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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAATCGAGGAAACTGGCAGACGATTCAGAGACACTGTTCTTGCGCTTGGAGGTGGAAAGTCTCCGCTTGAGgtaatggcttctttcaatctcttgggggctgctttgtttcgcagcaagtctgttaaaaaaaatggaattgtgctctgcag

Basic information

species Zea mays
transcript GRMZM2G133919_T01
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G133919_T01 (Zea mays), 5'ss of exon 16
lower sequence: LOC_Os02g58340.1 (Oryza sativa), 5'ss of exon 16
GCAATCGAGGAAACTGGCAGACGATTCAGAGACACTGTTCTTGCGCTTGGAGGTGGAAAGTCTCCGCTTGAGgtaa-----tggcttctttca----atctcttggg--ggctgctttgttt-cgcagcaagtctgt-taaaaaaaatgga----attgtgctctgcag----------------------------------------
||||| |||||||||||||||||||||||||| || || |||||||||||||||||||| ||||| || ||||||      |||   |||| |    ||||||||    || |||||| |||  |||  |||  | | ||||    || |     | |    | ||  |                                        
GCAATTGAGGAAACTGGCAGACGATTCAGAGAAACAGTCCTTGCGCTTGGAGGTGGAAAATCTCCACTCGAGgtaggcttctggtgcctttgacagcatctcttgacatggatgctttatttgtgcaataagcgtatgtaaagggcatagtttgcactaacttatgtggaataagacgacgtacgctaactctggaaatgaaaatgcag
















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|32943210|gb|CF048029.1|CF048029
EST:     GATTCAGAGACACTGTTCTTGCGCTTGGAGGTGGAAAGTCTCCGCTTGAG                         GTGTTCGTTTCATTCCGAGGACGGGAGCCTTCGCCTGAACCACTTCTTAGA
genomic: GATTCAGAGACACTGTTCTTGCGCTTGGAGGTGGAAAGTCTCCGCTTGAGgtaatggctt ... tgctctgcagGTGTTCGTTTCATTCCGAGGACGGGAGCCTTCGCCTGAACCACTTCTTAGA
EST: gi|14243309|gb|BG841007.2|BG841007
EST:     GATTCAGAGACACTGTTCTTGCGCTTGGAGGTGGAAAGTCTCCGCTTGAG                         GTGTTCGTTTCATTCCGAGGACGGGAGCCTTCGCCTGAACCACTTCTTAGA
genomic: GATTCAGAGACACTGTTCTTGCGCTTGGAGGTGGAAAGTCTCCGCTTGAGgtaatggctt ... tgctctgcagGTGTTCGTTTCATTCCGAGGACGGGAGCCTTCGCCTGAACCACTTCTTAGA
EST: gi|5871243|gb|AW017714.1|AW017714
EST:     GATTCAGAGACACTGTTCTTGCGCTTGGAGGTGGAAAGTCTCCGCTTGAG                         GTGTTCGTTTCATTCCGAGGACGGGAGCCTTCGCCTGAACCACTTCTTAGA
genomic: GATTCAGAGACACTGTTCTTGCGCTTGGAGGTGGAAAGTCTCCGCTTGAGgtaatggctt ... tgctctgcagGTGTTCGTTTCATTCCGAGGACGGGAGCCTTCGCCTGAACCACTTCTTAGA
EST: gi|40335046|gb|CK369116.1|CK369116
EST:     GATTCAGAGACACTGTTCTTGCGCTTGGAGGTGGAAAGTCTCCGCTTGAG                         GTGTTCGTTTCATTCCGAGGACGGGAGCCTTCGCCTGAACCACTTCTTAGA
genomic: GATTCAGAGACACTGTTCTTGCGCTTGGAGGTGGAAAGTCTCCGCTTGAGgtaatggctt ... tgctctgcagGTGTTCGTTTCATTCCGAGGACGGGAGCCTTCGCCTGAACCACTTCTTAGA
EST: gi|116824661|gb|EC868295.1|EC868295
EST:     GATTCAGAGACACTGTTCTTGCGCTTGGAGGTGGAAAGTCTCCGCTTGAG                         GTGTTCGTTTCATTCCGAGGACGGGAGCCTTCACCTGAACCACTTCTTAGA
genomic: GATTCAGAGACACTGTTCTTGCGCTTGGAGGTGGAAAGTCTCCGCTTGAGgtaatggctt ... tgctctgcagGTGTTCGTTTCATTCCGAGGACGGGAGCCTTCGCCTGAACCACTTCTTAGA
EST: gi|14244905|gb|BG842843.2|BG842843
EST:     GATTCAGAGACACTGTTCTTGCGCTTGGAGGTGGAAAGTCTCCGCTTGAG                         GTGTTCGTTTCATTCCGAGGACGGGAGCCTTCGCCTGAACCACTTCTTAGA
genomic: GATTCAGAGACACTGTTCTTGCGCTTGGAGGTGGAAAGTCTCCGCTTGAGgtaatggctt ... tgctctgcagGTGTTCGTTTCATTCCGAGGACGGGAGCCTTCGCCTGAACCACTTCTTAGA
EST: gi|6020894|gb|AW065822.1|AW065822
EST:     GATTCAGAGACACTGTTCTTGCGCTTGGAGGTGGAAAGTCTCCGCTTGAG                         GTGTTCGTTTCATTCCGAGGACGGGAGCCTTCGCCTGAACCACTTCTTAGA
genomic: GATTCAGAGACACTGTTCTTGCGCTTGGAGGTGGAAAGTCTCCGCTTGAGgtaatggctt ... tgctctgcagGTGTTCGTTTCATTCCGAGGACGGGAGCCTTCGCCTGAACCACTTCTTAGA
EST: gi|485666|gb|T18736.1|T18736
EST:     GATTCAGAGACACTGTTCTTGCGCTTGGAGGTGGAAAGTCTCCGCTTGAG                         GTGTTCGTTTCATTCCGAGGACGGGAGCCTTCACCTGAACCACTTCTTAGA
genomic: GATTCAGAGACACTGTTCTTGCGCTTGGAGGTGGAAAGTCTCCGCTTGAGgtaatggctt ... tgctctgcagGTGTTCGTTTCATTCCGAGGACGGGAGCCTTCGCCTGAACCACTTCTTAGA
EST: gi|60401020|gb|DN233827.1|DN233827
EST:     GATTCAGAGACACTGTTCTTGCGCTTGGAGGTGGAAAGTCTCCGCTTGAG                         GTGTTCGTTTCATTCCGAGGACGGGAGCCTTCGCCTGAACCACTTCTTAGA
genomic: GATTCAGAGACACTGTTCTTGCGCTTGGAGGTGGAAAGTCTCCGCTTGAGgtaatggctt ... tgctctgcagGTGTTCGTTTCATTCCGAGGACGGGAGCCTTCGCCTGAACCACTTCTTAGA
EST: gi|15499190|gb|BI595703.1|BI595703
EST:     TGCGCTTGGAGGTGGAAAGTCTCCGCTTGAG                         GTGTTCGTTTCATTCCGAGGACGGGAGCCTTCGCCTGAACCACTTCTTAGA
genomic: TGCGCTTGGAGGTGGAAAGTCTCCGCTTGAGgtaatggctt ... tgctctgcagGTGTTCGTTTCATTCCGAGGACGGGAGCCTTCGCCTGAACCACTTCTTAGA
EST: gi|14242856|gb|BG840631.2|BG840631
EST:     GATTCAGAGACACTGTTCTTGCGCTTGGAGGTGGAAAGTCTCCGCTTGAG                         GTGTTCGTTTCATTCCGAGGACGGGAGCCTTCGCCTGAACCACTTCTTAGA
genomic: GATTCAGAGACACTGTTCTTGCGCTTGGAGGTGGAAAGTCTCCGCTTGAGgtaatggctt ... tgctctgcagGTGTTCGTTTCATTCCGAGGACGGGAGCCTTCGCCTGAACCACTTCTTAGA
EST: gi|32909083|gb|CF013895.1|CF013895
EST:     GATTCAGAGACACTGTTCTTGCGCTTGGAGGTGGAAAGTCTCCGCTTGAG                         GTGTTCGTTTCATTCCGAGGACGGGAGCCTTCGCCTGAACCACTTCTTAGA
genomic: GATTCAGAGACACTGTTCTTGCGCTTGGAGGTGGAAAGTCTCCGCTTGAGgtaatggctt ... tgctctgcagGTGTTCGTTTCATTCCGAGGACGGGAGCCTTCGCCTGAACCACTTCTTAGA
EST: gi|37382536|gb|CF628220.1|CF628220
EST:     GATTCAGAGACACTGTTCTTGCGCTTGGAGGTGGAAAGTCTCCGCTTGAG                         GTGTTCGTTTCATTCCGAGGACGGGAGCCTTCGCCTGAACCACTTCTTAGA
genomic: GATTCAGAGACACTGTTCTTGCGCTTGGAGGTGGAAAGTCTCCGCTTGAGgtaatggctt ... tgctctgcagGTGTTCGTTTCATTCCGAGGACGGGAGCCTTCGCCTGAACCACTTCTTAGA
EST: gi|31997605|gb|CD661676.1|CD661676
EST:     GATTCAGAGACACTGTTCTTGCGCTTGGAGGTGGAAAGTCTCCGCTTGAG                         GTGTTCGTTTCATTCCGAGGACGGGAGCCTTCGCCTGAACCACTTCTTAGA
genomic: GATTCAGAGACACTGTTCTTGCGCTTGGAGGTGGAAAGTCTCCGCTTGAGgtaatggctt ... tgctctgcagGTGTTCGTTTCATTCCGAGGACGGGAGCCTTCGCCTGAACCACTTCTTAGA
EST: gi|78021291|gb|DV489678.1|DV489678
EST:     GATTCAGAGACACTGTTCTTGCGCTTGGAGGTGGAAAGTCTCCGCTTGAG                         GTGTTCGTTTCATTCCGAGGACGGGAGCCTTCGCCTGAACCACTTCTTAGA
genomic: GATTCAGAGACACTGTTCTTGCGCTTGGAGGTGGAAAGTCTCCGCTTGAGgtaatggctt ... tgctctgcagGTGTTCGTTTCATTCCGAGGACGGGAGCCTTCGCCTGAACCACTTCTTAGA
EST: gi|40336438|gb|CK370508.1|CK370508
EST:     GATTCAGAGACACTGTTCTTGCGCTTGGAGGTGGAAAGTCTCCGCTTGAG                         GTGTTCGTTTCATTCCGAGGACGGGAGCCTTCGCCTGAACCACTTCTTAGA
genomic: GATTCAGAGACACTGTTCTTGCGCTTGGAGGTGGAAAGTCTCCGCTTGAGgtaatggctt ... tgctctgcagGTGTTCGTTTCATTCCGAGGACGGGAGCCTTCGCCTGAACCACTTCTTAGA
EST: gi|149075397|gb|EE163911.2|EE163911
EST:     GATTCAGAGACACTGTTCTTGCGCTTGGAGGTGGAAAGTCTCCGCTTGAG                         GTGTTCGTTTCATTCCGAGGACGGGAGCCTTCGCCTGAACCACTTCTTAGA
genomic: GATTCAGAGACACTGTTCTTGCGCTTGGAGGTGGAAAGTCTCCGCTTGAGgtaatggctt ... tgctctgcagGTGTTCGTTTCATTCCGAGGACGGGAGCCTTCGCCTGAACCACTTCTTAGA
EST: gi|33097696|gb|CF057656.1|CF057656
EST:     GATTCAGAGACACTGTTCTTGCGCTTGGAGGTGGAAAGTCTCCGCTTGAG                         GTGTTCGTTTCATTCCGAGGACGGGAGCCTTCGCCTGAACCACTTCTTAGA
genomic: GATTCAGAGACACTGTTCTTGCGCTTGGAGGTGGAAAGTCTCCGCTTGAGgtaatggctt ... tgctctgcagGTGTTCGTTTCATTCCGAGGACGGGAGCCTTCGCCTGAACCACTTCTTAGA
EST: gi|213178852|gb|FM187713.1|FM187713
EST:     GATTCAGAGACACTGTTCTTGCGCTTGGAGGTGGAAAGTCTCCGCTTGAG                         GTGTTCGTTTCATTCCGAGGACGGGAGCCTTCGCCTGAACCACTTCTTAGA
genomic: GATTCAGAGACACTGTTCTTGCGCTTGGAGGTGGAAAGTCTCCGCTTGAGgtaatggctt ... tgctctgcagGTGTTCGTTTCATTCCGAGGACGGGAGCCTTCGCCTGAACCACTTCTTAGA
EST: gi|28982897|gb|BQ538418.2|BQ538418
EST:     GATTCAGAGACACTGTTCTTGCGCTTGGAGGTGGAAAGTCTCCGCTTGAG                         GTGTTCGTTTCATTCCGAGGACGGGAGCCTTCGCCTGAACCACTTCTTAGA
genomic: GATTCAGAGACACTGTTCTTGCGCTTGGAGGTGGAAAGTCTCCGCTTGAGgtaatggctt ... tgctctgcagGTGTTCGTTTCATTCCGAGGACGGGAGCCTTCGCCTGAACCACTTCTTAGA
EST: gi|29543522|gb|CB603904.1|CB603904
EST:     GATTCAGAGACACTGTTCTTGCGCTTGGAGGTGGAAAGTCTCCGCTTGAG                         GTGTTCGTTTCATTCCGAGGACGGGAGCCTTCGCCTGAACCACTTCTTAGA
genomic: GATTCAGAGACACTGTTCTTGCGCTTGGAGGTGGAAAGTCTCCGCTTGAGgtaatggctt ... tgctctgcagGTGTTCGTTTCATTCCGAGGACGGGAGCCTTCGCCTGAACCACTTCTTAGA
EST: gi|149009255|gb|EE153869.2|EE153869
EST:     GATTCAGAGACACTGTTCTTGCGCTTGGAGGTGGAAAGTTTCCGCTTGAG                         GTGTTCGTTTCATTCCGAGGACGGGAGCCTTCGCCTGAACCACTTTTTAGA
genomic: GATTCAGAGACACTGTTCTTGCGCTTGGAGGTGGAAAGTCTCCGCTTGAGgtaatggctt ... tgctctgcagGTGTTCGTTTCATTCCGAGGACGGGAGCCTTCGCCTGAACCACTTCTTAGA
EST: gi|14244353|gb|BG842414.2|BG842414
EST:     GATTCAGAGACACTGTTCTTGCGCTTGGAGGTGGAAAGTCTCCGCTTGAG                         GTGTTCGTTTCATTCCGAGGACGGGAGCCTTCGCCTGAACCACTTCTTAGA
genomic: GATTCAGAGACACTGTTCTTGCGCTTGGAGGTGGAAAGTCTCCGCTTGAGgtaatggctt ... tgctctgcagGTGTTCGTTTCATTCCGAGGACGGGAGCCTTCGCCTGAACCACTTCTTAGA
EST: gi|40335258|gb|CK369328.1|CK369328
EST:     GATTCAGAGACACTGTTCTTGCGCTTGGAGGTGGAAAGTCTCCGCTTGAG                         GTGTTCGTTTCATTCCGAGGACGGGAGCCTTCGCCTGAACCACTTCTTAGA
genomic: GATTCAGAGACACTGTTCTTGCGCTTGGAGGTGGAAAGTCTCCGCTTGAGgtaatggctt ... tgctctgcagGTGTTCGTTTCATTCCGAGGACGGGAGCCTTCGCCTGAACCACTTCTTAGA
EST: gi|15589996|gb|BI674612.1|BI674612
EST:     GATTCAGAGACACTGTTCTTGCGCTTGGAGGTGGAAAGTCTCCGCTTGAG                         GTGTTCGTTTCATTCCGAGGACGGGAGCCTTCGCCTGAACCACTTCTTAGA
genomic: GATTCAGAGACACTGTTCTTGCGCTTGGAGGTGGAAAGTCTCCGCTTGAGgtaatggctt ... tgctctgcagGTGTTCGTTTCATTCCGAGGACGGGAGCCTTCGCCTGAACCACTTCTTAGA
EST: gi|71758760|gb|DR956697.1|DR956697
EST:     GATTCAGAGACACTGTTCTTGCGCTGGGAGGGGGAAAGTCTCCGCTTGAG                         GTGTTCGTTTCATTCCGAGGAGGGGAGCCTTCGCCTGAACCACTTCTTAGA
genomic: GATTCAGAGACACTGTTCTTGCGCTTGGAGGTGGAAAGTCTCCGCTTGAGgtaatggctt ... tgctctgcagGTGTTCGTTTCATTCCGAGGACGGGAGCCTTCGCCTGAACCACTTCTTAGA
EST: gi|67022921|gb|CO451670.1|CO451670
EST:     GATTCAGAGACACTGTTCTTGCGCTTGGAGGTGGAAAGTCTCCGCTTGAG                         GTGTTCGTTTCATTCCGAGGACGGGAGCCTTCGCCTGAACCACTTCTTAGA
genomic: GATTCAGAGACACTGTTCTTGCGCTTGGAGGTGGAAAGTCTCCGCTTGAGgtaatggctt ... tgctctgcagGTGTTCGTTTCATTCCGAGGACGGGAGCCTTCGCCTGAACCACTTCTTAGA
EST: gi|110220920|gb|EC902818.1|EC902818
EST:     GATTCAGAGACACTGTTCTTGCGCTTGGAGGTGGAAAGTTTCCGCTTGAG                         GTGTTCGTTTCATTCCGAGGACGGGAGCCTTCGCCTGAACCACTTTTTAGA
genomic: GATTCAGAGACACTGTTCTTGCGCTTGGAGGTGGAAAGTCTCCGCTTGAGgtaatggctt ... tgctctgcagGTGTTCGTTTCATTCCGAGGACGGGAGCCTTCGCCTGAACCACTTCTTAGA
EST: gi|32843192|gb|CD982873.1|CD982873
EST:     GATTCAGGGACACTGTTCTTGCGCTTGGAGGTGGAAAGTCTCCGCTTGAG                         GTGTTCGTTTCATTCCGAGGACGGGAGCCTTCGCCTGAACCACTTCTTAGA
genomic: GATTCAGAGACACTGTTCTTGCGCTTGGAGGTGGAAAGTCTCCGCTTGAGgtaatggctt ... tgctctgcagGTGTTCGTTTCATTCCGAGGACGGGAGCCTTCGCCTGAACCACTTCTTAGA

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), 47 (downstream exon)
Score: 229

GCAATCGAGGAAACTGGCAGACGATTCAGAGACACTGTTCTTGCGCTTGGAGGTGGAAAGTCTCCGCTTGAGgtaatggctt ... tgctctgcagGTGTTCGTTTCATTCCGAGGACGGGAGCCTTCGCCTGAACCACTTCTTAGACAAAACGGCTTGCTTCCTGTTGCTGCCTAGTGCCCCAAAGATTTCTCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 161

GCAATCGAGGAAACTGGCAGACGATTCAGAGACACTGTTCTTGCGCTTGGAGGTGGAAAGTCTCCGCTTGAGgtaatggctt ... tgctctgcagGTGTTCGTTTCATTCCGAGGACGGGAGCCTTCGCCTGAACCACTTCTTAGACAAAACGGCTTGCTTCCTGTTGCTGCCTAGTGCCCCAAAGATTTCTCTG


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 97

GCAATCGAGGAAACTGGCAGACGATTCAGAGACACTGTTCTTGCGCTTGGAGGTGGAAAGTCTCCGCTTGAGgtaatggctt ... tgctctgcagGTGTTCGTTTCATTCCGAGGACGGGAGCCTTCGCCTGAACCACTTCTTAGACAAAACGGCTTGCTTCCTGTTGCTGCCTAGTGCCCCAAAGATTTCTCTG


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 180

GCAATCGAGGAAACTGGCAGACGATTCAGAGACACTGTTCTTGCGCTTGGAGGTGGAAAGTCTCCGCTTGAGgtaatggctt ... tgctctgcagGTGTTCGTTTCATTCCGAGGACGGGAGCCTTCGCCTGAACCACTTCTTAGACAAAACGGCTTGCTTCCTGTTGCTGCCTAGTGCCCCAAAGATTTCTCTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAATCGAGGAAACTGGCAGACGATTCAGAGACACTGTTCTTGCGCTTGGAGGTGGAAAGTCTCCGCTTGAGgtaatggcttctttcaatctcttgggggctgctttgtttcgcagcaagtctgttaaaaaaaatggaattgtgctctgcag

- - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA