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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactatagcttgaacattgtctatcttgttggcatcagagccttggctccgtgctgaatgtctcttttccatatattattgcagTACATCAAGCTTGTGGCTCCAGCGTCCAGAGGATGCGTCACTGATGAGTAGGCTGTGTTACATTCTGTTAGGTTGTGCACATGATGTGTTTTCAATCAAA

Basic information

species Zea mays
transcript GRMZM2G014069_T01
intron # 13
splice site 3'
intron type U2

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|211042827|gb|FL411666.1|FL411666
EST:     GGAAATGGACCCCACCGCCATACAAGTCGACCAGTGGAGCTCTTTGGAAG                         TACATCAAGCTTGTGGCTCCAGCGTCCAGAGGATGCGTCACTGATGAGTAG
genomic: GGAAATGGACCCCACCGCCATACAAGTCGACCAGTGGAGCTCTTTGGAAGgtactatagc ... attattgcagTACATCAAGCTTGTGGCTCCAGCGTCCAGAGGATGCGTCACTGATGAGTAG
EST: gi|149101994|gb|EE188015.2|EE188015
EST:     GGAAATGGACCCCACCGCCATACAAGTCGACCAGTGGAGCTCTTTGGAAG                         TACATCAAGCTTGTGGCTCCAGCGTCCAGAGGATGCGTCACTGATGAGTAG
genomic: GGAAATGGACCCCACCGCCATACAAGTCGACCAGTGGAGCTCTTTGGAAGgtactatagc ... attattgcagTACATCAAGCTTGTGGCTCCAGCGTCCAGAGGATGCGTCACTGATGAGTAG
EST: gi|71311152|gb|DR791882.1|DR791882
EST:     GGAAATGGACCCCACCGCCATACAAGTCGACCAGTGGAGCTCTTTGGAAG                         TACATCAAGCTTGTGGCTCCAGCGTCCAGAGGATGCGTCACTGATGAGTAG
genomic: GGAAATGGACCCCACCGCCATACAAGTCGACCAGTGGAGCTCTTTGGAAGgtactatagc ... attattgcagTACATCAAGCTTGTGGCTCCAGCGTCCAGAGGATGCGTCACTGATGAGTAG
EST: gi|9953481|gb|BE640064.1|BE640064
EST:     GGAAATGGACCCCACCGCCATACAAGTCGACCAGTGGAGCTCTTTGGAAG                         TACATCAAGCTTGTGGCTCCAGCGTCCAGAGGATGCGTCACTGATGAGTAG
genomic: GGAAATGGACCCCACCGCCATACAAGTCGACCAGTGGAGCTCTTTGGAAGgtactatagc ... attattgcagTACATCAAGCTTGTGGCTCCAGCGTCCAGAGGATGCGTCACTGATGAGTAG
EST: gi|50337747|gb|CO532873.1|CO532873
EST:     GGAAATGGACCCCACCGCCATACAAGTCGACCAGTGGAGCTCTTTGGAAG                         TACATCAAGCTTGTGGCTCCAGCGTCCAGAGGATGCGTCACTGATGAGTAG
genomic: GGAAATGGACCCCACCGCCATACAAGTCGACCAGTGGAGCTCTTTGGAAGgtactatagc ... attattgcagTACATCAAGCTTGTGGCTCCAGCGTCCAGAGGATGCGTCACTGATGAGTAG
EST: gi|211152609|gb|FL453070.1|FL453070
EST:     GGAAATGGACCCCMCCGCCATACAAGTCGACCAGTGGAGCTCTTTGGAAG                         TACATCAAGCTTGTGGCTCCAGCGTCCAGAGGATGCGTCACTGATGAGTAG
genomic: GGAAATGGACCCCACCGCCATACAAGTCGACCAGTGGAGCTCTTTGGAAGgtactatagc ... attattgcagTACATCAAGCTTGTGGCTCCAGCGTCCAGAGGATGCGTCACTGATGAGTAG
EST: gi|5688808|gb|AI941823.1|AI941823
EST:     GGAAATGGACCCCACCGCCATACAAGTCGACCAGTGGAGCTCTTTGGAAG                         TACATCAAGCTTGTGGCTCCAGCGTCCAGAGGATGCGTCACTGATGAGTAG
genomic: GGAAATGGACCCCACCGCCATACAAGTCGACCAGTGGAGCTCTTTGGAAGgtactatagc ... attattgcagTACATCAAGCTTGTGGCTCCAGCGTCCAGAGGATGCGTCACTGATGAGTAG
EST: gi|45568073|gb|CK985888.1|CK985888
EST:     GGAAATGGACCCCACCGCCATACAAGTCGACCAGTGGAGCTCTTTGGAAG                         TACATCAAGCTTGTGGCTCCAGCGTCCTGAGGATGCGTCACTGATGAGTAG
genomic: GGAAATGGACCCCACCGCCATACAAGTCGACCAGTGGAGCTCTTTGGAAGgtactatagc ... attattgcagTACATCAAGCTTGTGGCTCCAGCGTCCAGAGGATGCGTCACTGATGAGTAG
EST: gi|74234928|gb|DT642842.1|DT642842
EST:     GGAAATGGACCCCACCGCCATACAAGTCGACCAGTGGAGCTCTTTGGAAG                         TACATCAAGCTTGTGGCTCCAGCGTCCAGAGGATGCGTCACTGATGAGTAG
genomic: GGAAATGGACCCCACCGCCATACAAGTCGACCAGTGGAGCTCTTTGGAAGgtactatagc ... attattgcagTACATCAAGCTTGTGGCTCCAGCGTCCAGAGGATGCGTCACTGATGAGTAG
EST: gi|5895787|gb|AW037033.1|AW037033
EST:     GGAAATGGACCCCACCGCCATACAAGTCGACCAGTGGAGCTCTTTGGAAG                         TACATCAAGCTTGTGGCTCCAGCGTCCAGAGGATGCGTCACTGATGAGTAG
genomic: GGAAATGGACCCCACCGCCATACAAGTCGACCAGTGGAGCTCTTTGGAAGgtactatagc ... attattgcagTACATCAAGCTTGTGGCTCCAGCGTCCAGAGGATGCGTCACTGATGAGTAG

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: 46 (upstream exon), 47 (downstream exon)
Score: 213

GAGGGTAATCGATGTTGACCTTACCGAACAGCAGCTCGAAGAAAGGCGGAGGAAATGGACCCCACCGCCATACAAGTCGACCAGTGGAGCTCTTTGGAAGgtactatagc ... attattgcagTACATCAAGCTTGTGGCTCCAGCGTCCAGAGGATGCGTCACTGATGAGTAGGCTGTGTTACATTCTGTTAGGTTGTGCACATGATGTGTTTTCAATCAAA


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 109

GAGGGTAATCGATGTTGACCTTACCGAACAGCAGCTCGAAGAAAGGCGGAGGAAATGGACCCCACCGCCATACAAGTCGACCAGTGGAGCTCTTTGGAAGgtactatagc ... attattgcagTACATCAAGCTTGTGGCTCCAGCGTCCAGAGGATGCGTCACTGATGAGTAGGCTGTGTTACATTCTGTTAGGTTGTGCACATGATGTGTTTTCAATCAAA


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 96

GAGGGTAATCGATGTTGACCTTACCGAACAGCAGCTCGAAGAAAGGCGGAGGAAATGGACCCCACCGCCATACAAGTCGACCAGTGGAGCTCTTTGGAAGgtactatagc ... attattgcagTACATCAAGCTTGTGGCTCCAGCGTCCAGAGGATGCGTCACTGATGAGTAGGCTGTGTTACATTCTGTTAGGTTGTGCACATGATGTGTTTTCAATCAAA


Block sizes: 44 (upstream exon), 47 (downstream exon)
Score: 113

GAGGGTAATCGATGTTGACCTTACCGAACAGCAGCTCGAAGAAAGGCGGAGGAAATGGACCCCACCGCCATACAAGTCGACCAGTGGAGCTCTTTGGAAGgtactatagc ... attattgcagTACATCAAGCTTGTGGCTCCAGCGTCCAGAGGATGCGTCACTGATGAGTAGGCTGTGTTACATTCTGTTAGGTTGTGCACATGATGTGTTTTCAATCAAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggcatcagagccttggctccgtgctgaatgtctcttttccatatattattgcagTACATCAAGCTTGTGGCTCCAGCGTCCAGAGGATGCGTCACTGATGAGTAGGCTGTGTTACATTCTGTTAGGTTGTGCACATGATGTGTTTTCAATCAAA
                                   ttttccatatattatt  TA-rich tract