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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatattttcagagaatgtaaccacagtcaccatattagatctatgctttcttttgatgtttatccatttttctttcacgacactagCTTACATATGCTCTATATTGAAGAACCAAAGGTGCTGATCAGCGGCAACGATTTCTATGCATTTCCTCGCATTGATCAAAATAAAAAGCGGATAGCATGG

Basic information

species Zea mays
transcript GRMZM2G120302_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G120302_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os06g11180.1 (Oryza sativa), 3'ss of exon 4
gtaatattttcagagaatgtaaccacagtcaccatattagatctatgc-------tttcttttgatgtt----tatccatttttctttcacgacactagCTTACATATGCTCTATATTGAAGAACCAAAGGTGCTGATCAGCGGCAACGATTTCTATGCATTTCCTCGCATTGATCAAAATAAAAAGCGGATAGCATGG-----------------------
|||| | | |  || |   | |  ||  |||| |  ||| |||||||        || ||| | || ||    ||||   |||| ||  | || | |        | |  ||| |||||||||||||||||||||||| || ||||| || |||||||| |||||||| ||||| || ||||| ||||| || ||||||                       
gtaagactatacgaaatgtttataactttcacaaagttaaatctatgtgtgcgtgttgcttgtaattttctcatatctgctttttttgtaaga-attcttactttttttttctgtattgaagAACCAAAGGTGCTGATTAGTGGCAATGACTTCTATGCTTTTCCTCGTATTGACCATAATAACAAGCGTATGGCATGGATAGAGTGGAGTCATCCAAATAT
















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|148964888|gb|EC906051.2|EC906051
EST:     TCCCACCACAACAATTGCTGCTATAAACTTGAGTGGCAGTGATGTTCATG                         CTTACATATGCTCTATATTGAAGAACCAAAGGTGCTGATCAGCGGCAACGA
genomic: TCCCACCACAACAATTGCTGCTATAAACTTGAGTGGCAGTGATGTTCATGgtaatatttt ... acgacactagCTTACATATGCTCTATATTGAAGAACCAAAGGTGCTGATCAGCGGCAACGA




















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 3 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 42 (downstream exon)
Score: 8

ATCGTCGAAAGGATAGCTTGAATCCCACCACAACAATTGCTGCTATAAACTTGAGTGGCAGTGATGTTCATGgtaatatttt ... acgacactagCTTACATATGCTCTATATTGAAGAACCAAAGGTGCTGATCAGCGGCAACGATTTCTATGCATTTCCTCGCATTGATCAAAATAAAAAGCGGATAGCATGG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 12

ATCGTCGAAAGGATAGCTTGAATCCCACCACAACAATTGCTGCTATAAACTTGAGTGGCAGTGATGTTCATGgtaatatttt ... acgacactagCTTACATATGCTCTATATTGAAGAACCAAAGGTGCTGATCAGCGGCAACGATTTCTATGCATTTCCTCGCATTGATCAAAATAAAAAGCGGATAGCATGG


Block sizes: 23 (upstream exon), 44 (downstream exon)
Score: 7

ATCGTCGAAAGGATAGCTTGAATCCCACCACAACAATTGCTGCTATAAACTTGAGTGGCAGTGATGTTCATGgtaatatttt ... acgacactagCTTACATATGCTCTATATTGAAGAACCAAAGGTGCTGATCAGCGGCAACGATTTCTATGCATTTCCTCGCATTGATCAAAATAAAAAGCGGATAGCATGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atattagatctatgctttcttttgatgtttatccatttttctttcacgacactagCTTACATATGCTCTATATTGAAGAACCAAAGGTGCTGATCAGCGGCAACGATTTCTATGCATTTCCTCGCATTGATCAAAATAAAAAGCGGATAGCATGG
                   ttttgat  putative branch site (score: 7)
                               tccatttttctttcac  putative PPT
                                  atttttcttt  TA-rich tract