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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGATGTCCCCGTCGTAGGAATCGTCACTCGCCTGACAGCCCAAAAGGGGATCCACCTGATCAAGCATGCGATTCACCGTACACTCGAACGGAACGGACAGgtcattcgatcccttgcattgcatggcacatatatagaacttggaacattctttctttccttaattattcgtgcctttctgtcatcttgaaatgaaactaattaagaatgccatatgtttggtttccag

Basic information

species Zea mays
transcript GRMZM2G141399_T01
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G141399_T01 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os08g09230.1 (Oryza sativa), 5'ss of exon 12
CGATGTCCCCGTCGTAGGAATCGTCACTCGCCTGACAGCCCAAAAGGGGATCCACCTGATCAAGCATGCGATTCACCGTACACTCGAACGGAACGGACAGgtcattcgatcccttgca-ttgcatggcacatatatagaacttggaacattctttctttccttaattattcgtgcctttctgtcatcttgaaatgaaactaattaagaatgccatatgtttggtttccag
 ||||||||| | || |||||| ||||||| ||||||||||| ||||| |||||||| || || |||||  |||| || ||||| ||||| || |||||||| | ||  |   |  || |    | |    |   |||||||||      | || | || |  |||||||  ||||   || ||    |||||  |              |  || |||||| |||  ||
TGATGTCCCCATTGTTGGAATCATCACTCGTCTGACAGCCCAGAAGGGTATCCACCTCATTAAACATGCACTTCATCGGACACTTGAACGCAATGGACAGgttaatcatttgatgacaatcttctagtgtctccctagaacttg-----cttttccctttcgcaattatttttgccgacctatc----tgaaacaa--------------gtgatgtgtttgctttttag
















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|67021517|gb|CO450266.1|CO450266
EST:     TCCACCTGATCAAGCATGCGATTCACCGTACACTCGAACGGAACGGACAG                         GTGGTTTTGCTTGGTTCAGCGCCGGACTCTCGAATCCAAGCTGATTTTGTC
genomic: TCCACCTGATCAAGCATGCGATTCACCGTACACTCGAACGGAACGGACAGgtcattcgat ... tggtttccagGTGGTTTTGCTTGGTTCAGCGCCGGACTCTCGAATCCAAGCTGATTTTGTC
EST: gi|31352858|gb|CD437215.1|CD437215
EST:     TCCACCTGATCAAGCATGCGATTCACCGTACACTCGAACGGAACGGACAG                         GTGGTTTTGCTTGGTTCAGCGCCGGACTCTCGAATCCAAGCTGATTTTGTC
genomic: TCCACCTGATCAAGCATGCGATTCACCGTACACTCGAACGGAACGGACAGgtcattcgat ... tggtttccagGTGGTTTTGCTTGGTTCAGCGCCGGACTCTCGAATCCAAGCTGATTTTGTC
EST: gi|32835013|gb|CD974691.1|CD974691
EST:     GTACACTCGAACGGAACGGACAG                         GTGGTTTTGCTTGGTTCAGCGCCGGACTCTCGAATCCAAGCTGATTTTGTC
genomic: GTACACTCGAACGGAACGGACAGgtcattcgat ... tggtttccagGTGGTTTTGCTTGGTTCAGCGCCGGACTCTCGAATCCAAGCTGATTTTGTC
EST: gi|13149461|gb|BG319783.1|BG319783
EST:     TCCACCTGATCAAGCATGCGATTCACCGTACACTCGAACGGAACGGACAG                         GTGGTTTTGCTTGGTTCAGCGCCGGACTCTCGAATCCAAGCTGATTTTGTC
genomic: TCCACCTGATCAAGCATGCGATTCACCGTACACTCGAACGGAACGGACAGgtcattcgat ... tggtttccagGTGGTTTTGCTTGGTTCAGCGCCGGACTCTCGAATCCAAGCTGATTTTGTC
EST: gi|32833105|gb|CD972783.1|CD972783
EST:     ACACTCGAACGGAACGGACAG                         GTGGTTTTGCTTGGTTCAGCGCCGGACTCTCGAATCCAAGCTGATTTTGTC
genomic: ACACTCGAACGGAACGGACAGgtcattcgat ... tggtttccagGTGGTTTTGCTTGGTTCAGCGCCGGACTCTCGAATCCAAGCTGATTTTGTC
EST: gi|31361027|gb|CD445384.1|CD445384
EST:     TCCACCTGATCAAGCATGCGATTCACCGTACACTCGAACGGAACGGACAG                         GTGGGTTTGCTTGGTTCAGCGCCGGAC
genomic: TCCACCTGATCAAGCATGCGATTCACCGTACACTCGAACGGAACGGACAGgtcattcgat ... tggtttccagGTGGTTTTGCTTGGTTCAGCGCCGGAC
EST: gi|67014870|gb|CO443619.1|CO443619
EST:     TCCACCTGATCAAGCATGCGATTCACCGTACACTCGAACGGAACGGACAG                         GTGGTTTTGCTTGGTTCAGCGCCGGACTCTCGAATCCAAGCTGATTTTGTC
genomic: TCCACCTGATCAAGCATGCGATTCACCGTACACTCGAACGGAACGGACAGgtcattcgat ... tggtttccagGTGGTTTTGCTTGGTTCAGCGCCGGACTCTCGAATCCAAGCTGATTTTGTC
EST: gi|31351712|gb|CD436069.1|CD436069
EST:     TCCACCTGATCAAGCATGCGATTCACCGTACACTCGAACGGAACGGACAG                         GTGGTTTTGCTTGGTTCAGCGCCGGACTCTCGAATCCAAGCTGATTTTGTC
genomic: TCCACCTGATCAAGCATGCGATTCACCGTACACTCGAACGGAACGGACAGgtcattcgat ... tggtttccagGTGGTTTTGCTTGGTTCAGCGCCGGACTCTCGAATCCAAGCTGATTTTGTC
EST: gi|24769423|gb|CA404552.1|CA404552
EST:     TCCACCTGATCAAGCATGCGATTCACCGTACACTCGAACGGAACGGACAG                         GTGGTTTTGCTTGGTTCAGCGCCGGACTCTCGAATCCAAGCTGATTTTGTC
genomic: TCCACCTGATCAAGCATGCGATTCACCGTACACTCGAACGGAACGGACAGgtcattcgat ... tggtttccagGTGGTTTTGCTTGGTTCAGCGCCGGACTCTCGAATCCAAGCTGATTTTGTC

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: 45 (upstream exon), 40 (downstream exon)
Score: 34

CGATGTCCCCGTCGTAGGAATCGTCACTCGCCTGACAGCCCAAAAGGGGATCCACCTGATCAAGCATGCGATTCACCGTACACTCGAACGGAACGGACAGgtcattcgat ... tggtttccagGTGGTTTTGCTTGGTTCAGCGCCGGACTCTCGAATCCAAGCTGATTTTGTCAACCTGGCGAATAAGCTCCACGGCGTAAACCATGGGCAAGTGAGGCTTT


Block sizes: 46 (upstream exon), 32 (downstream exon)
Score: 9

CGATGTCCCCGTCGTAGGAATCGTCACTCGCCTGACAGCCCAAAAGGGGATCCACCTGATCAAGCATGCGATTCACCGTACACTCGAACGGAACGGACAGgtcattcgat ... tggtttccagGTGGTTTTGCTTGGTTCAGCGCCGGACTCTCGAATCCAAGCTGATTTTGTCAACCTGGCGAATAAGCTCCACGGCGTAAACCATGGGCAAGTGAGGCTTT


Block sizes: 42 (upstream exon), 8 (downstream exon)
Score: 1

CGATGTCCCCGTCGTAGGAATCGTCACTCGCCTGACAGCCCAAAAGGGGATCCACCTGATCAAGCATGCGATTCACCGTACACTCGAACGGAACGGACAGgtcattcgat ... tggtttccagGTGGTTTTGCTTGGTTCAGCGCCGGACTCTCGAATCCAAGCTGATTTTGTCAACCTGGCGAATAAGCTCCACGGCGTAAACCATGGGCAAGTGAGGCTTT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 58

CGATGTCCCCGTCGTAGGAATCGTCACTCGCCTGACAGCCCAAAAGGGGATCCACCTGATCAAGCATGCGATTCACCGTACACTCGAACGGAACGGACAGgtcattcgat ... tggtttccagGTGGTTTTGCTTGGTTCAGCGCCGGACTCTCGAATCCAAGCTGATTTTGTCAACCTGGCGAATAAGCTCCACGGCGTAAACCATGGGCAAGTGAGGCTTT