGCCACAAATGGTACAAAACTTGAAAGCTCAAGCATGGACTGATGAGgtgaggagct ... atgcacccagGATCTGTTAGATGCTCTGAATCAACTAGAGGTGGGACTCAAAGAAAACCTC
EST: gi|5901299|gb|AW042399.1|AW042399
EST:     AACTTGAAAGCTCAAGCATGGACTGATGAG                         GATCTGTTAGATGCTCTGAATCAACTAGAGGTGGGACTCAAAGAAAACCTT
genomic: AACTTGAAAGCTCAAGCATGGACTGATGAGgtgaggagct ... atgcacccagGATCTGTTAGATGCTCTGAATCAACTAGAGGTGGGACTCAAAGAAAACCTC
EST: gi|5325216|gb|AI783407.1|AI783407
EST:     GATTGCCACAAATGGTACAAAACTTGAAAGCTCAAGCATGGACTGATGAG                         GATCTGTTAGATGCTCTGAATCAACTAGAGGTGGGACTCAAAGAAAACCTT
genomic: GATTGCCACAAATGGTACAAAACTTGAAAGCTCAAGCATGGACTGATGAGgtgaggagct ... atgcacccagGATCTGTTAGATGCTCTGAATCAACTAGAGGTGGGACTCAAAGAAAACCTC
EST: gi|5296243|gb|AI782923.1|AI782923
EST:     CTCAAGCATGGACTGATGAG                         GATCTGTTAGATGCTCTGAATCAACTAGAGGTGGGACTCAAAGAAAACCTT
genomic: CTCAAGCATGGACTGATGAGgtgaggagct ... atgcacccagGATCTGTTAGATGCTCTGAATCAACTAGAGGTGGGACTCAAAGAAAACCTC
EST: gi|149089817|gb|EE179093.2|EE179093
EST:     GATTGCCACAAATGGTACAAAACTTGAAAGCTCAAGCATGGACTGATGAG                         GATCTGTTAGATGCTCTGAATCAACTAGAGGTGGGACTCAAAGAAAACCTC
genomic: GATTGCCACAAATGGTACAAAACTTGAAAGCTCAAGCATGGACTGATGAGgtgaggagct ... atgcacccagGATCTGTTAGATGCTCTGAATCAACTAGAGGTGGGACTCAAAGAAAACCTC
EST: gi|6194895|gb|AW146999.1|AW146999
EST:     GATTGCCACAAATGGTACAAAACTTGAAAGCTCAAGCATGGACTGATGAG                         GATCTGGTAGATGCTCTGAATCAACTAGAGGTGGGACTCAAAGAAAACCTT
genomic: GATTGCCACAAATGGTACAAAACTTGAAAGCTCAAGCATGGACTGATGAGgtgaggagct ... atgcacccagGATCTGTTAGATGCTCTGAATCAACTAGAGGTGGGACTCAAAGAAAACCTC
EST: gi|60350326|gb|DN217299.1|DN217299
EST:     GATTGCCACAAATGGTACAAAACTTGAAAGCTCAAGCATGGACTGATGAG                         GATCTGTTAGATGCTCTGAATCAACTAGAGGTGGGACTCAAAGAAAACCTC
genomic: GATTGCCACAAATGGTACAAAACTTGAAAGCTCAAGCATGGACTGATGAGgtgaggagct ... atgcacccagGATCTGTTAGATGCTCTGAATCAACTAGAGGTGGGACTCAAAGAAAACCTC
EST: gi|89247015|gb|DY618801.1|DY618801
EST:     GATTGCCACAAATGGTACAAAACTTGAAAGCTCAAGCATGGACTGATGAG                         GATCTGTTAGATGCTCTGAATCAACTAGAGGTGGGACTCAAAGAAAACCTC
genomic: GATTGCCACAAATGGTACAAAACTTGAAAGCTCAAGCATGGACTGATGAGgtgaggagct ... atgcacccagGATCTGTTAGATGCTCTGAATCAACTAGAGGTGGGACTCAAAGAAAACCTC
EST: gi|6020588|gb|AW065621.1|AW065621
EST:     GATTGCCACAAATGGTACAAAACTTGAAAGCTCAAGCATGGACTGATGAG                         GATCTGTTAGATGCTCTGAATCAACTAGAGGTGGGACTCAAAGAAAACCTT
genomic: GATTGCCACAAATGGTACAAAACTTGAAAGCTCAAGCATGGACTGATGAGgtgaggagct ... atgcacccagGATCTGTTAGATGCTCTGAATCAACTAGAGGTGGGACTCAAAGAAAACCTC
EST: gi|18170707|gb|BM340547.1|BM340547
EST:     GATTGCCACAAATGGTACAAAACTTGAAAGCTCAAGCATGGACTGATGAG                         GATCTGTTAGATGCTCTGAATCAACTAGAGGTGGGACTCAAAGAAAACCTC
genomic: GATTGCCACAAATGGTACAAAACTTGAAAGCTCAAGCATGGACTGATGAGgtgaggagct ... atgcacccagGATCTGTTAGATGCTCTGAATCAACTAGAGGTGGGACTCAAAGAAAACCTC
EST: gi|61119705|gb|DN560666.1|DN560666
EST:     GATTGCCACAAATGGTACAAAACTTGAAAGCTCAAGCATGGACTGATGAG                         GATCTGTTAGATGCTCTGAATCAACTAGAGGTGGGACTCAAAGAAAACCTC
genomic: GATTGCCACAAATGGTACAAAACTTGAAAGCTCAAGCATGGACTGATGAGgtgaggagct ... atgcacccagGATCTGTTAGATGCTCTGAATCAACTAGAGGTGGGACTCAAAGAAAACCTC
EST: gi|32851780|gb|CD991461.1|CD991461
EST:     GGACTGATNAG                         GATCTGTTAGATGCTCTGAATCANCTAGAGGTGGGACTCAAAGAAAACCTC
genomic: GGACTGATGAGgtgaggagct ... atgcacccagGATCTGTTAGATGCTCTGAATCAACTAGAGGTGGGACTCAAAGAAAACCTC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 247

