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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactccctacttacagtttcttcagtgtttgaattagtagtgaaacattgtctagggaaccatgatctcattttcaaagttacagttcatttattggatattctttggtgcaaacatatacttcttctatttctcttgaatccactgattgcctttgtgctgcagTACATAGTGAAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTTATGGCATTTGACGTACCGCCTCCTCGTGGTCCTCTCTG

Basic information

species Zea mays
transcript GRMZM2G077233_T06
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G077233_T04 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os01g18630.1 (Oryza sativa), 3'ss of exon 10
gtaactccctacttacagtttcttcagtgtttgaattagtagtgaaacattgtctagggaaccatgatctcattttcaaagttacagttcatttattggatattctttggtgcaaacatatacttcttctatttctcttgaatccactgattgcctttgtgctgcagTACATAGTGAAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTTATGGCATTTGACGTACCGCCTCCTCGTGGTCCTCTCTG
                                                                     |   |  |  ||| |||   || ||     ||  ||||  |   | ||  || ||| |||||  ||||      ||   |  | | |      |||||||| ||||||||||||||||   ||| |||||| | |||||||| ||||| ||||| || ||||| || ||||| || || || |||||
--------------------------------------------------------------------gtggctccctcagtgaca---cacttggcccatcctcttaagc-tatactcatgctt-ttctaaatctca-----ccgtcgtcttcttcaactatgcagTACGTAGTGAAGCTGGAGCAGCAAGGTCAAACTGTTTGCATCAGCGGGTTCATGGCGTTCGACGTGCCACCTCCACGCGGCCCACTCTG
















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|32839637|gb|CD979318.1|CD979318
EST:     ATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACCAGAGCAG                         TACATAGTGAAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTT
genomic: ATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACCAGAGCAGgtaactccct ... tgtgctgcagTACATAGTGAAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTT
EST: gi|78179647|gb|DV550020.1|DV550020
EST:     ATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACCAGAGCAG                         TACATAGTGAAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTT
genomic: ATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACCAGAGCAGgtaactccct ... tgtgctgcagTACATAGTGAAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTT
EST: gi|91876412|gb|EB406369.1|EB406369
EST:     ATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACCAGAGCAG                         TACATAGTGAAGCTGGAGCAAGCAGGCCAAACTATCTGCATCAGTGGGTTT
genomic: ATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACCAGAGCAGgtaactccct ... tgtgctgcagTACATAGTGAAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTT
EST: gi|67023174|gb|CO451923.1|CO451923
EST:     ATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACCAGAGCAG                         TACATAGTGAAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTT
genomic: ATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACCAGAGCAGgtaactccct ... tgtgctgcagTACATAGTGAAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTT
EST: gi|211078124|gb|FL447287.1|FL447287
EST:     ATCTTGCATTCACCATAGCAAACAAGACTTTCACTTTAACACCAGAGCAG                         TACATAGTGAATCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTT
genomic: ATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACCAGAGCAGgtaactccct ... tgtgctgcagTACATAGTGAAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTT
EST: gi|24768386|gb|CA403515.1|CA403515
EST:     ATCTTGCATTCACCATAGCAAATAAGACTTTCCCCTTAACACCAGAGCAG                         TACATAGTGAAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTT
genomic: ATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACCAGAGCAGgtaactccct ... tgtgctgcagTACATAGTGAAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTT
EST: gi|24768986|gb|CA404115.1|CA404115
EST:     ATCTTGCATTCACCATAGCAAATAAGACTTTCACCTTAACACCAGAGCAG                         TACATAGTGAAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTT
genomic: ATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACCAGAGCAGgtaactccct ... tgtgctgcagTACATAGTGAAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTT
EST: gi|83278626|gb|DV942634.1|DV942634
EST:     ATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACCAGAGCAG                         TACATAGTGAAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTT
genomic: ATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACCAGAGCAGgtaactccct ... tgtgctgcagTACATAGTGAAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTT
EST: gi|76289739|gb|DV029307.1|DV029307
EST:     ATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACCAGAGCAG                         TACATAGTGAAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTT
genomic: ATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACCAGAGCAGgtaactccct ... tgtgctgcagTACATAGTGAAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTT
EST: gi|14242980|gb|BG840151.2|BG840151
EST:     ATCTTGCATTCACCATAGCAAATAAGACTTTCACCTTAACACCAGAGCAG                         TACATAGTGAAGCTAGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTT
genomic: ATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACCAGAGCAGgtaactccct ... tgtgctgcagTACATAGTGAAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTT
EST: gi|32839672|gb|CD979353.1|CD979353
EST:     ATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACCAGAGCAG                         TACATAGTGAAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTT
genomic: ATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACCAGAGCAGgtaactccct ... tgtgctgcagTACATAGTGAAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTT
EST: gi|211384116|gb|FL248479.1|FL248479
EST:     ATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACCAGAGCAG                         TACATAGTGAAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTT
genomic: ATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACCAGAGCAGgtaactccct ... tgtgctgcagTACATAGTGAAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTT
EST: gi|60346328|gb|DN213301.1|DN213301
EST:     ATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACCAGAGCAG                         TACATAGTGAAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTT
genomic: ATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACCAGAGCAGgtaactccct ... tgtgctgcagTACATAGTGAAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTT
EST: gi|116822883|gb|EC866344.1|EC866344
EST:     ATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACCAGAGCAG                         T-----G--AAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTT
genomic: ATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACCAGAGCAGgtaactccct ... tgtgctgcagTACATAGTGAAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTT
EST: gi|76291014|gb|DV030582.1|DV030582
EST:     ATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACCAGAGCAG                         TACATAGTGAAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTT
genomic: ATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACCAGAGCAGgtaactccct ... tgtgctgcagTACATAGTGAAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTT
EST: gi|78023269|gb|DV491656.1|DV491656
EST:     ATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACCAGAGCAG                         TACATAGTGAAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTT
genomic: ATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACCAGAGCAGgtaactccct ... tgtgctgcagTACATAGTGAAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTT
EST: gi|60396697|gb|DN229564.1|DN229564
EST:     ATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACCAGAGCAG                         TACATAGTGAAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTT
genomic: ATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACCAGAGCAGgtaactccct ... tgtgctgcagTACATAGTGAAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTT
EST: gi|31250410|gb|CD219434.1|CD219434
EST:     ATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACCAGAGCAG                         TACATAGTGAAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTT
genomic: ATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACCAGAGCAGgtaactccct ... tgtgctgcagTACATAGTGAAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTT
EST: gi|8577168|gb|BE129805.1|BE129805
EST:     ATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACCAGAGCAG                         TACATAGTGAAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTT
genomic: ATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACCAGAGCAGgtaactccct ... tgtgctgcagTACATAGTGAAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTT
EST: gi|109637704|gb|EC591249.1|EC591249
EST:     ATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACCAGAGCAG                         TACATAGTGAAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTT
genomic: ATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACCAGAGCAGgtaactccct ... tgtgctgcagTACATAGTGAAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTT
EST: gi|32840610|gb|CD980291.1|CD980291
EST:     ATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACCAGAGCAG                         TACATAGTGAAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTT
genomic: ATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACCAGAGCAGgtaactccct ... tgtgctgcagTACATAGTGAAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTT
EST: gi|32858947|gb|CD998628.1|CD998628
EST:     ATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACCAGAGCAG                         TACATAGTGAAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTT
genomic: ATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACCAGAGCAGgtaactccct ... tgtgctgcagTACATAGTGAAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTT
EST: gi|5915565|gb|AW053206.1|AW053206
EST:     ATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACCAGAGCAG                         TACATAGTGAAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTT
genomic: ATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACCAGAGCAGgtaactccct ... tgtgctgcagTACATAGTGAAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTT
EST: gi|60348336|gb|DN215309.1|DN215309
EST:     ATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACCAGAGCAG                         TACATAGTGAAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTT
genomic: ATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACCAGAGCAGgtaactccct ... tgtgctgcagTACATAGTGAAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTT

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: 48 (upstream exon), 49 (downstream exon)
Score: 410

CCCCAATGGCGAGTCAACTGTTGATTGCCATCAGATCTCAAAGATGCCAAATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACCAGAGCAGgtaactccct ... tgtgctgcagTACATAGTGAAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTTATGGCATTTGACGTACCGCCTCCTCGTGGTCCTCTCTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 551

CCCCAATGGCGAGTCAACTGTTGATTGCCATCAGATCTCAAAGATGCCAAATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACCAGAGCAGgtaactccct ... tgtgctgcagTACATAGTGAAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTTATGGCATTTGACGTACCGCCTCCTCGTGGTCCTCTCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 753

CCCCAATGGCGAGTCAACTGTTGATTGCCATCAGATCTCAAAGATGCCAAATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACCAGAGCAGgtaactccct ... tgtgctgcagTACATAGTGAAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTTATGGCATTTGACGTACCGCCTCCTCGTGGTCCTCTCTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 461

CCCCAATGGCGAGTCAACTGTTGATTGCCATCAGATCTCAAAGATGCCAAATCTTGCATTCACCATAGCAAACAAGACTTTCACCTTAACACCAGAGCAGgtaactccct ... tgtgctgcagTACATAGTGAAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTTATGGCATTTGACGTACCGCCTCCTCGTGGTCCTCTCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaacatatacttcttctatttctcttgaatccactgattgcctttgtgctgcagTACATAGTGAAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTTATGGCATTTGACGTACCGCCTCCTCGTGGTCCTCTCTG
                                cactgat  putative branch site (score: 461)
                                      ttgccttt  CT-rich tract
     atatactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaactccctacttacagtttcttcagtgtttgaattagtagtgaaacattgtctagggaaccatgatctcattttcaaagttacagttcatttattggatattctttggtgcaaacatatacttcttctatttctcttgaatccactgattgcctttgtgctgcagTACATAGTGAAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTTATGGCATTTGACGTACCGCCTCCTCGTGGTCCTCTCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC