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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaccccaaatctaaccttctattcttctgttatgctcctagtcctagatatgttcaggttttcaataataattaggacactaaggaacctgccatctattctcacattaagctattcaaaaatgaaataattttgttctcattcactgcagTTAGAAGGAGAAGCAACTGCACGGGCAATCCGTTTAGCTAAGTTCATCAATACGCCACTGTATGTTGTTCATGTGATGAGCATCGACGCAATGGATGAGA

Basic information

species Zea mays
transcript GRMZM2G020002_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G020002_T03 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g59340.2 (Oryza sativa), 3'ss of exon 8
gtaaccccaaatctaaccttctattcttctgttatgctcctagtcctagatatgtt---cag-------gttttc---aataataattaggaca--ctaaggaacctgccatct------attctcacattaagctattcaaaaatgaa---ataattttg------ttctcattcactgcagTTAGAAGGAGAAGCAACTGCACGGGCAATCCGTTTAGCTAAGTTCATCAATACGCCACTGTATGTTGTTCATGTGATGAGCATCGACGCAATGGATGAGA
||||   || |   |  ||||   | | |||||||||   |    || ||||||||   |||       ||||||    | |||| | | | ||   |   ||||  | ||         |||     |||        |||  | | |   |||   |||      ||||  ||| |||||||| ||||| ||||||||||| |||||||| || ||||| |||||  ||||||| ||| ||||||||||||||||||||||||| || |||||||||||||
gtaatttcacactaactcttcgcatttactgttatgcctatttatcttgatatgttggacagatcaagtgttttcttatacaatattcaagtcaatttggtgaactagacacaccatgaaatttgtgtattttctctcacaaggaaggatagataccattgagctgcttcttgttccctgcagTTGGAAGGGGAAGCAACTGCTCGGGCAATTCGATTAGCCAAGTTTGTCAATACACCATTGTATGTTGTTCATGTGATGAGCATTGATGCAATGGATGAGA
















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|149082368|gb|EE171552.2|EE171552
EST:     ACCTTGGGATAACTGGTCCAGAAGGGCATGCTCTCTCAAGGCCTCCAATT                         TTAGAAGGAGAAGCAACTGCACGGGCAATCCGTTTAGCTAAG
genomic: ACCTTGGGATAACTGGTCCAGAAGGGCATGCTCTCTCAAGGCCTCCAATTgtaaccccaa ... ttcactgcagTTAGAAGGAGAAGCAACTGCACGGGCAATCCGTTTAGCTAAG
EST: gi|18659090|gb|BM500149.1|BM500149
EST:     ACCTTGGGATAACTGGTCCAGAAGGGCATGCTCTCTCAAGGCCTCCAATT                         TTAGAAGGAGAAGCAACTGCACGGGCAATCCGTTTAGCTAAGTTCATCAAT
genomic: ACCTTGGGATAACTGGTCCAGAAGGGCATGCTCTCTCAAGGCCTCCAATTgtaaccccaa ... ttcactgcagTTAGAAGGAGAAGCAACTGCACGGGCAATCCGTTTAGCTAAGTTCATCAAT
EST: gi|31355355|gb|CD439712.1|CD439712
EST:     ACCTTGGGATAACTGGTCCAGAAGGGCATGCTCTCTCAAGGCCTCCAATT                         TTAGAAGGAGAAGCAACTGCACGGGCAATCCGTTTGGCGAAGTTCATCAAT
genomic: ACCTTGGGATAACTGGTCCAGAAGGGCATGCTCTCTCAAGGCCTCCAATTgtaaccccaa ... ttcactgcagTTAGAAGGAGAAGCAACTGCACGGGCAATCCGTTTAGCTAAGTTCATCAAT

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), 44 (downstream exon)
Score: 69

TCATGCAGAGAATGGTGATGCTGTTGCCGAGGGACAACAGCGGATGATTGACCTTGGGATAACTGGTCCAGAAGGGCATGCTCTCTCAAGGCCTCCAATTgtaaccccaa ... ttcactgcagTTAGAAGGAGAAGCAACTGCACGGGCAATCCGTTTAGCTAAGTTCATCAATACGCCACTGTATGTTGTTCATGTGATGAGCATCGACGCAATGGATGAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 320

TCATGCAGAGAATGGTGATGCTGTTGCCGAGGGACAACAGCGGATGATTGACCTTGGGATAACTGGTCCAGAAGGGCATGCTCTCTCAAGGCCTCCAATTgtaaccccaa ... ttcactgcagTTAGAAGGAGAAGCAACTGCACGGGCAATCCGTTTAGCTAAGTTCATCAATACGCCACTGTATGTTGTTCATGTGATGAGCATCGACGCAATGGATGAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 296

TCATGCAGAGAATGGTGATGCTGTTGCCGAGGGACAACAGCGGATGATTGACCTTGGGATAACTGGTCCAGAAGGGCATGCTCTCTCAAGGCCTCCAATTgtaaccccaa ... ttcactgcagTTAGAAGGAGAAGCAACTGCACGGGCAATCCGTTTAGCTAAGTTCATCAATACGCCACTGTATGTTGTTCATGTGATGAGCATCGACGCAATGGATGAGA


Block sizes: 44 (upstream exon), 48 (downstream exon)
Score: 120

TCATGCAGAGAATGGTGATGCTGTTGCCGAGGGACAACAGCGGATGATTGACCTTGGGATAACTGGTCCAGAAGGGCATGCTCTCTCAAGGCCTCCAATTgtaaccccaa ... ttcactgcagTTAGAAGGAGAAGCAACTGCACGGGCAATCCGTTTAGCTAAGTTCATCAATACGCCACTGTATGTTGTTCATGTGATGAGCATCGACGCAATGGATGAGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattctcacattaagctattcaaaaatgaaataattttgttctcattcactgcagTTAGAAGGAGAAGCAACTGCACGGGCAATCCGTTTAGCTAAGTTCATCAATACGCCACTGTATGTTGTTCATGTGATGAGCATCGACGCAATGGATGAGA
  ttctcac  putative branch site (score: 120)
                                  ttttgttctcattc  putative PPT
         attaagctattcaaaa  TA-rich tract