CCGCAATTTGCTGGCAAAGGGTGCATTTGCTGCCCAGATGATCGATCTTGGATTGCCACAAATGGTACAAAACTTGAAAGCTCAAGCATGGACTGATGAGgtgaggagct ... atgcacccagGATCTGTTAGATGCTCTGAATCAACTAGAGGTGGGACTCAAAGAAAACCTCAAGAAGTTGAGTTCCTTTGATAAGTACAAACAGCAAGTTCTTCTTGGTC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 302

CCGCAATTTGCTGGCAAAGGGTGCATTTGCTGCCCAGATGATCGATCTTGGATTGCCACAAATGGTACAAAACTTGAAAGCTCAAGCATGGACTGATGAGgtgaggagct ... atgcacccagGATCTGTTAGATGCTCTGAATCAACTAGAGGTGGGACTCAAAGAAAACCTCAAGAAGTTGAGTTCCTTTGATAAGTACAAACAGCAAGTTCTTCTTGGTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 245

CCGCAATTTGCTGGCAAAGGGTGCATTTGCTGCCCAGATGATCGATCTTGGATTGCCACAAATGGTACAAAACTTGAAAGCTCAAGCATGGACTGATGAGgtgaggagct ... atgcacccagGATCTGTTAGATGCTCTGAATCAACTAGAGGTGGGACTCAAAGAAAACCTCAAGAAGTTGAGTTCCTTTGATAAGTACAAACAGCAAGTTCTTCTTGGTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 318

CCGCAATTTGCTGGCAAAGGGTGCATTTGCTGCCCAGATGATCGATCTTGGATTGCCACAAATGGTACAAAACTTGAAAGCTCAAGCATGGACTGATGAGgtgaggagct ... atgcacccagGATCTGTTAGATGCTCTGAATCAACTAGAGGTGGGACTCAAAGAAAACCTCAAGAAGTTGAGTTCCTTTGATAAGTACAAACAGCAAGTTCTTCTTGGTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgtttttgcacctttttgtgctaactgcaatttgctattatttatgcacccagGATCTGTTAGATGCTCTGAATCAACTAGAGGTGGGACTCAAAGAAAACCTCAAGAAGTTGAGTTCCTTTGATAAGTACAAACAGCAAGTTCTTCTTGGTC
                    tgctaac  putative branch site (score: 318)
                              aatttgctattattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgtgaatgtatcgccgtttagtatgtgctcaggttgagcttgtatgtgtttttgcacctttttgtgctaactgcaatttgctattatttatgcacccagGATCTGTTAGATGCTCTGAATCAACTAGAGGTGGGACTCAAAGAAAACCTCAAGAAGTTGAGTTCCTTTGATAAGTACAAACAGCAAGTTCTTCTTGGTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- gtgaatg
- - - - - - - - - - - - tgtgctc
- - - - - - - - - - - - - - - - - - gagcttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aactgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctatt