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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAGTTGAAGGCTGAAAGAGTATCGAACTGGTTCTCGCATCTTGCTGAAAGTTCAGACGTGAAAGCTCTACCAAACGGTCTTTCGCTGCTCCTTAACAAGgtaattttctttctaccttgaggaaaccttatttttgtttctaagatcaacatcctaaattcttaattctggtacag

Basic information

species Zea mays
transcript GRMZM2G377341_T01
intron # 29
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G377341_T01 (Zea mays), 5'ss of exon 29
lower sequence: LOC_Os10g21910.2 (Oryza sativa), 5'ss of exon 1
GGAGTTGAAGGCTGAAAGAGTATCGAACTGGTTCTCGCATCTTGCTGAAAGTTCAGACGTGAAAGCTCTACCAAACGGTCTTTCGCTGCTCCTTAACAAGgtaattttctttcta-----ccttgagga---aaccttatttttgtttctaagatcaacatcctaaat-tcttaattctggtacag--------------------
|||||||||||||||||||||||| || ||| |||||| ||| ||||||||  | || ||||||||| | ||||| ||||||||  |  | |||||||||||||  ||  ||| |      | ||| |     | ||| | | |||| |||       |||| |  || || ||| ||   |  |                     
GGAGTTGAAGGCTGAAAGAGTATCCAAGTGGCTCTCGCGTCTCGCTGAAAGCCCTGATGTGAAAGCTTTGCCAAATGGTCTTTCAATTGTTCTTAACAAGgtaagctttcttcaaacacttcctgaagctatgatcttttctctgtt-ctatttctgtcatcatgtatctcataagtcgattctaattcctcgatttcttgttcag
















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|5915461|gb|AW053102.1|AW053102
EST:     GTTCAGACGTGAAAGCTCTACCAAACGGTCTTTCGCTGCTCCTTAACAAG                         ATGAATCCTTTGAAGAGGGAGCAGGTCATTGATGGCCTCAGGCAGCTTCTT
genomic: GTTCAGACGTGAAAGCTCTACCAAACGGTCTTTCGCTGCTCCTTAACAAGgtaattttct ... tctggtacagATGAATCCTTTGAAGAGGGAGCAGGTCATTGATGGCCTCAGGCAGCTTCTT
EST: gi|211185925|gb|FL329927.1|FL329927
EST:     GTTCAGACGTGAAAGCTCTACCAAACGGTCTTTCGCTGCTCCTTAACAAG                         ATGAATCCTTTGAAGAGGGAGCAGGTCATTGATGACCTCAGGCAGCTTCTT
genomic: GTTCAGACGTGAAAGCTCTACCAAACGGTCTTTCGCTGCTCCTTAACAAGgtaattttct ... tctggtacagATGAATCCTTTGAAGAGGGAGCAGGTCATTGATGGCCTCAGGCAGCTTCTT
EST: gi|4609505|gb|AI600344.1|AI600344
EST:     GTTCAGACGTGAAAGCTCTACCAAACGGTCTTTCGCTGCTCCTTAACAAG                         ATGAATCCTTTGAAGAGGGAGCAGGTCATTGATGGCCTCAGGCAGCTTNTT
genomic: GTTCAGACGTGAAAGCTCTACCAAACGGTCTTTCGCTGCTCCTTAACAAGgtaattttct ... tctggtacagATGAATCCTTTGAAGAGGGAGCAGGTCATTGATGGCCTCAGGCAGCTTCTT
EST: gi|211121231|gb|FL444932.1|FL444932
EST:     GTTCAGACGTGAAAGCTCTACCAAACGGTCTTTCGCTGCTCCTTAACAAG                         ATGAATCCTTTGAAGAGGGAGCAGGTCATTGATGGCCTCAGGCAGCTTCTT
genomic: GTTCAGACGTGAAAGCTCTACCAAACGGTCTTTCGCTGCTCCTTAACAAGgtaattttct ... tctggtacagATGAATCCTTTGAAGAGGGAGCAGGTCATTGATGGCCTCAGGCAGCTTCTT
EST: gi|5714106|gb|AI944091.1|AI944091
EST:     GTTCAGACGTGAAAGCTCTACCAAACGGTCTTTCGCTGCTCCTTAACAAG                         ATGAATCCTTTGAAGAGGGAGCAGGTCATTGATGGCCTCAGGCAGCTTCTT
genomic: GTTCAGACGTGAAAGCTCTACCAAACGGTCTTTCGCTGCTCCTTAACAAGgtaattttct ... tctggtacagATGAATCCTTTGAAGAGGGAGCAGGTCATTGATGGCCTCAGGCAGCTTCTT
EST: gi|16925530|gb|BM078598.1|BM078598
EST:     GTTCAGACGTGAAAGCTCTACCAAACGGTCTTTCGCTGCTCCTTAACAAG                         ATGAATCCTTTGAAGAGGGAGCAGGTCATTGATGGCCTCAGGCAGCTTCTT
genomic: GTTCAGACGTGAAAGCTCTACCAAACGGTCTTTCGCTGCTCCTTAACAAGgtaattttct ... tctggtacagATGAATCCTTTGAAGAGGGAGCAGGTCATTGATGGCCTCAGGCAGCTTCTT
EST: gi|18177498|gb|BM378708.1|BM378708
EST:     GTTCAGACGTGAAAGCTCTACCAAACGGTCTTTCGCTGCTCCTTAACAAG                         ATGAATCCTTTGAAGAGGGAGCAGGTCATTGATGGCCTCAGGCAGCTTCTT
genomic: GTTCAGACGTGAAAGCTCTACCAAACGGTCTTTCGCTGCTCCTTAACAAGgtaattttct ... tctggtacagATGAATCCTTTGAAGAGGGAGCAGGTCATTGATGGCCTCAGGCAGCTTCTT
EST: gi|6195020|gb|AW147124.1|AW147124
EST:     GTTCAGACGTGAAAGCTCTACCAACCGGTCTTTCGCTGCTCCTTACCAAG                         ATGAATCCTTTGAAGAGGGAGCAGGTCATTGATGGCCTCAGGCAGCTTCTT
genomic: GTTCAGACGTGAAAGCTCTACCAAACGGTCTTTCGCTGCTCCTTAACAAGgtaattttct ... tctggtacagATGAATCCTTTGAAGAGGGAGCAGGTCATTGATGGCCTCAGGCAGCTTCTT
EST: gi|13177904|gb|BG349087.1|BG349087
EST:     GTTCAGACGTGAAAGCTCTACCAAACGGTCTTTCGCTGCTCCTTAACAAG                         ATGAATCCTTTGAAGAGGGAGCAGGTCATTGATGGCCTCAGGCAGCTTCTT
genomic: GTTCAGACGTGAAAGCTCTACCAAACGGTCTTTCGCTGCTCCTTAACAAGgtaattttct ... tctggtacagATGAATCCTTTGAAGAGGGAGCAGGTCATTGATGGCCTCAGGCAGCTTCTT
EST: gi|211270874|gb|FL478604.1|FL478604
EST:     GTTCAGACGTGAAAGCTCTACCAAACGGTCTTTCGCTGCTCCTTAACAAG                         ATGAATCCTTTGAAGAGGGAGCAGGTCATTGATGGCCTCAGGCAGCTTYTT
genomic: GTTCAGACGTGAAAGCTCTACCAAACGGTCTTTCGCTGCTCCTTAACAAGgtaattttct ... tctggtacagATGAATCCTTTGAAGAGGGAGCAGGTCATTGATGGCCTCAGGCAGCTTCTT
EST: gi|33095984|gb|CF055978.1|CF055978
EST:     GTTCAGACGTGAAAGCTCTACCAAACGGTCTTTCGCTGCTCCTTAACAAG                         ATGAATCCTTTGAAGAGGGAGCAGGTCATTGATGGCCTCAGGCAGCTTCTT
genomic: GTTCAGACGTGAAAGCTCTACCAAACGGTCTTTCGCTGCTCCTTAACAAGgtaattttct ... tctggtacagATGAATCCTTTGAAGAGGGAGCAGGTCATTGATGGCCTCAGGCAGCTTCTT
EST: gi|5714112|gb|AI944097.1|AI944097
EST:     GTTCAGACGTGAAAGCTCTACCAAACGGTCTTTCGCTGCTCCTTAACAAG                         ATGAATCCTTTGAAGAGGGAGCAGGTCATTGATGGCCTCAGGCAGCTTCTT
genomic: GTTCAGACGTGAAAGCTCTACCAAACGGTCTTTCGCTGCTCCTTAACAAGgtaattttct ... tctggtacagATGAATCCTTTGAAGAGGGAGCAGGTCATTGATGGCCTCAGGCAGCTTCTT
EST: gi|60397138|gb|DN229954.1|DN229954
EST:     GTTCAGACGTGAAAGCTCTACCAAACGGTCTTTCGCTGCTCCTTAACAAG                         ATGAATCCTTTGAAGAGGGAGCAGGTCATTGATGGCCTCAGGCAGCTTCTT
genomic: GTTCAGACGTGAAAGCTCTACCAAACGGTCTTTCGCTGCTCCTTAACAAGgtaattttct ... tctggtacagATGAATCCTTTGAAGAGGGAGCAGGTCATTGATGGCCTCAGGCAGCTTCTT
EST: gi|60344241|gb|DN211214.1|DN211214
EST:     GTTCAGACGTGAAAGCTCTACCAAACGGTCTTTCGCTGCTCCTTAACAAG                         ATGAATCCTTTGAAGAGGGAGCAGGTCATTGATGGCCTCAGGCAGCTTCTT
genomic: GTTCAGACGTGAAAGCTCTACCAAACGGTCTTTCGCTGCTCCTTAACAAGgtaattttct ... tctggtacagATGAATCCTTTGAAGAGGGAGCAGGTCATTGATGGCCTCAGGCAGCTTCTT
EST: gi|7135830|gb|AW498288.1|AW498288
EST:     GTTCAGACGTGAAAGCTCTACCAAACGGTCTTTCGCTGCTCCTTAACAAG                         ATGAATCCTTTGAAGAGGGAGCAGGTCATTGATGGCCTCAGGCAGCTTCTT
genomic: GTTCAGACGTGAAAGCTCTACCAAACGGTCTTTCGCTGCTCCTTAACAAGgtaattttct ... tctggtacagATGAATCCTTTGAAGAGGGAGCAGGTCATTGATGGCCTCAGGCAGCTTCTT
EST: gi|12968531|gb|BG265477.1|BG265477
EST:     GTTCAGACGTGAAAGCTCTACCAAACGGTCTTTCGCTGCTCCTTAACAAG                         ATGAATCCTTTGAAGAGGGAGCAGGTCATTGATGGCCTCAGGCAGCTTCTT
genomic: GTTCAGACGTGAAAGCTCTACCAAACGGTCTTTCGCTGCTCCTTAACAAGgtaattttct ... tctggtacagATGAATCCTTTGAAGAGGGAGCAGGTCATTGATGGCCTCAGGCAGCTTCTT
EST: gi|113703683|gb|EE681187.1|EE681187
EST:     GTTCAGACGTGAAAGCTCTACCAAACGGTCTTTCGCTGCTCCTTAACAAG                         ATGAATCCTTTGAAGAGGGAGCAGGTCATTGATGGCCTCAGGCAGCTTCTT
genomic: GTTCAGACGTGAAAGCTCTACCAAACGGTCTTTCGCTGCTCCTTAACAAGgtaattttct ... tctggtacagATGAATCCTTTGAAGAGGGAGCAGGTCATTGATGGCCTCAGGCAGCTTCTT
EST: gi|37385646|gb|CF629976.1|CF629976
EST:     GTTCAGACGTGAAAGCTCTACCAAACGGTCTTTCGCTGCTCCTTAACAAG                         ATGAATCCTTTGAAGAGGGAGCAGGTCATTGATGGCCTCAGGCAGCTTCTT
genomic: GTTCAGACGTGAAAGCTCTACCAAACGGTCTTTCGCTGCTCCTTAACAAGgtaattttct ... tctggtacagATGAATCCTTTGAAGAGGGAGCAGGTCATTGATGGCCTCAGGCAGCTTCTT
EST: gi|40303405|gb|CK347792.1|CK347792
EST:     GTTCAGACGTGAAAGCTCTACCAAACGGTCTTTCGCTGCTCCTTAACAAG                         ATGAATCCTTTGAAGAGGGAGCAGGTCATT-ATGGCCTCAGGCAGCTTCTT
genomic: GTTCAGACGTGAAAGCTCTACCAAACGGTCTTTCGCTGCTCCTTAACAAGgtaattttct ... tctggtacagATGAATCCTTTGAAGAGGGAGCAGGTCATTGATGGCCTCAGGCAGCTTCTT
EST: gi|33097774|gb|CF057734.1|CF057734
EST:     GTTCAGACGTGAAAGCTCTACCAAACGGTCTTTCGCTGCTCCTTAACAAG                         ATGAATCCTTTGAAGAGGGAGCAGGTCATTGATGGCCTCAGGCAGCTTCTT
genomic: GTTCAGACGTGAAAGCTCTACCAAACGGTCTTTCGCTGCTCCTTAACAAGgtaattttct ... tctggtacagATGAATCCTTTGAAGAGGGAGCAGGTCATTGATGGCCTCAGGCAGCTTCTT
EST: gi|5740341|gb|AI948031.1|AI948031
EST:     GTTCAGACGTGAAAGCTCTACCAAACGGTCTTTCGCTGCTCCTTAACAAG                         ATGAATCCTTTGAAGAGGGACCAGGTCATTGATGGCCTCAGGCAGCTTCTT
genomic: GTTCAGACGTGAAAGCTCTACCAAACGGTCTTTCGCTGCTCCTTAACAAGgtaattttct ... tctggtacagATGAATCCTTTGAAGAGGGAGCAGGTCATTGATGGCCTCAGGCAGCTTCTT
EST: gi|78022421|gb|DV490808.1|DV490808
EST:     GTTCAGACGTGAAAGCTCTACCAAACGGTCTTTCGCTGCTCCTTAACAAG                         ATGAATCCTTTGAAGAGGGAGCAGGTCATTGATGGCCTCAGGCAGCTTCTT
genomic: GTTCAGACGTGAAAGCTCTACCAAACGGTCTTTCGCTGCTCCTTAACAAGgtaattttct ... tctggtacagATGAATCCTTTGAAGAGGGAGCAGGTCATTGATGGCCTCAGGCAGCTTCTT
EST: gi|71770490|gb|DR968427.1|DR968427
EST:     GTTCAGACGTGAAAGCTTTACCAAACGGTCTTTCGCTGCTCCTTAACAAG                         ATGAATCCTTTGAAGAGGGAGCAGGTCATTGATGGCCTCAGGCAGCTTCTT
genomic: GTTCAGACGTGAAAGCTCTACCAAACGGTCTTTCGCTGCTCCTTAACAAGgtaattttct ... tctggtacagATGAATCCTTTGAAGAGGGAGCAGGTCATTGATGGCCTCAGGCAGCTTCTT
EST: gi|113703526|gb|EE681030.1|EE681030
EST:     GTTCAGACGTGAAAGCTCTACCAAACGGTCTTTCGCTGCTCCTTAACAAG                         ATGAATCCTTTGAAGAGGGAGCAGGTCATTGATGGCCTCAGGCAGCTTCTT
genomic: GTTCAGACGTGAAAGCTCTACCAAACGGTCTTTCGCTGCTCCTTAACAAGgtaattttct ... tctggtacagATGAATCCTTTGAAGAGGGAGCAGGTCATTGATGGCCTCAGGCAGCTTCTT
EST: gi|16926000|gb|BM079068.1|BM079068
EST:     GTTCAGACGTGAAAGCTCTACCAAACGGTCTTTCGCTGCTCCTTAACAAG                         ATGAATCCTTTGAAGAGGGAGCAGGTCATTGATGGCCTCAGGCAGCTTCTT
genomic: GTTCAGACGTGAAAGCTCTACCAAACGGTCTTTCGCTGCTCCTTAACAAGgtaattttct ... tctggtacagATGAATCCTTTGAAGAGGGAGCAGGTCATTGATGGCCTCAGGCAGCTTCTT

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: 46 (upstream exon), 45 (downstream exon)
Score: 84

GGAGTTGAAGGCTGAAAGAGTATCGAACTGGTTCTCGCATCTTGCTGAAAGTTCAGACGTGAAAGCTCTACCAAACGGTCTTTCGCTGCTCCTTAACAAGgtaattttct ... tctggtacagATGAATCCTTTGAAGAGGGAGCAGGTCATTGATGGCCTCAGGCAGCTTCTTGGTTGATCGATGGTGGCAAAGTGGAGCATGAAGCCCTGTTTAGTTGGGA


Block sizes: 46 (upstream exon), 43 (downstream exon)
Score: 84

GGAGTTGAAGGCTGAAAGAGTATCGAACTGGTTCTCGCATCTTGCTGAAAGTTCAGACGTGAAAGCTCTACCAAACGGTCTTTCGCTGCTCCTTAACAAGgtaattttct ... tctggtacagATGAATCCTTTGAAGAGGGAGCAGGTCATTGATGGCCTCAGGCAGCTTCTTGGTTGATCGATGGTGGCAAAGTGGAGCATGAAGCCCTGTTTAGTTGGGA


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 32

GGAGTTGAAGGCTGAAAGAGTATCGAACTGGTTCTCGCATCTTGCTGAAAGTTCAGACGTGAAAGCTCTACCAAACGGTCTTTCGCTGCTCCTTAACAAGgtaattttct ... tctggtacagATGAATCCTTTGAAGAGGGAGCAGGTCATTGATGGCCTCAGGCAGCTTCTTGGTTGATCGATGGTGGCAAAGTGGAGCATGAAGCCCTGTTTAGTTGGGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 449

GGAGTTGAAGGCTGAAAGAGTATCGAACTGGTTCTCGCATCTTGCTGAAAGTTCAGACGTGAAAGCTCTACCAAACGGTCTTTCGCTGCTCCTTAACAAGgtaattttct ... tctggtacagATGAATCCTTTGAAGAGGGAGCAGGTCATTGATGGCCTCAGGCAGCTTCTTGGTTGATCGATGGTGGCAAAGTGGAGCATGAAGCCCTGTTTAGTTGGGA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAGTTGAAGGCTGAAAGAGTATCGAACTGGTTCTCGCATCTTGCTGAAAGTTCAGACGTGAAAGCTCTACCAAACGGTCTTTCGCTGCTCCTTAACAAGgtaattttctttctaccttgaggaaaccttatttttgtttctaagatcaacatcctaaattcttaattctggtacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT