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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataattatagtattctatatttttcttactgcaatatatatggttttgttagaactatccaatagttgttaatgattattttttttgcttccagGGAATGATTCTCTTGTGGGATACTGATTCCGGGCTCGCTCAGCTTGACAAGTACTTGCATAGTAATGATACTCATGTTGTTGCTGGAGCTTTGCTAGGTA

Basic information

species Zea mays
transcript GRMZM2G155384_T01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G155384_T03 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os02g05340.1 (Oryza sativa), 3'ss of exon 14
-------gtataattat-agtattctatatttttcttactgcaat-atatatggttttgttagaactatccaatagttgt--taatgattattttttttgcttccagGGAATGATTCTCTTGTGGGATACTGATTCCGGGCTCGCTCAGCTTGACAAGTACTTGCATAGTAATGATACTCATGTTGTTGCTGGAGCTTTGCTAGGTA
         ||  ||||   ||||  | |   |    |   || | | |  ||  ||  |||  |||   ||| | |  |   ||   |  | |||     || |||||||||||||||||||||||||||||||| || || |||||||||||||||||||| |||||||||||| ||||||||||||||||||||||||||||||
gtaagttacattgttattgatatttgacaaactctacaaaccattgacaactgagttcttta--actggtcaacaataataacaaaagtactgtttcaccttttcagGGAATGATTCTCTTGTGGGATACTGATTCTGGACTTGCTCAGCTTGACAAGTACTTACATAGTAATGATGCTCATGTTGTTGCTGGAGCTTTGCTAGGTA

upper sequence: GRMZM2G155384_T03 (Zea mays), 3'ss of exon 14
lower sequence: GLYMA06G44340.1 (Glycine max), 3'ss of exon 14
gtataattatagtattctatatttttcttactgcaatatatatggttt-tgttagaactatccaatagttgttaatgattattttttttgcttccagGGAATGATTCTCTTGTGGGATACTGATTCCGGGCTCGCTCAGCTTGACAAGTACTTGCATAGTAATGATACTCATGTTGTTGCTGGAGCTTTGCTAGGTA
           ||||   || || ||   |   |||| | | |  |   || | | || ||  ||   |  ||  | |   |  | | |  |  ||||| |||||| |  | ||||||  ||| || || || |||||  ||||||||||||| ||||||||||||| ||||||  ||||||| || || || ||  
-----------gtatga-attttcttaccaaaacaatttttcttatccgtggttggaccatataaatttcatttttaagactagtgtatcatgacagGGTATGATTTTACTCTGGGATGTTGACTCGGGACTTGCTCAAATTGACAAGTACTTCCATAGTAATGATAATCATGTCATTGCTGGTGCATTACTGGGAG

upper sequence: GRMZM2G155384_T03 (Zea mays), 3'ss of exon 14
lower sequence: GLYMA12G13410.1 (Glycine max), 3'ss of exon 14
gtataattatagtattctatatttttcttactgcaatatatatggttttgttagaactatccaatagttgttaatgattattttttttgcttccagGGAATGATTCTCTTGTGGGATACTGATTCCGGGCTCGCTCAGCTTGACAAGTACTTGCATAGTAATGATACTCATGTTGTTGCTGGAGCTTTGCTAGGTA
           |||     | | || |  |    ||| |   |     ||   | || ||  ||   |  || |  |   |  | | |  |  ||||| |||||| |  | ||||||  ||| || || || |||||  ||||||||||||| ||||||||||||| ||||||  ||||||| || || || ||| 
-----------gtacgaattttcttaccaaaacaaattttcttatccatgggtgtaccatataaatttcatttacaacactagtgtatcatgacagGGTATGATTTTACTCTGGGATGTTGACTCGGGACTTGCTCAAATTGACAAGTACTTCCATAGTAATGATAATCATGTCATTGCTGGTGCATTACTGGGTG

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|33093842|gb|CF053836.1|CF053836
EST:     GGTTATTCAAGAACAAGGAACATGGAAAAGCTAGTGCAGCAGCTAGTCTG                         GGAATGATTCTCTTGTGGGATACTGATTCCCGGCCCGCTCAGCTTGACAAG
genomic: GGTTATTCAAGAACAAGGAACATGGAAAAGCTAGTGCAGCAGCTAGTCTGgtataattat ... ttgcttccagGGAATGATTCTCTTGTGGGATACTGATTCCGGGCTCGCTCAGCTTGACAAG
EST: gi|32934754|gb|CF039566.1|CF039566
EST:     GGTTATTCAAGAACAAGGAACATGGAAAAGCTAGTGCAGCAGCTAGTCTG                         GGAATGATTCTCTTGTGGGATACTGATTCCGGGCTCGCTCAACTTGACAAG
genomic: GGTTATTCAAGAACAAGGAACATGGAAAAGCTAGTGCAGCAGCTAGTCTGgtataattat ... ttgcttccagGGAATGATTCTCTTGTGGGATACTGATTCCGGGCTCGCTCAGCTTGACAAG
EST: gi|32834497|gb|CD974175.1|CD974175
EST:     GGTTATTCAAGAACAAGGAACATGGAAAAGCTAGTGCAGCAGCTAGTCTG                         GGAATGATTCTCTTGTGGGATACTGATTCCGGGCTCGCTCAGCTTGACAAG
genomic: GGTTATTCAAGAACAAGGAACATGGAAAAGCTAGTGCAGCAGCTAGTCTGgtataattat ... ttgcttccagGGAATGATTCTCTTGTGGGATACTGATTCCGGGCTCGCTCAGCTTGACAAG
EST: gi|32833976|gb|CD973654.1|CD973654
EST:     GGTTATTCAAGAACAAGGAACATGGAAAAGCTAGTGCAGCAGCTAGTCTG                         GGAATGATTCTCTTGTGGGATACTGATTCCGGGCTCGCTCAGCTTGACAAG
genomic: GGTTATTCAAGAACAAGGAACATGGAAAAGCTAGTGCAGCAGCTAGTCTGgtataattat ... ttgcttccagGGAATGATTCTCTTGTGGGATACTGATTCCGGGCTCGCTCAGCTTGACAAG

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), 48 (downstream exon)
Score: 336

GTTGATGACCGCTCCATCTGATTCATCCAGCAGCGGGTCTTCCGGAAATTGGTTATTCAAGAACAAGGAACATGGAAAAGCTAGTGCAGCAGCTAGTCTGgtataattat ... ttgcttccagGGAATGATTCTCTTGTGGGATACTGATTCCGGGCTCGCTCAGCTTGACAAGTACTTGCATAGTAATGATACTCATGTTGTTGCTGGAGCTTTGCTAGGTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 229

GTTGATGACCGCTCCATCTGATTCATCCAGCAGCGGGTCTTCCGGAAATTGGTTATTCAAGAACAAGGAACATGGAAAAGCTAGTGCAGCAGCTAGTCTGgtataattat ... ttgcttccagGGAATGATTCTCTTGTGGGATACTGATTCCGGGCTCGCTCAGCTTGACAAGTACTTGCATAGTAATGATACTCATGTTGTTGCTGGAGCTTTGCTAGGTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 149

GTTGATGACCGCTCCATCTGATTCATCCAGCAGCGGGTCTTCCGGAAATTGGTTATTCAAGAACAAGGAACATGGAAAAGCTAGTGCAGCAGCTAGTCTGgtataattat ... ttgcttccagGGAATGATTCTCTTGTGGGATACTGATTCCGGGCTCGCTCAGCTTGACAAGTACTTGCATAGTAATGATACTCATGTTGTTGCTGGAGCTTTGCTAGGTA


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

GTTGATGACCGCTCCATCTGATTCATCCAGCAGCGGGTCTTCCGGAAATTGGTTATTCAAGAACAAGGAACATGGAAAAGCTAGTGCAGCAGCTAGTCTGgtataattat ... ttgcttccagGGAATGATTCTCTTGTGGGATACTGATTCCGGGCTCGCTCAGCTTGACAAGTACTTGCATAGTAATGATACTCATGTTGTTGCTGGAGCTTTGCTAGGTA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atggttttgttagaactatccaatagttgttaatgattattttttttgcttccagGGAATGATTCTCTTGTGGGATACTGATTCCGGGCTCGCTCAGCTTGACAAGTACTTGCATAGTAATGATACTCATGTTGTTGCTGGAGCTTTGCTAGGTA
                           tgttaat  putative branch site (score: 214)
                                    ttattttttttgcttc  putative PPT
                     aatagttgttaatgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtataattatagtattctatatttttcttactgcaatatatatggttttgttagaactatccaatagttgttaatgattattttttttgcttccagGGAATGATTCTCTTGTGGGATACTGATTCCGGGCTCGCTCAGCTTGACAAGTACTTGCATAGTAATGATACTCATGTTGTTGCTGGAGCTTTGCTAGGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT