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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAAGAAGTTGCTCCTTGGGAAAAAGAGATCATAACTGATCCTAGTACTCCAAAGCCTAATCCAAATCCGTTCAGTTATGAACATCAGGCTAAAACCGATgtaagtgcagctcttcagatatgaacatgttgactagacggatatcatttaagatgattttcttttccctgattaatttctttctttcag

Basic information

species Zea mays
transcript GRMZM2G134396_T03
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G134396_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os07g49270.1 (Oryza sativa), 5'ss of exon 5
AGAAGAAGTTGCTCCTTGGGAAAAAGAGATCATAACTGATCCTAGTACTCCAAAGCCTAATCCAAATCCGTTCAGTTATGAACATCAGGCTAAAACCGATgtaagtgcagctcttcagatatga-acatgttgactagacgg-atatcatttaagatgattttcttttccctgatt--aatttctttctttcag
||||||||||||||| ||||| || || |||||||||||||||||||||||||| |||||||| || || |||  ||| || || ||| ||||||| || || ||||    ||   | || |    ||| || || | ||   |  |  |          ||||| | | || |||    |||| ||| |||||
AGAAGAAGTTGCTCCATGGGAGAAGGAAATCATAACTGATCCTAGTACTCCAAAACCTAATCCTAACCCTTTCTATTACGAGCAGCAGACTAAAACTGAAgtgagtgtgtttccctatattttctgcatattaacgatacaacacgttttcctgctctgctttctgtactctaattttgttttccttccttcag
















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|71772853|gb|DR970776.1|DR970776
EST:     CAAAGCCTAATCCAAATCCGTTCAGTTATGAACATCAGGCTAAAACCGAT                         CACCATTTCGAAATGGTTGATGGCGTCATTCATGTGTACCCCAATAAAGAT
genomic: CAAAGCCTAATCCAAATCCGTTCAGTTATGAACATCAGGCTAAAACCGATgtaagtgcag ... tttctttcagCACCATTTCGAAATGGTTGATGGCGTCATTCATGTGTACCCCAATAAAGAT
EST: gi|19058010|gb|BM736677.1|BM736677
EST:     CAAAGCCTAATCCAAATCCGTTCAGTTATGAACATCAGGCTAAAACCGAT                         CACCATTTCGAAATGGTTGATGGCGTCATTCATGTGTACCCCAATAAAGAT
genomic: CAAAGCCTAATCCAAATCCGTTCAGTTATGAACATCAGGCTAAAACCGATgtaagtgcag ... tttctttcagCACCATTTCGAAATGGTTGATGGCGTCATTCATGTGTACCCCAATAAAGAT
EST: gi|50336750|gb|CO531876.1|CO531876
EST:     CAAAGCCTAATCCAAATCCGTTCAGTTATGAACATCAGGCTAAAACCGAT                         CACCATTTCGAAATGGTTGATGGCGTCATTCATGTGTACCCCAATAAAGAT
genomic: CAAAGCCTAATCCAAATCCGTTCAGTTATGAACATCAGGCTAAAACCGATgtaagtgcag ... tttctttcagCACCATTTCGAAATGGTTGATGGCGTCATTCATGTGTACCCCAATAAAGAT
EST: gi|22490387|gb|BU050310.1|BU050310
EST:     CAAAGCCTAATCCAAATCCGTTCAGTTATGAACATCAGGCTAAAACCGAT                         CACCATTTCGAAATGGTTGATGGCGTCATTCATGTGTACCCCAATAAAGAT
genomic: CAAAGCCTAATCCAAATCCGTTCAGTTATGAACATCAGGCTAAAACCGATgtaagtgcag ... tttctttcagCACCATTTCGAAATGGTTGATGGCGTCATTCATGTGTACCCCAATAAAGAT
EST: gi|87153046|gb|DY397835.1|DY397835
EST:     CAAAGCCTAATCCAAATCCGTTCAGTTATGAACATCAGGCTAAAACCGAT                         CACCATTTCGAAATGGTTGATGGCGTCATTCATGTGTACCCCAATAAAGAT
genomic: CAAAGCCTAATCCAAATCCGTTCAGTTATGAACATCAGGCTAAAACCGATgtaagtgcag ... tttctttcagCACCATTTCGAAATGGTTGATGGCGTCATTCATGTGTACCCCAATAAAGAT

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: 135

AGAAGAAGTTGCTCCTTGGGAAAAAGAGATCATAACTGATCCTAGTACTCCAAAGCCTAATCCAAATCCGTTCAGTTATGAACATCAGGCTAAAACCGATgtaagtgcag ... tttctttcagCACCATTTCGAAATGGTTGATGGCGTCATTCATGTGTACCCCAATAAAGATT


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 130

AGAAGAAGTTGCTCCTTGGGAAAAAGAGATCATAACTGATCCTAGTACTCCAAAGCCTAATCCAAATCCGTTCAGTTATGAACATCAGGCTAAAACCGATgtaagtgcag ... tttctttcagCACCATTTCGAAATGGTTGATGGCGTCATTCATGTGTACCCCAATAAAGATT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 164

AGAAGAAGTTGCTCCTTGGGAAAAAGAGATCATAACTGATCCTAGTACTCCAAAGCCTAATCCAAATCCGTTCAGTTATGAACATCAGGCTAAAACCGATgtaagtgcag ... tttctttcagCACCATTTCGAAATGGTTGATGGCGTCATTCATGTGTACCCCAATAAAGATT


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 92

AGAAGAAGTTGCTCCTTGGGAAAAAGAGATCATAACTGATCCTAGTACTCCAAAGCCTAATCCAAATCCGTTCAGTTATGAACATCAGGCTAAAACCGATgtaagtgcag ... tttctttcagCACCATTTCGAAATGGTTGATGGCGTCATTCATGTGTACCCCAATAAAGATT