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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcattggactttgtggtttgccaaatccactatcaaatatactgtttcttaagaacattaaaatccgattgatatgtcatataatttgcctcttaaatatatttcctttgcagGTCTCTCGGTTGAGGCTTCTAGGGGATAATGTACATTCCACAAGGATTGCTTTTGTTGAATTTGTCCAT

Basic information

species Zea mays
transcript GRMZM2G051043_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G051043_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os01g11120.1 (Oryza sativa), 3'ss of exon 7
gtgagcattggactttgtggtttgccaaatccactatcaaatatactgtt-tcttaagaacattaaaatccgattgatatgtcata----taatttgcc-tcttaaatatatttcctttgcagGTCTCTCGGTTGAGGCTTCTAGGGGATAATGTACATTCCACAAGGATTGCTTTTGTTGAATTTGTCCAT
                      |      | | |||  |  | ||||||  | ||    | | | || |     |||| || || |    |||| ||   | | |||||| ||  |||||||||||||||| ||||| ||||||||||||||||||||||| |||||||||||||||||||| |||||||||
---------------------ctctttttttccctagtagctgtactgtcatattttatatagtgaatt--agctgatctggcacaaacctaatatgttgtataaaatatgttctctttgcagGTCTCTCGTTTGAGACTTCTAGGGGATAATGTACATTCTACAAGGATTGCTTTTGTTGAGTTTGTCCAT
















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|5058613|gb|AI737089.1|AI737089
EST:     GTTACTCAGTTAGATGTAAAGAAATTCTTTGAAGAACTTTGCGGTGAG                         GTCTCTCGGTTGAGGCTTCTAGGGGATAATGTACATTCCACAAGGATTGCT
genomic: GTTACTCAGTTAGATGTAAAGAAATTCTTTGAAGAACTTTGCGGTGAGgtgagcattg ... tcctttgcagGTCTCTCGGTTGAGGCTTCTAGGGGATAATGTACATTCCACAAGGATTGCT
EST: gi|78180075|gb|DV550448.1|DV550448
EST:     GTTACTCAGTTAGATGTAAAGAAATTCTTTGAAGAACTTTGCGGTGAG                         GTCTCTCGGTTGAGGCTTCTAGGGGATAATGTACATTCCACAAGGATTGCT
genomic: GTTACTCAGTTAGATGTAAAGAAATTCTTTGAAGAACTTTGCGGTGAGgtgagcattg ... tcctttgcagGTCTCTCGGTTGAGGCTTCTAGGGGATAATGTACATTCCACAAGGATTGCT
EST: gi|108823990|gb|EC277998.1|EC277998
EST:     GTTACTCAGTTAGATGTAAAGAAATTCTTTGAAGAACTTTGCGGTGAG                         GTCTCTCGGTTGAGGCTTCTAGGGGATAATGTACATTCCACAAGGATTGCT
genomic: GTTACTCAGTTAGATGTAAAGAAATTCTTTGAAGAACTTTGCGGTGAGgtgagcattg ... tcctttgcagGTCTCTCGGTTGAGGCTTCTAGGGGATAATGTACATTCCACAAGGATTGCT
EST: gi|108953255|gb|EC364659.1|EC364659
EST:     GTTACTCAGTTAGATGTAAAGAAATTCTTTGAAGAACTTTGCGGTGAG                         GTCTCTCGGTTGAAGCTTCTAGGGGGATAATGT
genomic: GTTACTCAGTTAGATGTAAAGAAATTCTTTGAAGAACTTTGCGGTGAGgtgagcattg ... tcctttgcagGTCTCTCGGTTGAGGCTTCTAGGGG-ATAATGT
EST: gi|61236519|gb|DN586269.1|DN586269
EST:     GTTACTCAGTTAGATGTAAAGAAATTCTTTGAAGAACTTTGCGGTGAG                         GTCTCTCGGTTGAGGCTTCTAGGGGATAATGTACATTCCACAAGGATTGCT
genomic: GTTACTCAGTTAGATGTAAAGAAATTCTTTGAAGAACTTTGCGGTGAGgtgagcattg ... tcctttgcagGTCTCTCGGTTGAGGCTTCTAGGGGATAATGTACATTCCACAAGGATTGCT
EST: gi|12046008|gb|BF728043.1|BF728043
EST:     GTTACTCAGTTAGATGTAAAGAAATTCTTTGAAGAACTTTGCGGTGAG                         GTCTCTCGGTTGAGGCTTCTAGGGGATAATGTACATTCCACAAGGATTGCT
genomic: GTTACTCAGTTAGATGTAAAGAAATTCTTTGAAGAACTTTGCGGTGAGgtgagcattg ... tcctttgcagGTCTCTCGGTTGAGGCTTCTAGGGGATAATGTACATTCCACAAGGATTGCT
EST: gi|28983351|gb|BQ538610.2|BQ538610
EST:     TTTGAAGAACTTTACGGTGAG                         GTCTCTCGGTTGAGGCTTCTAGGGGATAATGTACATTCCACAAGGATTGCT
genomic: TTTGAAGAACTTTGCGGTGAGgtgagcattg ... tcctttgcagGTCTCTCGGTTGAGGCTTCTAGGGGATAATGTACATTCCACAAGGATTGCT
EST: gi|38502629|gb|CF972489.1|CF972489
EST:     GTTACTCAGTTAGATGTAAAGAAATTCTTTGAAGAACTTTGCGGTGAG                         GTCTCTCGGTTGAGGCTTCTAGGGGATAATGTACATTCCACAAGGATTGCT
genomic: GTTACTCAGTTAGATGTAAAGAAATTCTTTGAAGAACTTTGCGGTGAGgtgagcattg ... tcctttgcagGTCTCTCGGTTGAGGCTTCTAGGGGATAATGTACATTCCACAAGGATTGCT
EST: gi|4730460|gb|AI649626.1|AI649626
EST:     GTTACTCAGTTAGATGTAAAGAAATTCTTTGAAGAACTTTGCGGTGAG                         GTCTCTCGGTTGAGGCTTCTAGGGGATAATGTACATTCCACAAG
genomic: GTTACTCAGTTAGATGTAAAGAAATTCTTTGAAGAACTTTGCGGTGAGgtgagcattg ... tcctttgcagGTCTCTCGGTTGAGGCTTCTAGGGGATAATGTACATTCCACAAG
EST: gi|33771172|gb|CF272833.1|CF272833
EST:     GTTACTCAGTTAGATGTAAAGAAATTCTTTGAAGAACTTTGCGGTGAG                         GTCTCTCGGTTGAGGCTTCTAGGGGATAATGTACATTCCACAAGGATTGCT
genomic: GTTACTCAGTTAGATGTAAAGAAATTCTTTGAAGAACTTTGCGGTGAGgtgagcattg ... tcctttgcagGTCTCTCGGTTGAGGCTTCTAGGGGATAATGTACATTCCACAAGGATTGCT
EST: gi|6827432|gb|AW331075.1|AW331075
EST:     GTTACTCAGTTAGATGTAAAGAAATTCTTTGAAGAACTTTGCGGTGAG                         GTCTCTCGGTTGAGGCTTCTAGGGGATAATGTACATTCCACAAGGATTGCT
genomic: GTTACTCAGTTAGATGTAAAGAAATTCTTTGAAGAACTTTGCGGTGAGgtgagcattg ... tcctttgcagGTCTCTCGGTTGAGGCTTCTAGGGGATAATGTACATTCCACAAGGATTGCT

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: 138

GTTACTCAGTTAGATGTAAAGAAATTCTTTGAAGAACTTTGCGGTGAGgtgagcattg ... tcctttgcagGTCTCTCGGTTGAGGCTTCTAGGGGATAATGTACATTCCACAAGGATTGCTTTTGTTGAATTTGTCCAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 116

GTTACTCAGTTAGATGTAAAGAAATTCTTTGAAGAACTTTGCGGTGAGgtgagcattg ... tcctttgcagGTCTCTCGGTTGAGGCTTCTAGGGGATAATGTACATTCCACAAGGATTGCTTTTGTTGAATTTGTCCAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 206

GTTACTCAGTTAGATGTAAAGAAATTCTTTGAAGAACTTTGCGGTGAGgtgagcattg ... tcctttgcagGTCTCTCGGTTGAGGCTTCTAGGGGATAATGTACATTCCACAAGGATTGCTTTTGTTGAATTTGTCCAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 144

GTTACTCAGTTAGATGTAAAGAAATTCTTTGAAGAACTTTGCGGTGAGgtgagcattg ... tcctttgcagGTCTCTCGGTTGAGGCTTCTAGGGGATAATGTACATTCCACAAGGATTGCTTTTGTTGAATTTGTCCAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaaatccgattgatatgtcatataatttgcctcttaaatatatttcctttgcagGTCTCTCGGTTGAGGCTTCTAGGGGATAATGTACATTCCACAAGGATTGCTTTTGTTGAATTTGTCCAT
        gattgat  putative branch site (score: 144)
                                         tatttccttt  putative PPT
                                  ttaaatatatttcctt  TA-rich tract