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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtttttattttagctgcagtcttgagttcttggttgcaaggcctacactgtaaattgagataccctacttacgttttttatttgtatgtttttccagGCACTTGCTCAAATGAAGTCAATAAACTTGTTAGGAGTCCAGCAAATATGCAGGAATTCGATAGCTCTGGAACAG

Basic information

species Zea mays
transcript GRMZM2G327394_T01
intron # 22
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G327394_T01 (Zea mays), 3'ss of exon 22
lower sequence: LOC_Os08g22864.2 (Oryza sativa), 3'ss of exon 21
--gtttgtttttatt--ttagctgcagtcttgagttcttggttgcaaggcctacactgtaaattgagataccctacttacgttttttatttgtatgtttttccagGCACTTGCTCAAATGAAGTCAATAAACTTGTTAGGAGTCCAGCAAATATGCAGGAATTCGATAGCTCTGGAACAG
  |  ||  |  |||   ||  |   |     |    |||||| |  ||  |||  || | |||      | || || || |   || |  | |   |||| |||||||| ||||| |||||||| || || |||||||| ||||| ||||||||||| ||||| ||||| || ||||||
ctgactgcctcgattagctaattaaggctggtacggtttggtttcttgg--tactatg-atattcttgctcactgctaacttgaattgt--gaaatatttttcagGCACTCGCTCAGATGAAGTCGATCAATTTGTTAGGGGTCCAACAAATATGCAGAAATTCTATAGCACTAGAACAG
















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|113700911|gb|EE678415.1|EE678415
EST:     ATTACATATTTGGTGGGATTTCCAGTGTTGCTGCTAATGCATCAATAAAG                         GCACTTGCTCAAATGAAGTCAATAAACTTGTTAGGAGTCCAGCAAATATGC
genomic: ATTACATATTTGGTGGGATTTCCAGTGTTGCTGCTAATGCATCAATAAAGgtttgttttt ... gtttttccagGCACTTGCTCAAATGAAGTCAATAAACTTGTTAGGAGTCCAGCAAATATGC




















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: 114

TGCACGACGGGATGAAGAAATGGCTCCTTATATCACGGAATCAGAAAGGAATTACATATTTGGTGGGATTTCCAGTGTTGCTGCTAATGCATCAATAAAGgtttgttttt ... gtttttccagGCACTTGCTCAAATGAAGTCAATAAACTTGTTAGGAGTCCAGCAAATATGCAGGAATTCGATAGCTCTGGAACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 141

TGCACGACGGGATGAAGAAATGGCTCCTTATATCACGGAATCAGAAAGGAATTACATATTTGGTGGGATTTCCAGTGTTGCTGCTAATGCATCAATAAAGgtttgttttt ... gtttttccagGCACTTGCTCAAATGAAGTCAATAAACTTGTTAGGAGTCCAGCAAATATGCAGGAATTCGATAGCTCTGGAACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 94

TGCACGACGGGATGAAGAAATGGCTCCTTATATCACGGAATCAGAAAGGAATTACATATTTGGTGGGATTTCCAGTGTTGCTGCTAATGCATCAATAAAGgtttgttttt ... gtttttccagGCACTTGCTCAAATGAAGTCAATAAACTTGTTAGGAGTCCAGCAAATATGCAGGAATTCGATAGCTCTGGAACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 123

TGCACGACGGGATGAAGAAATGGCTCCTTATATCACGGAATCAGAAAGGAATTACATATTTGGTGGGATTTCCAGTGTTGCTGCTAATGCATCAATAAAGgtttgttttt ... gtttttccagGCACTTGCTCAAATGAAGTCAATAAACTTGTTAGGAGTCCAGCAAATATGCAGGAATTCGATAGCTCTGGAACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctacactgtaaattgagataccctacttacgttttttatttgtatgtttttccagGCACTTGCTCAAATGAAGTCAATAAACTTGTTAGGAGTCCAGCAAATATGCAGGAATTCGATAGCTCTGGAACAG
                       tacttac  putative branch site (score: 123)
                                            tgtttttcc  putative PPT
                               ttttttatttgtatgt  TA-rich tract