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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATGGAAGCGCAAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTATACAATCATAAGgtacataatacacaacatttagaaccaaataaaattctgcttctttttgttatggtagcctcccttcagtagattactctctttgttttgcacgtctaaa...

Basic information

species Zea mays
transcript GRMZM2G068244_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G068244_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os03g60740.1 (Oryza sativa), 5'ss of exon 5
GTATGGAAGCGCAAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTATACAATCATAAGgtacataatacacaacatttagaaccaaataaaattctgcttctttttgttatggtagcctcccttcagtagattactctctttgttttgca--cgtctaaa-
|| |||||||||||  |||||||||||||||||||||||||| ||||||||||||| |||||||||    | || || |     | ||| |   |||       ||  ||| |  ||| | ||   |||  |   ||  |||      || | |   || | |  
GTTTGGAAGCGCAAGTCAGAACAGTATTTGGCAGACAGTGGAGTCCCTTATACAATAATAAGgtaccacctgcataagacaagaagccatacgtaatagcctgactaattggtccggttggcttaattcgct---ttgttcttgaaacttaggaaatgtttgatt

upper sequence: GRMZM2G068244_T01 (Zea mays), 5'ss of exon 5
lower sequence: Vv08s0007g00530.t01 (Vitis vinifera), 5'ss of exon 5
GTATGGAAGCGCAAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTATACAATCATAAGgtacataatacacaacatttagaa---ccaaataaaattctgcttctttttgttatggtagcctcccttcagtagattactctctttgttttgcacgtctaaa
|| |||||| | ||||| ||||||||||| ||||||  |||||| ||||| ||||| |||||||||||   ||  || ||||  |    |  |||||   |  | | |||  |   |         |  |||  ||| ||| | | |   |     |    |   
GTTTGGAAGAGAAAAGCTGAACAGTATTTAGCAGACTCTGGAATACCTTACACAATTATAAGgtacatctaacttaatatttccagtttctcaataactgttagttacttgatacaacatggttgacttttctctaggttattatgtggataacatattctt---
















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|60397802|gb|DN230618.1|DN230618
EST:     AAAGCAGAACAGTATTTGGCAAACAGTGGAATCCCTTATACAATCATAAG                         GCCAGGAGGTCTTCAAGACAAGGACGGAGGAGTGAGAGAGCTACTTGTGGG
genomic: AAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTATACAATCATAAGgtacataata ... taaattttagGCCAGGAGGTCTACAAGACAAGGACGGAGGAGTGAGAGAGCTACTTGTGGG
EST: gi|32922742|gb|CF027554.1|CF027554
EST:     AAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTATACAATCATAAG                         GCCAGGAGGTCTACAAGACAAGGACGGAGGAGTGAGAGAGCTACTAGTGGG
genomic: AAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTATACAATCATAAGgtacataata ... taaattttagGCCAGGAGGTCTACAAGACAAGGACGGAGGAGTGAGAGAGCTACTTGTGGG
EST: gi|20803051|gb|BQ294101.1|BQ294101
EST:     AAAGCAGAACAGTATTTGGCAAACAGTGGAATCCCTTATACAATCATAAG                         GCCAGGAGGTCTTCAAGACAAGGACGGAGGAGTGAGAGAGCTACTTGTGGG
genomic: AAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTATACAATCATAAGgtacataata ... taaattttagGCCAGGAGGTCTACAAGACAAGGACGGAGGAGTGAGAGAGCTACTTGTGGG
EST: gi|32922646|gb|CF027458.1|CF027458
EST:     AAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTATACAATCATAAG                         GCCAGGGGGTCTACAAGACAAGGACGGAGGAGTGAGAGAGCTACTTA-GGA
genomic: AAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTATACAATCATAAGgtacataata ... taaattttagGCCAGGAGGTCTACAAGACAAGGACGGAGGAGTGAGAGAGCTACTTGTGGG
EST: gi|211113405|gb|FL349341.1|FL349341
EST:     AAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTATACAATCATAAG                         GCCAGGAGGTCTACAAGACAAGGACGGAGGAGTGAGAGAGCTACTTGTGGG
genomic: AAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTATACAATCATAAGgtacataata ... taaattttagGCCAGGAGGTCTACAAGACAAGGACGGAGGAGTGAGAGAGCTACTTGTGGG
EST: gi|32922752|gb|CF027564.1|CF027564
EST:     AAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTATACAATCATAAG                         GCCAGGAGGTCTACAAGACAAGGACGGAGGAGTGAGAGAGC-ACAAGATGG
genomic: AAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTATACAATCATAAGgtacataata ... taaattttagGCCAGGAGGTCTACAAGACAAGGACGGAGGAGTGAGAGAGCTACTTG-TGG
EST: gi|32923432|gb|CF028244.1|CF028244
EST:     AAAGCAGACCAGTATTTGGCAGACAGTGGAATCCCTTATACAATCATAAG                         GCCAGGAGGTCTACAAGACAAGGACGGAGGAGTGAGAGAGCTACTTGTGGG
genomic: AAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTATACAATCATAAGgtacataata ... taaattttagGCCAGGAGGTCTACAAGACAAGGACGGAGGAGTGAGAGAGCTACTTGTGGG
EST: gi|32923376|gb|CF028188.1|CF028188
EST:     AAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTATACAATCATAAG                         GCCAGGAGGTCTACAAGACAAGGACGGAGGAGTGAGAGAGCTACTTGTGGG
genomic: AAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTATACAATCATAAGgtacataata ... taaattttagGCCAGGAGGTCTACAAGACAAGGACGGAGGAGTGAGAGAGCTACTTGTGGG
EST: gi|60339573|gb|DN206546.1|DN206546
EST:     AAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTATACAATCATAAG                         GCCAGGAGGTCTACAAGACAAGGACGGAGGAGTGAGAGAGCTACTTGTGGG
genomic: AAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTATACAATCATAAGgtacataata ... taaattttagGCCAGGAGGTCTACAAGACAAGGACGGAGGAGTGAGAGAGCTACTTGTGGG
EST: gi|211283841|gb|FL366659.1|FL366659
EST:     AAAGCAGAACAGTATTTGGCAAACAGTGGAATCCCTTATACAATCATAAG                         GCCAGGAGGTCTTCAAGACAAGGACGGANGAGTGAGAGAGCTACTTTGTGG
genomic: AAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTATACAATCATAAGgtacataata ... taaattttagGCCAGGAGGTCTACAAGACAAGGACGGAGGAGTGAGAGAGCTACTT-GTGG
EST: gi|211537318|gb|FL320573.1|FL320573
EST:     AAAGCAGAACAGTATTTGGCAAACAGTGGAATCCCTTATACAATCATAAG                         GCCAGGAAGTCT
genomic: AAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTATACAATCATAAGgtacataata ... taaattttagGCCAGGAGGTCT
EST: gi|60343124|gb|DN210097.1|DN210097
EST:     AAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTATACAATCATAAG                         GCCAGGAGGTCTACAAGACAAGGACGGAGGAGTGAGAGAGCTACTTGTGGG
genomic: AAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTATACAATCATAAGgtacataata ... taaattttagGCCAGGAGGTCTACAAGACAAGGACGGAGGAGTGAGAGAGCTACTTGTGGG
EST: gi|32923449|gb|CF028261.1|CF028261
EST:     AAAGCAGACCAGTATTTGGCAGACAGTGGAATCCCTTATACAATCATAAG                         GCCAGGAGGTCTACAAGACAAGGACGGAGGAGTGAGAGAGCTACTTGTGGG
genomic: AAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTATACAATCATAAGgtacataata ... taaattttagGCCAGGAGGTCTACAAGACAAGGACGGAGGAGTGAGAGAGCTACTTGTGGG
EST: gi|211278086|gb|FL458575.1|FL458575
EST:     AAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTATACAATCATAAG                         GCCAGGAGGTCTACAAGACAAGGACGGAGGAGTGAGAGAGCTACTTGTGGG
genomic: AAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTATACAATCATAAGgtacataata ... taaattttagGCCAGGAGGTCTACAAGACAAGGACGGAGGAGTGAGAGAGCTACTTGTGGG
EST: gi|211193544|gb|FL459435.1|FL459435
EST:     AAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTATACAATCATAAG                         GCCAGGAGGTCTACAAGACAAGGACGGAGGAKTGAGAGAGCTACTTGTGGG
genomic: AAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTATACAATCATAAGgtacataata ... taaattttagGCCAGGAGGTCTACAAGACAAGGACGGAGGAGTGAGAGAGCTACTTGTGGG
EST: gi|32911901|gb|CF016713.1|CF016713
EST:     AAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTATACAATCATAAG                         GCCAGGAGGTCTACAAGACAAGGACGGAGGAGTGAGAGAGTTACTTGTGGG
genomic: AAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTATACAATCATAAGgtacataata ... taaattttagGCCAGGAGGTCTACAAGACAAGGACGGAGGAGTGAGAGAGCTACTTGTGGG
EST: gi|32844239|gb|CD983920.1|CD983920
EST:     AAAGCAGAACAGTATTTGGCAGACAGTGGAGTCCCTTATACAATCATAAG                         GCCAGGAGGTCTACAAGACAAGGACGGAGGAGTGAGAGAGTTACTTGTGGG
genomic: AAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTATACAATCATAAGgtacataata ... taaattttagGCCAGGAGGTCTACAAGACAAGGACGGAGGAGTGAGAGAGCTACTTGTGGG
EST: gi|16379519|gb|BI993001.1|BI993001
EST:     AGTATTTGGCAGACAGTGGAATCCCTTATCCAATCATAAG                         GCCAGGAGGTCTACAAGACAAGGACGGAGGAGTGAGAGAGCTACTTGTGGG
genomic: AGTATTTGGCAGACAGTGGAATCCCTTATACAATCATAAGgtacataata ... taaattttagGCCAGGAGGTCTACAAGACAAGGACGGAGGAGTGAGAGAGCTACTTGTGGG
EST: gi|60396304|gb|DN229173.1|DN229173
EST:     AAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTATACAATCATAAG                         GCCAGGAGGTCTACAAGACAAGGACGGAGGAGTGAGAGAGCTACTTGTGGG
genomic: AAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTATACAATCATAAGgtacataata ... taaattttagGCCAGGAGGTCTACAAGACAAGGACGGAGGAGTGAGAGAGCTACTTGTGGG
EST: gi|78023137|gb|DV491524.1|DV491524
EST:     AAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTATACAATCATAAG                         GCCAGGAGGTCTACAAGACAAGGACGGAGGAGTGAGAGAGCTACTTGTGGG
genomic: AAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTATACAATCATAAGgtacataata ... taaattttagGCCAGGAGGTCTACAAGACAAGGACGGAGGAGTGAGAGAGCTACTTGTGGG
EST: gi|32920219|gb|CF025031.1|CF025031
EST:     AAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTATACAATCATAAG                         GCCAGGAGGTCTACAAGACAAGGACGGAGGAGTGAGAGAGCTACTTGTGGG
genomic: AAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTATACAATCATAAGgtacataata ... taaattttagGCCAGGAGGTCTACAAGACAAGGACGGAGGAGTGAGAGAGCTACTTGTGGG
EST: gi|116825576|gb|EC869314.1|EC869314
EST:     AAAGCAGAACAGTATTTGGCAAACAGTGGAATCCCTTATACAATCATAAG                         GCCAGGAGGTCTACAAGACAAGGACGGAGGAGTGAGAGAGCTACTTGTGGG
genomic: AAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTATACAATCATAAGgtacataata ... taaattttagGCCAGGAGGTCTACAAGACAAGGACGGAGGAGTGAGAGAGCTACTTGTGGG

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: 37 (upstream exon), 49 (downstream exon)
Score: 152

GTATGGAAGCGCAAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTATACAATCATAAGgtacataata ... taaattttagGCCAGGAGGTCTACAAGACAAGGACGGAGGAGTGAGAGAGCTACTTGTGGGGAAAGACGATGAACTTCTCCAGACTGACACAAAGTCGATTCCTAGAGCC


Block sizes: 37 (upstream exon), 49 (downstream exon)
Score: 715

GTATGGAAGCGCAAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTATACAATCATAAGgtacataata ... taaattttagGCCAGGAGGTCTACAAGACAAGGACGGAGGAGTGAGAGAGCTACTTGTGGGGAAAGACGATGAACTTCTCCAGACTGACACAAAGTCGATTCCTAGAGCC


Block sizes: 37 (upstream exon), 49 (downstream exon)
Score: 234

GTATGGAAGCGCAAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTATACAATCATAAGgtacataata ... taaattttagGCCAGGAGGTCTACAAGACAAGGACGGAGGAGTGAGAGAGCTACTTGTGGGGAAAGACGATGAACTTCTCCAGACTGACACAAAGTCGATTCCTAGAGCC


Block sizes: 37 (upstream exon), 49 (downstream exon)
Score: 292

GTATGGAAGCGCAAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTATACAATCATAAGgtacataata ... taaattttagGCCAGGAGGTCTACAAGACAAGGACGGAGGAGTGAGAGAGCTACTTGTGGGGAAAGACGATGAACTTCTCCAGACTGACACAAAGTCGATTCCTAGAGCC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTATGGAAGCGCAAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTATACAATCATAAGgtacataatacacaacatttagaaccaaataaaattctgcttctttttgttatggtagcctcccttcagtagattactctctttgttttgcacgtctaaa

- - - - - - - - - - - - - - - - - - AGTGGA
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