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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGTGATGATACAGTGGATTTCATTGGACATGCACTTGCTCTTCATAGAGATGATCGCTATCTTGATGAACCGGCACTTGATACAGTGAAAAGGATGAAAgtaagtcttggccagagttgcttcctagttgttactatggataaacttgtgcttcctaatggtttgaatgtgttttctttatatagttctgttatacttatctatcgtgtgcttttag

Basic information

species Zea mays
transcript GRMZM2G435373_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G435373_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os05g23860.1 (Oryza sativa), 5'ss of exon 6
AAGTGATGATACAGTGGATTTCATTGGACATGCACTTGCTCTTCATAGAGATGATCGCTATCTTGATGAACCGGCACTTGATACAGTGAAAAGGATGAAAgtaagtcttggccagagttgcttcctagttgttactatggataaact-tgtgcttcctaatggtt--tgaatgtgttttctttatatagttctgttatactt--atctatcgtgtgcttttag
|||||| ||||| ||||||||||| || |||||||||||||||||||||||||||||||| ||| ||||||| ||| ||||||| || |||||||||||||||||| |||  || || | | |     |||||  ||    |   ||  |    ||||  || |   ||||| |   | ||||||  |||||  ||| | ||   |   |  | | ||| |||
AAGTGACGATACCGTGGATTTCATCGGTCATGCACTTGCTCTTCATAGAGATGATCGCTACCTTAATGAACCAGCAATTGATACTGTAAAAAGGATGAAAgtaagtattgatcaaagct-cctgtagattgttcgtagtcttctgctacggatatcctgctgttctctgaatattcatgctttatgaagttcaattacattttagtgctttatctacttgtag

upper sequence: GRMZM2G435373_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os05g34540.1 (Oryza sativa), 5'ss of exon 6
AAGTGATGATACAGTGGATTTCATTGGACATGCACTTGCTCTTCATAGAGATGATCGCTATCTTGATGAACCGGCACTTGATACAGTGAAAAGGATGAAAgtaagtcttggccagagttgcttcctagttgttactatggataaacttgtgcttcctaatggtttgaatgtgttttctttatatagttctgttatacttatctatcgtgtgcttttag
|||||| ||||| ||||||||||| || ||||||||||||||||||||||||||||| || ||  ||||||| ||| ||||||| || ||||||||||||||||||||||     ||||   |    ||| | | |||   |   ||  |   |||||    |     |   | |  |  | |   |   | |  | |  |    |            
AAGTGACGATACTGTGGATTTCATCGGCCATGCACTTGCTCTTCATAGAGATGATCGTTACCTAAATGAACCAGCAATTGATACTGTAAAAAGGATGAAAgtaagtcttgtttgtagtttgct----gttatcagtatcc-tctgctcata--tcctaccattccattttcatctcttaaacaccttcaggctgcattagttagcca-----------
















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|149050331|gb|EE048608.2|EE048608
EST:     ATGATCGCTATCTTGATGAACCGGCACTTGATACAGTGAAAAGGATGAAA                         CTATATTCAGAGTCTCTTGCGCGCTTTCAAGGAGGCTCGCCATATATCTAT
genomic: ATGATCGCTATCTTGATGAACCGGCACTTGATACAGTGAAAAGGATGAAAgtaagtcttg ... gtgcttttagCTATATTCAGAGTCTCTTGCGCGCTTTCAAGGAGGCTCGCCATATATCTAT
EST: gi|32846965|gb|CD986646.1|CD986646
EST:     ATGATCGCTATCTTGATGAACCGGCACTTGATACAGTGAAAAGGATGAAA                         CTATATTCAGAGTCTCTTGCGCGCTTTCAAGGAGGCTCGCCATATATCTAT
genomic: ATGATCGCTATCTTGATGAACCGGCACTTGATACAGTGAAAAGGATGAAAgtaagtcttg ... gtgcttttagCTATATTCAGAGTCTCTTGCGCGCTTTCAAGGAGGCTCGCCATATATCTAT
EST: gi|6031345|gb|AW076202.1|AW076202
EST:     ATGATCGCTATCTTGATGAACCGGCACTTGATACAGNGAAAAGGATGAAA                         CTATATTCAGAGTCTCTTGCGCGCTTTCAAGGAGGCTCGCCATATATCTAT
genomic: ATGATCGCTATCTTGATGAACCGGCACTTGATACAGTGAAAAGGATGAAAgtaagtcttg ... gtgcttttagCTATATTCAGAGTCTCTTGCGCGCTTTCAAGGAGGCTCGCCATATATCTAT
EST: gi|32938598|gb|CF043417.1|CF043417
EST:     ATGATCGCTATCTTGATGAACCGGCACTTGATACAGTGAAAAGGATGAAA                         CTATATTCAGAGTCTCTTGCGCGCTTTCAAGGAGGCTCGCCATATATCTAT
genomic: ATGATCGCTATCTTGATGAACCGGCACTTGATACAGTGAAAAGGATGAAAgtaagtcttg ... gtgcttttagCTATATTCAGAGTCTCTTGCGCGCTTTCAAGGAGGCTCGCCATATATCTAT
EST: gi|33094579|gb|CF054573.1|CF054573
EST:     ATGATCGCTATCTTGATGAACCGGCACTTGATACAGTGAAAAGGATGAAA                         CTATATTCAGAGTCTCTTGCGCGCTTTCAAGGAGGCTCGCCATATATCTAT
genomic: ATGATCGCTATCTTGATGAACCGGCACTTGATACAGTGAAAAGGATGAAAgtaagtcttg ... gtgcttttagCTATATTCAGAGTCTCTTGCGCGCTTTCAAGGAGGCTCGCCATATATCTAT
EST: gi|149098467|gb|EE184446.2|EE184446
EST:     ATGATCGCTATCTTGATGAACCGGCACTTGATACAGTGAAAAGGATGAAA                         CTATATTCAGAGTCTCTTGCGCGCTTTNCA-GGAGGCTCGCCATATATCTA
genomic: ATGATCGCTATCTTGATGAACCGGCACTTGATACAGTGAAAAGGATGAAAgtaagtcttg ... gtgcttttagCTATATTCAGAGTCTCTTGCGCGCTTT-CAAGGAGGCTCGCCATATATCTA
EST: gi|32939909|gb|CF044728.1|CF044728
EST:     ATGATCGCTATCTTGATGAACCGGCACTTGATACAGTGAAAAGGATGAAA                         CTATATTCAGAGTCTCTTGCGCGCTTTCAAGGAGGCTCGCCATATATCTAT
genomic: ATGATCGCTATCTTGATGAACCGGCACTTGATACAGTGAAAAGGATGAAAgtaagtcttg ... gtgcttttagCTATATTCAGAGTCTCTTGCGCGCTTTCAAGGAGGCTCGCCATATATCTAT
EST: gi|32856054|gb|CD995735.1|CD995735
EST:     ATGATCGCTATCTTGATGAACTGGCACTTGATACAGTGAAAAGGATGAAA                         CTATATTCAGAGTCTCTTGCGCGCTTTCAAGGAGGCTCGCCATATATCTAT
genomic: ATGATCGCTATCTTGATGAACCGGCACTTGATACAGTGAAAAGGATGAAAgtaagtcttg ... gtgcttttagCTATATTCAGAGTCTCTTGCGCGCTTTCAAGGAGGCTCGCCATATATCTAT
EST: gi|32932660|gb|CF037472.1|CF037472
EST:     ATGATCGCTATCTTGATGAACCGGCACTTGATACAGTGAAAAGGATGAAA                         CTATATTCAGAGTCTCTTGCGCGCTTTCAAGGAGGCTCGCCATATATCTAT
genomic: ATGATCGCTATCTTGATGAACCGGCACTTGATACAGTGAAAAGGATGAAAgtaagtcttg ... gtgcttttagCTATATTCAGAGTCTCTTGCGCGCTTTCAAGGAGGCTCGCCATATATCTAT
EST: gi|47962286|gb|CN844995.1|CN844995
EST:     ATGATCGCTATCTTGATGAACCGGCACTTGATACAGTGAAAAGGATGAAA                         CTATATTCAGAGTCTCTTGCGCGCTTTCAAGGAGGCTCGCCATATATCTAT
genomic: ATGATCGCTATCTTGATGAACCGGCACTTGATACAGTGAAAAGGATGAAAgtaagtcttg ... gtgcttttagCTATATTCAGAGTCTCTTGCGCGCTTTCAAGGAGGCTCGCCATATATCTAT
EST: gi|211034436|gb|FL381555.1|FL381555
EST:     ATGATCGCTATCTTGATGAACCGGCACTTGATACAGTGAAAAGGATGAAA                         CTATATTCAGAGTCTCTTGCGCGCTTTCAAGGAGGCTCGCCATATATCTAT
genomic: ATGATCGCTATCTTGATGAACCGGCACTTGATACAGTGAAAAGGATGAAAgtaagtcttg ... gtgcttttagCTATATTCAGAGTCTCTTGCGCGCTTTCAAGGAGGCTCGCCATATATCTAT
EST: gi|211144299|gb|FL377140.1|FL377140
EST:     ATGATCGCTATCTTGATGAACCGGCACTTGATACAGTGAAAAGGATGAAA                         CTATATTCAGAGTCTCTTGCGCGCTTTCAAGGAGGCTCGCCATATATCTAT
genomic: ATGATCGCTATCTTGATGAACCGGCACTTGATACAGTGAAAAGGATGAAAgtaagtcttg ... gtgcttttagCTATATTCAGAGTCTCTTGCGCGCTTTCAAGGAGGCTCGCCATATATCTAT
EST: gi|211445979|gb|FL406296.1|FL406296
EST:     ATGATCGCTATCTTGATGAACCGGCACTTGATACAGTGAAAAGGATGAAA                         CTATATTCAGAGTCTCTTGCGCGCTTTCAAGGAGGCTCGCCATATATCTAT
genomic: ATGATCGCTATCTTGATGAACCGGCACTTGATACAGTGAAAAGGATGAAAgtaagtcttg ... gtgcttttagCTATATTCAGAGTCTCTTGCGCGCTTTCAAGGAGGCTCGCCATATATCTAT
EST: gi|211259815|gb|FL426651.1|FL426651
EST:     ATGATCGCTATCTTGATGAACCGGCACTTGATACAGTGAAAAGGATGAAA                         CTATATTCAGAGTCTCTTGCGCGCTTTCAAGGAGGCTCGCCATATATCTAT
genomic: ATGATCGCTATCTTGATGAACCGGCACTTGATACAGTGAAAAGGATGAAAgtaagtcttg ... gtgcttttagCTATATTCAGAGTCTCTTGCGCGCTTTCAAGGAGGCTCGCCATATATCTAT
EST: gi|32932658|gb|CF037470.1|CF037470
EST:     ATGATCGCTATCTTGATGAACCGGCACTTGATACAGTGAAAAGGATGAAA                         CTATATTCAGAGTCTCTTGCGCGCTTTCAAGGAGGCTCGCCATATATCTAT
genomic: ATGATCGCTATCTTGATGAACCGGCACTTGATACAGTGAAAAGGATGAAAgtaagtcttg ... gtgcttttagCTATATTCAGAGTCTCTTGCGCGCTTTCAAGGAGGCTCGCCATATATCTAT
EST: gi|211346475|gb|FL413228.1|FL413228
EST:     ATGATCGCTATCTTGATGAACCGGCACTTGATACAGTGAAAAGGATGAAA                         CTATATTCAGAGTCTCTTGCGCGCTTTCAAGGAGGCTCGCCATATATCTAT
genomic: ATGATCGCTATCTTGATGAACCGGCACTTGATACAGTGAAAAGGATGAAAgtaagtcttg ... gtgcttttagCTATATTCAGAGTCTCTTGCGCGCTTTCAAGGAGGCTCGCCATATATCTAT
EST: gi|33104315|gb|CF064275.1|CF064275
EST:     ATGATCGCTATCTTGATGAACCGGCACTTGATACAGTGAAAAGGATGAAA                         CTATATTCAGAGTCTCTTGCGCGCTTTCAAGGAGGCTCGCCATATATCTAT
genomic: ATGATCGCTATCTTGATGAACCGGCACTTGATACAGTGAAAAGGATGAAAgtaagtcttg ... gtgcttttagCTATATTCAGAGTCTCTTGCGCGCTTTCAAGGAGGCTCGCCATATATCTAT
EST: gi|32939179|gb|CF043998.1|CF043998
EST:     ATGATCGCTATCTTGATGAACCGGCACTTGATACAGTGAAAAGGATGAAA                         CTATATTCAGAGTCTCTTGCGCGCTTTCAAGGAGGCTCGCCATATATCTAT
genomic: ATGATCGCTATCTTGATGAACCGGCACTTGATACAGTGAAAAGGATGAAAgtaagtcttg ... gtgcttttagCTATATTCAGAGTCTCTTGCGCGCTTTCAAGGAGGCTCGCCATATATCTAT

