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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTACTGTGTTCAGAGAACCAATTATATGCAAAAACGTTCCAAGGCTTGTTCCAGgtatttagcaaaaatatgaaactaccctgcatttttgtgtgcaataatggtttccccctaaattgaaatgtttgtgaaatcag

Basic information

species Zea mays
transcript GRMZM2G033515_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G033515_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os01g46610.1 (Oryza sativa), 5'ss of exon 6
GTACTGTGTTCAGAGAACCAATTATATGCAAAAACGTTCCAAGGCTTGTTCCAGgtatttagcaaaaatatgaaactaccctgcatttttgtgtgcaataatggtttccccctaa-attgaaatgtttgtgaaatcag
| ||||| |||||||| ||||||||||||||||| || |||||||||||||||||||||||   |  ||||||| |||  ||   || |||  || | |||  |||   |  ||| ||||||   ||  ||||| |||
GCACTGTATTCAGAGAGCCAATTATATGCAAAAATGTCCCAAGGCTTGTTCCAGgtatttaa-gaggatatgaatctattct---ttattgaatgaactaa--gttcatctgtaacattgaaccattgatgaaaccag
















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|67021863|gb|CO450612.1|CO450612
EST:     TGTGTTCAGAGAACCAATTATATGCAAAAACGTTCCAAGGCTTGTTCCAG                         GATGGACGAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAGTACC
genomic: TGTGTTCAGAGAACCAATTATATGCAAAAACGTTCCAAGGCTTGTTCCAGgtatttagca ... gtgaaatcagGATGGACGAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAGTACC
EST: gi|31353696|gb|CD438053.1|CD438053
EST:     TGTGTTCAGAGAACCAATTATATGCAAAAACGTTCCAAGGCTTGTTCCAG                         GATGGACGAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAGTACC
genomic: TGTGTTCAGAGAACCAATTATATGCAAAAACGTTCCAAGGCTTGTTCCAGgtatttagca ... gtgaaatcagGATGGACGAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAGTACC
EST: gi|84980627|gb|DW530976.1|DW530976
EST:     TGTGTTCAGAGAACCAATTATATGCAAAAACGTTCCAAGGCTTGTTCCAG                         GATGGACGAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAGTACC
genomic: TGTGTTCAGAGAACCAATTATATGCAAAAACGTTCCAAGGCTTGTTCCAGgtatttagca ... gtgaaatcagGATGGACGAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAGTACC
EST: gi|61119247|gb|DN560208.1|DN560208
EST:     TGTGTTCAGAGAACCAATTATATGCAAAAACGTTCCAAGGCTTGTTCCAG                         GATGGACGAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAGTACC
genomic: TGTGTTCAGAGAACCAATTATATGCAAAAACGTTCCAAGGCTTGTTCCAGgtatttagca ... gtgaaatcagGATGGACGAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAGTACC
EST: gi|78092177|gb|DV520551.1|DV520551
EST:     TGTGTTCAGAGAACCAATTATATGCAAAAACGTTCCAAGGCTTGTTCCAG                         GATGGACGAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAGTACC
genomic: TGTGTTCAGAGAACCAATTATATGCAAAAACGTTCCAAGGCTTGTTCCAGgtatttagca ... gtgaaatcagGATGGACGAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAGTACC

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: 44 (upstream exon), 46 (downstream exon)
Score: 12

GTACTGTGTTCAGAGAACCAATTATATGCAAAAACGTTCCAAGGCTTGTTCCAGgtatttagca ... gtgaaatcagGATGGACGAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAGTACCGAGCTACTGATGCAGTTCTGAAGGGGCCTGGGAAGCTGAAGCTAGTTTT


Block sizes: 44 (upstream exon), 46 (downstream exon)
Score: 23

GTACTGTGTTCAGAGAACCAATTATATGCAAAAACGTTCCAAGGCTTGTTCCAGgtatttagca ... gtgaaatcagGATGGACGAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAGTACCGAGCTACTGATGCAGTTCTGAAGGGGCCTGGGAAGCTGAAGCTAGTTTT


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 29

GTACTGTGTTCAGAGAACCAATTATATGCAAAAACGTTCCAAGGCTTGTTCCAGgtatttagca ... gtgaaatcagGATGGACGAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAGTACCGAGCTACTGATGCAGTTCTGAAGGGGCCTGGGAAGCTGAAGCTAGTTTT


Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 47

GTACTGTGTTCAGAGAACCAATTATATGCAAAAACGTTCCAAGGCTTGTTCCAGgtatttagca ... gtgaaatcagGATGGACGAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAGTACCGAGCTACTGATGCAGTTCTGAAGGGGCCTGGGAAGCTGAAGCTAGTTTT