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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATATTCCGGGGACTAGCTTATATTCATACTGTACCAGGAATTTGTCACCGAGATATTAAGCCTCAGAATATCTTGgtatgctggtttagtgttttttatgctaagcatgtgcttgttcccgcttcttgttcatgacgttcagttggaaaatgctggccttctctttttcttattgtttgatag

Basic information

species Zea mays
transcript GRMZM2G043350_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G043350_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os06g35530.1 (Oryza sativa), 5'ss of exon 5
ATATTCCGGGGACTAGCTTATATTCATACTGTACCAGGAATTTGTCACCGAGATATTAAGCCTCAGAATATCTTGgtatgctggtttagtgttttttatgctaagcatgtgcttgttcccgcttcttgttcatgacgttcagttggaaaatgctggccttctctttttcttattgtttgatag
|||||||| ||| ||||||| ||||| ||||| || ||| |||||||||||||||| ||||| || |||||||||||||||   |||       ||  | | |||| | | | ||||           ||||    | |      |||||| || |  ||   || |  | || |        
ATATTCCGCGGATTAGCTTACATTCACACTGTTCCTGGAGTTTGTCACCGAGATATAAAGCCACAAAATATCTTGgtatgccctttt------cttcttaccaagcgtat-catgtt-----------ttcacactgctgcagctgaaaattcttggttttgattgtgttgatag--------
















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|67015526|gb|CO444275.1|CO444275
EST:     ATACTGTACCAGGAATTTGTCACCGAGATATTAAGCCTCAGAA-ATCTTG                         GTGGATCCTCTTTCC-ACCAAGTCAAGGTTTGTGACTTCGGGAGTGCTAAN
genomic: ATACTGTACCAGGAATTTGTCACCGAGATATTAAGCCTCAGAATATCTTGgtatgctggt ... tgtttgatagGTGGATCCTCTTTCCCACCAAGTCAAGGTTTGTGACTTCGGGAGTGCTAAA
EST: gi|71446526|gb|DR827576.1|DR827576
EST:     ATACTGTACCAGGAATTTGTCACCGAGATATTAAGCCTCAGAATATCTTG                         GTGGATCCTCTTTCCCACCAAGTCAAGGTTTGTGACTTCGGGAGTGCTAAA
genomic: ATACTGTACCAGGAATTTGTCACCGAGATATTAAGCCTCAGAATATCTTGgtatgctggt ... tgtttgatagGTGGATCCTCTTTCCCACCAAGTCAAGGTTTGTGACTTCGGGAGTGCTAAA
EST: gi|148944449|gb|EC889564.2|EC889564
EST:     ATACTGTACCAGGAATTTGTCACCGAGATATTAAGCCTCAGAATATCTTG                         GTGGATCCTCTTTCCCACCAAGTCAAGGTTTGTGACTTCGGGAGTGCTAAA
genomic: ATACTGTACCAGGAATTTGTCACCGAGATATTAAGCCTCAGAATATCTTGgtatgctggt ... tgtttgatagGTGGATCCTCTTTCCCACCAAGTCAAGGTTTGTGACTTCGGGAGTGCTAAA
EST: gi|148952374|gb|EC898188.2|EC898188
EST:     ATACTGTACCAGGAATTTGTCACCGAGATATTAAGCCTCAGAATATCTTG                         GTGGATCCTCTTTCCCACCAAGTCAAGGTTTGTGACTTCGGGAGTGCTAAA
genomic: ATACTGTACCAGGAATTTGTCACCGAGATATTAAGCCTCAGAATATCTTGgtatgctggt ... tgtttgatagGTGGATCCTCTTTCCCACCAAGTCAAGGTTTGTGACTTCGGGAGTGCTAAA
EST: gi|71438041|gb|DR819091.1|DR819091
EST:     ATACTGTACCAGGAATTTGTCACCGAGATATTAAGCCTCAGAATATCTTG                         GTGGATCCTCTTTCCCACCAAGTCAAGGTTTGTGACTTCGGGAGTGCTAAA
genomic: ATACTGTACCAGGAATTTGTCACCGAGATATTAAGCCTCAGAATATCTTGgtatgctggt ... tgtttgatagGTGGATCCTCTTTCCCACCAAGTCAAGGTTTGTGACTTCGGGAGTGCTAAA
EST: gi|78092425|gb|DV520799.1|DV520799
EST:     ATACTGTACCAGGAATTTGTCACCGAGATATTAAGCCTCAGAATATCTTG                         GTGGATCCTCTTTCCCACCAAGTCAAGGTTTGTGACTTCGGGAGTGCTAAA
genomic: ATACTGTACCAGGAATTTGTCACCGAGATATTAAGCCTCAGAATATCTTGgtatgctggt ... tgtttgatagGTGGATCCTCTTTCCCACCAAGTCAAGGTTTGTGACTTCGGGAGTGCTAAA
EST: gi|50322397|gb|CO517523.1|CO517523
EST:     ATACTGTACCAGGAATTTGTCACCGAGATATTAAGCCTCAGAATATCTTG                         GTGGATCCTCTTTCCCACCAAGTCAAGGTTTGTGACTTCGGGAGTGCTAAA
genomic: ATACTGTACCAGGAATTTGTCACCGAGATATTAAGCCTCAGAATATCTTGgtatgctggt ... tgtttgatagGTGGATCCTCTTTCCCACCAAGTCAAGGTTTGTGACTTCGGGAGTGCTAAA
EST: gi|149083957|gb|EE173340.2|EE173340
EST:     ATACTGTACCAGGAATTTGTCACCGAGATATTAAGCCTCAGAATATCTTG                         GTGGATCCTCTTTCCCCACCAAGTCAAGGTTTGTGACTTCGGGAGTGCTAA
genomic: ATACTGTACCAGGAATTTGTCACCGAGATATTAAGCCTCAGAATATCTTGgtatgctggt ... tgtttgatagGTGGATCCTCTTTCCC-ACCAAGTCAAGGTTTGTGACTTCGGGAGTGCTAA
EST: gi|31355327|gb|CD439684.1|CD439684
EST:     ATACTGTACCAGGAATTTGTCACCGAGATATTAAGCCTCAGAATATCTTG                         GTGGATCCTCTTTCCCACCAAGTCAAGGTTTGTGACTTCGGGAGTGCTAAA
genomic: ATACTGTACCAGGAATTTGTCACCGAGATATTAAGCCTCAGAATATCTTGgtatgctggt ... tgtttgatagGTGGATCCTCTTTCCCACCAAGTCAAGGTTTGTGACTTCGGGAGTGCTAAA
EST: gi|91055941|gb|EB166359.1|EB166359
EST:     ATACTGTACCAGGAATTTGTCACCGAGATATTAAGCCTCAGAATATCTTG                         GTGGATCCTCTTTCCCACCAAGTCAAGGTTTGTGACTTCGGGAGTGCTAAA
genomic: ATACTGTACCAGGAATTTGTCACCGAGATATTAAGCCTCAGAATATCTTGgtatgctggt ... tgtttgatagGTGGATCCTCTTTCCCACCAAGTCAAGGTTTGTGACTTCGGGAGTGCTAAA
EST: gi|149076229|gb|EE164829.2|EE164829
EST:     ATACTGTACCAGGAATTTGTCACCGAGATATTAAGCCTCAGAATATCTTG                         GTGGATCCTCTTTCCCACCAAGTCAAGGTTTGTGACTTCGGGAGTGCTAAA
genomic: ATACTGTACCAGGAATTTGTCACCGAGATATTAAGCCTCAGAATATCTTGgtatgctggt ... tgtttgatagGTGGATCCTCTTTCCCACCAAGTCAAGGTTTGTGACTTCGGGAGTGCTAAA
EST: gi|149112100|gb|EE295033.2|EE295033
EST:     ATACTGTACCAGGAATTTGTCACCGAGATATTAAGCCTCAGAATATCTTG                         GTGGATCCTCTTTCCCACCAAGTCAAGGTTTGTGACTTCGGGAGTGCTAAA
genomic: ATACTGTACCAGGAATTTGTCACCGAGATATTAAGCCTCAGAATATCTTGgtatgctggt ... tgtttgatagGTGGATCCTCTTTCCCACCAAGTCAAGGTTTGTGACTTCGGGAGTGCTAAA
EST: gi|149101575|gb|EE187701.2|EE187701
EST:     ATACTGTACCAGGAATTTGTCACCGAGATATTAAGCCTCAGAATATCTTG                         GTGGATCCTCTTTCCCACCAAGTCAAGGTTTGTGACTTCGGGAGTGCTAAA
genomic: ATACTGTACCAGGAATTTGTCACCGAGATATTAAGCCTCAGAATATCTTGgtatgctggt ... tgtttgatagGTGGATCCTCTTTCCCACCAAGTCAAGGTTTGTGACTTCGGGAGTGCTAAA

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: 412

ATATTCCGGGGACTAGCTTATATTCATACTGTACCAGGAATTTGTCACCGAGATATTAAGCCTCAGAATATCTTGgtatgctggt ... tgtttgatagGTGGATCCTCTTTCCCACCAAGTCAAGGTTTGTGACTTCGGGAGTGCTAAAATCTTG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 84

ATATTCCGGGGACTAGCTTATATTCATACTGTACCAGGAATTTGTCACCGAGATATTAAGCCTCAGAATATCTTGgtatgctggt ... tgtttgatagGTGGATCCTCTTTCCCACCAAGTCAAGGTTTGTGACTTCGGGAGTGCTAAAATCTTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 62

ATATTCCGGGGACTAGCTTATATTCATACTGTACCAGGAATTTGTCACCGAGATATTAAGCCTCAGAATATCTTGgtatgctggt ... tgtttgatagGTGGATCCTCTTTCCCACCAAGTCAAGGTTTGTGACTTCGGGAGTGCTAAAATCTTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 83

ATATTCCGGGGACTAGCTTATATTCATACTGTACCAGGAATTTGTCACCGAGATATTAAGCCTCAGAATATCTTGgtatgctggt ... tgtttgatagGTGGATCCTCTTTCCCACCAAGTCAAGGTTTGTGACTTCGGGAGTGCTAAAATCTTG