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: 304

AAGTGATGATACAGTGGATTTCATTGGACATGCACTTGCTCTTCATAGAGATGATCGCTATCTTGATGAACCGGCACTTGATACAGTGAAAAGGATGAAAgtaagtcttg ... gtgcttttagCTATATTCAGAGTCTCTTGCGCGCTTTCAAGGAGGCTCGCCATATATCTATCCATTGTATGGTCTGGGTGAGCTACCACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 315

AAGTGATGATACAGTGGATTTCATTGGACATGCACTTGCTCTTCATAGAGATGATCGCTATCTTGATGAACCGGCACTTGATACAGTGAAAAGGATGAAAgtaagtcttg ... gtgcttttagCTATATTCAGAGTCTCTTGCGCGCTTTCAAGGAGGCTCGCCATATATCTATCCATTGTATGGTCTGGGTGAGCTACCACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 329

AAGTGATGATACAGTGGATTTCATTGGACATGCACTTGCTCTTCATAGAGATGATCGCTATCTTGATGAACCGGCACTTGATACAGTGAAAAGGATGAAAgtaagtcttg ... gtgcttttagCTATATTCAGAGTCTCTTGCGCGCTTTCAAGGAGGCTCGCCATATATCTATCCATTGTATGGTCTGGGTGAGCTACCACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 214

AAGTGATGATACAGTGGATTTCATTGGACATGCACTTGCTCTTCATAGAGATGATCGCTATCTTGATGAACCGGCACTTGATACAGTGAAAAGGATGAAAgtaagtcttg ... gtgcttttagCTATATTCAGAGTCTCTTGCGCGCTTTCAAGGAGGCTCGCCATATATCTATCCATTGTATGGTCTGGGTGAGCTACCACAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGTGATGATACAGTGGATTTCATTGGACATGCACTTGCTCTTCATAGAGATGATCGCTATCTTGATGAACCGGCACTTGATACAGTGAAAAGGATGAAAgtaagtcttggccagagttgcttcctagttgttactatggataaacttgtgcttcctaatggtttgaatgtgttttctttatatagttctgttatacttatctatcgtgtgcttttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG