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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactccattgctaggatacaattttatcttggtcaatttatgctattgagaagaattcctcccccttactgtgggttatttgccaaatccagTCTGCACTTCTGAAGAAGGCTGAAGACGCTGAGATTGACACAGCAGAGCAAAGTGCTATAAAGCTACGCAGTCAGCAACAAACTTCCAGTGCTCTTGTTG

Basic information

species Zea mays
transcript GRMZM2G092741_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G092741_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g02150.2 (Oryza sativa), 3'ss of exon 17
-----------------------------------------------------------------------------------------------------gtaactccattgctaggatacaattttatct-tggtcaatttatgctattgagaagaattcctcccccttactgtgggtt-atttgccaaatcc-agTCTGCACTTCTGAAGAAGGCTGAAGACGCTGAGATTGACACAGCAGAGCAAAGTGCTATAAAGCTACGCAGTCAGCAACAAACTTCCAGTGCTCTTGTTG
                                                                                                       |  |  | |   |   ||| || | |  | |  |  |||  | | ||| | ||  |||  |    |||||| ||| || | ||| | ||||  ||||||| ||  |||||||||||||||| |||||| ||||||||||||||||||||||||||||  |||| |||||||||||||| || |||||| ||||  
gtaaattttcatcctgttgcatgtatactcacagtttacggtattaaatcttcttctagccacatatattctcacactttagtgtatgaaatctgcatcttacatgtgtactctcaatttactatataacttatcttgcattcgttccattaacaatgatttgtttttcttactatggatttacttgtcgaatcttagTCTGCTCTGTTGAAGAAGGCTGAAGATGCTGAGGTTGACACAGCAGAGCAAAGTGCTATAAAATTACGAAGTCAGCAACAAACATCGAGTGCTATTGTCA
















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|32835885|gb|CD975563.1|CD975563
EST:     CCCTGAGCGTGAG                         TCTGCACTTCTGAAGAAGGCTGAAGACGCTGAGATTGACACAGCAGAGCAN
genomic: CCCTGAGCGTGAGgtaactccat ... ccaaatccagTCTGCACTTCTGAAGAAGGCTGAAGACGCTGAGATTGACACAGCAGAGCAA




















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), 49 (downstream exon)
Score: 300

TGAAATACAACAGAGAGCAGTTGAGTATTTTGAACTAAGCAGGAAAGGCCCTGCTTTGGCAGATGTGTTGGCTGAAATGCCAAAATTCCCTGAGCGTGAGgtaactccat ... ccaaatccagTCTGCACTTCTGAAGAAGGCTGAAGACGCTGAGATTGACACAGCAGAGCAAAGTGCTATAAAGCTACGCAGTCAGCAACAAACTTCCAGTGCTCTTGTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 252

TGAAATACAACAGAGAGCAGTTGAGTATTTTGAACTAAGCAGGAAAGGCCCTGCTTTGGCAGATGTGTTGGCTGAAATGCCAAAATTCCCTGAGCGTGAGgtaactccat ... ccaaatccagTCTGCACTTCTGAAGAAGGCTGAAGACGCTGAGATTGACACAGCAGAGCAAAGTGCTATAAAGCTACGCAGTCAGCAACAAACTTCCAGTGCTCTTGTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 330

TGAAATACAACAGAGAGCAGTTGAGTATTTTGAACTAAGCAGGAAAGGCCCTGCTTTGGCAGATGTGTTGGCTGAAATGCCAAAATTCCCTGAGCGTGAGgtaactccat ... ccaaatccagTCTGCACTTCTGAAGAAGGCTGAAGACGCTGAGATTGACACAGCAGAGCAAAGTGCTATAAAGCTACGCAGTCAGCAACAAACTTCCAGTGCTCTTGTTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 198

TGAAATACAACAGAGAGCAGTTGAGTATTTTGAACTAAGCAGGAAAGGCCCTGCTTTGGCAGATGTGTTGGCTGAAATGCCAAAATTCCCTGAGCGTGAGgtaactccat ... ccaaatccagTCTGCACTTCTGAAGAAGGCTGAAGACGCTGAGATTGACACAGCAGAGCAAAGTGCTATAAAGCTACGCAGTCAGCAACAAACTTCCAGTGCTCTTGTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatgctattgagaagaattcctcccccttactgtgggttatttgccaaatccagTCTGCACTTCTGAAGAAGGCTGAAGACGCTGAGATTGACACAGCAGAGCAAAGTGCTATAAAGCTACGCAGTCAGCAACAAACTTCCAGTGCTCTTGTTG
                         cccttac  putative branch site (score: 198)
                                      ttattt  TA-rich tract