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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgtttatcatatactgtaagtgtttgcaagaagaattagtctttgcgagatgggattgatttgcttgcttttgtagGGGAGCGGTGAGCCAAAACGCAAGGTCATCAAGCATAGCAAGCTTGAGAAGGACAAAGAGTTATTTCAACTAGCCCAGCAATACCACAAAGTGGTTGCAG

Basic information

species Zea mays
transcript GRMZM2G107731_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G107731_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g17930.3 (Oryza sativa), 3'ss of exon 2
--------------------------------gttgtttatcatatactgtaagtgtttg-caagaagaattagtctttgcgagatgggattgatttgcttgcttttgtagGGGAGCGGTGAGCCAAAACGCAAGGTCATCAAGCATAGCAAGCTTGAGAAGGACAAAGAGTTATTTCAACTAGCCCAGCAATACCACAAAGTGGTTGCAG
                                 |   | ||  |      |  || ||||  | |||| ||||||  |||| | | ||||||||| ||||||  |||||||||||| |||||||  || ||||||||| | ||  | |||||| | |||||||||| |||| | ||| |||| || |||   |||||||| ||||| ||||
gttgtcattgctgaggtttataggatctggacctgcctcattgtgctgcattggtttttgataggaaggattagtgcttgctaaacgggattgatctgcttgactttgtagGGGAGTGGTGAGCAGAAGCGCAAGGTCGTGAAAAAGAGCAAGGTAGAGAAGGACAGAGAGCTGTTTGAACTTGCGCAGGCGTACCACAAGGTGGTAGCAG

upper sequence: GRMZM2G107731_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g17930.1 (Oryza sativa), 3'ss of exon 2
-----------------gttgtttatcatatactgtaagtgtttg-caagaagaattagtctttgcgagatgggattgatttgcttgcttttgtagGGGAGCGGTGAGCCAAAACGCAAGGTCATCAAGCATAGCAAGCTTGAGAAGGACAAAGAGTTATTTCAACTAGCCCAGCAATACCACAAAGTGGTTGCAG
                  |   | ||  |      |  || ||||  | |||| ||||||  |||| | | ||||||||| ||||||  |||||||||||| |||||||  || ||||||||| | ||  | |||||| | |||||||||| |||| | ||| |||| || |||   |||||||| ||||| ||||
gtttataggatctggacctgcctcattgtgctgcattggtttttgataggaaggattagtgcttgctaaacgggattgatctgcttgactttgtagGGGAGTGGTGAGCAGAAGCGCAAGGTCGTGAAAAAGAGCAAGGTAGAGAAGGACAGAGAGCTGTTTGAACTTGCGCAGGCGTACCACAAGGTGGTAGCAG
















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|148937207|gb|EC881388.2|EC881388
EST:     ATCGTGCATCAGAGCAAGTGGGCGCTCCAAGTGATCAAAAGGTGGTCAAG                         GGGAGCGGTGAGCCAAAACGCAAGGTCATCAAGCATAGCAAGCTTGAGAAG
genomic: ATCGTGCATCAGAGCAAGTGGGCGCTCCAAGTGATCAAAAGGTGGTCAAGgttgtttatc ... gcttttgtagGGGAGCGGTGAGCCAAAACGCAAGGTCATCAAGCATAGCAAGCTTGAGAAG
EST: gi|78116277|gb|DV534664.1|DV534664
EST:     ATCGTGCATCAGAGCAAGTGGGCGCTCCAAGTGATCAAAAGGTGGTCAAG                         GGGAGCGGTGAGCCAAAACGCAAGGTCATCAAGCATAGCAAGCTTGAGAAG
genomic: ATCGTGCATCAGAGCAAGTGGGCGCTCCAAGTGATCAAAAGGTGGTCAAGgttgtttatc ... gcttttgtagGGGAGCGGTGAGCCAAAACGCAAGGTCATCAAGCATAGCAAGCTTGAGAAG
EST: gi|211002685|gb|FL029004.1|FL029004
EST:     ATCGTGCATCAGAGCAAGTGGGCGCTCCAAGTGATCAAAAGGTGGTCAAG                         GGGAGCGGTGAGCCAAAACGCAAGGTCATCAAGCATAGCAAGCTTGAGAAG
genomic: ATCGTGCATCAGAGCAAGTGGGCGCTCCAAGTGATCAAAAGGTGGTCAAGgttgtttatc ... gcttttgtagGGGAGCGGTGAGCCAAAACGCAAGGTCATCAAGCATAGCAAGCTTGAGAAG
EST: gi|148994670|gb|EE034191.2|EE034191
EST:     ATCGTGCATCAGAGCAAGTGGGCGCTCCAAGTGATCAAAAGGTGGTCAAG                         GGGAGCGGTGAGCCAAAACGCAAGGTCATCAAGCATAGCAAGCTTGAGAAG
genomic: ATCGTGCATCAGAGCAAGTGGGCGCTCCAAGTGATCAAAAGGTGGTCAAGgttgtttatc ... gcttttgtagGGGAGCGGTGAGCCAAAACGCAAGGTCATCAAGCATAGCAAGCTTGAGAAG
EST: gi|71436912|gb|DR817962.1|DR817962
EST:     ATCGTGCATCAGAGCAAGTGGGCGCTCCAAGTGATCAAAAGGTGGTCAAG                         GGGAGCGGTGAGCCAAAACGCAAGGTCATCAAGCATAGCAAGCTTGAGAAG
genomic: ATCGTGCATCAGAGCAAGTGGGCGCTCCAAGTGATCAAAAGGTGGTCAAGgttgtttatc ... gcttttgtagGGGAGCGGTGAGCCAAAACGCAAGGTCATCAAGCATAGCAAGCTTGAGAAG
EST: gi|31354731|gb|CD439088.1|CD439088
EST:     ATCGTGCATCAGAGCAAGTGGGCGCTCCAAGTGATC--AA-------AAG                         GGGAGCGGTGAGCCAAAACGCAAGGTCATCAAGCATAGCAAGCTTGAGAAG
genomic: ATCGTGCATCAGAGCAAGTGGGCGCTCCAAGTGATCAAAAGGTGGTCAAGgttgtttatc ... gcttttgtagGGGAGCGGTGAGCCAAAACGCAAGGTCATCAAGCATAGCAAGCTTGAGAAG
EST: gi|91874738|gb|EB404695.1|EB404695
EST:     ATCGTGCATCAGAGCAAGTGGGCGCTCCAAGTGATCAAAAGG-GG--A-G                         -----CGGTGAGCCCAAACGCAAGGTCATCAAGCATAGCAAGCTTGAAAAG
genomic: ATCGTGCATCAGAGCAAGTGGGCGCTCCAAGTGATCAAAAGGTGGTCAAGgttgtttatc ... gcttttgtagGGGAGCGGTGAGCCAAAACGCAAGGTCATCAAGCATAGCAAGCTTGAGAAG
EST: gi|149071351|gb|EE159746.2|EE159746
EST:     ATCGTGCATCAGAGCAAGTGGGCGCTCCAAGTGATCAAAAGG-GG--A-G                         -----CGGTGAGCCAAAACGCAAGGTCATCAAGCATAGCAAGCTTGAGAAG
genomic: ATCGTGCATCAGAGCAAGTGGGCGCTCCAAGTGATCAAAAGGTGGTCAAGgttgtttatc ... gcttttgtagGGGAGCGGTGAGCCAAAACGCAAGGTCATCAAGCATAGCAAGCTTGAGAAG
EST: gi|60358220|gb|DN225193.1|DN225193
EST:     ATCGTGCATCAGAGCAAGTGGGCGCTCCAAGTGATCAAAAGGTGGTCAAG                         GGGAGCGGTGAGCCAAAACGCAAGGTCATCAAGCATAGCAAGCTTGAGAAG
genomic: ATCGTGCATCAGAGCAAGTGGGCGCTCCAAGTGATCAAAAGGTGGTCAAGgttgtttatc ... gcttttgtagGGGAGCGGTGAGCCAAAACGCAAGGTCATCAAGCATAGCAAGCTTGAGAAG
EST: gi|91055771|gb|EB166189.1|EB166189
EST:     ATCGTGCATCAGAGCAAGTGGGCGCTCCAAGTGATCAAAAGG-GG--A-G                         -----CGGTGAGCCAAAACGCAAGGTCATCAAGCATAGCAAGCTTGAGAAG
genomic: ATCGTGCATCAGAGCAAGTGGGCGCTCCAAGTGATCAAAAGGTGGTCAAGgttgtttatc ... gcttttgtagGGGAGCGGTGAGCCAAAACGCAAGGTCATCAAGCATAGCAAGCTTGAGAAG
EST: gi|149103903|gb|EE289318.2|EE289318
EST:     ATCGTGCATCAGAGCAAGTGGGCGCTCCAAGTGATCAAAAGGTGGTCAAG                         GGGAGCGGTGAGCCAAAACGCAAGGTCATCAAGCATAGCAAGCTTTGAGAA
genomic: ATCGTGCATCAGAGCAAGTGGGCGCTCCAAGTGATCAAAAGGTGGTCAAGgttgtttatc ... gcttttgtagGGGAGCGGTGAGCCAAAACGCAAGGTCATCAAGCATAGCAAGCTT-GAGAA
EST: gi|149081200|gb|EE170309.2|EE170309
EST:     ATCGTGCATCAGAGCAAGTGGGCGCTCCAAGTGATCAAAAGG-GG--A-G                         -----CGGTGAGCCAAAACGCAAGGTCATCAAGCATAGCAAGCTTGAGAAG
genomic: ATCGTGCATCAGAGCAAGTGGGCGCTCCAAGTGATCAAAAGGTGGTCAAGgttgtttatc ... gcttttgtagGGGAGCGGTGAGCCAAAACGCAAGGTCATCAAGCATAGCAAGCTTGAGAAG
EST: gi|71774542|gb|DR972420.1|DR972420
EST:     ATCGTGCATCAGAGCAAGTGGGCGCTCCAAGTGATCAAAAGG-GG--A-G                         -----CGGTGAGCCAAAACGCAAGGTCATCAAGCATAGCAAGCTTGAGAAG
genomic: ATCGTGCATCAGAGCAAGTGGGCGCTCCAAGTGATCAAAAGGTGGTCAAGgttgtttatc ... gcttttgtagGGGAGCGGTGAGCCAAAACGCAAGGTCATCAAGCATAGCAAGCTTGAGAAG
EST: gi|149027108|gb|EE046399.2|EE046399
EST:     ATCGTGCATCAGAGCAAGTGGGCGCTCCAAGTGATCAAAAGGTGGTCAAG                         GGGAGCGGTGAGCAAAAACGCAAGGTCATCAAGCATAGCAAGCTTGAGAAG
genomic: ATCGTGCATCAGAGCAAGTGGGCGCTCCAAGTGATCAAAAGGTGGTCAAGgttgtttatc ... gcttttgtagGGGAGCGGTGAGCCAAAACGCAAGGTCATCAAGCATAGCAAGCTTGAGAAG
EST: gi|148961119|gb|EE011825.2|EE011825
EST:     ATCGTGCATCAGAGCAAGTGGGCGCTCCAAGTGATCAAAAGGTGGTCAAG                         GGGAGCGGTGAGCCAAAACGCAAGGTCATCAAGCATAGCAAGCTTGAGAAG
genomic: ATCGTGCATCAGAGCAAGTGGGCGCTCCAAGTGATCAAAAGGTGGTCAAGgttgtttatc ... gcttttgtagGGGAGCGGTGAGCCAAAACGCAAGGTCATCAAGCATAGCAAGCTTGAGAAG
EST: gi|50326867|gb|CO521993.1|CO521993
EST:     ATCGTGCATCAGAGCAAGTGGGCGCTCCAAGTGATCAAAAGG-GG--A-G                         -----CGGTGAGCCAAAACGCAAGGTCATCAAGCATAGCAAGCTTGAGAAG
genomic: ATCGTGCATCAGAGCAAGTGGGCGCTCCAAGTGATCAAAAGGTGGTCAAGgttgtttatc ... gcttttgtagGGGAGCGGTGAGCCAAAACGCAAGGTCATCAAGCATAGCAAGCTTGAGAAG

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: 36 (upstream exon), 48 (downstream exon)
Score: 34

GTGAAGGATCCTTGAAGGAAAATCGTGCATCAGAGCAAGTGGGCGCTCCAAGTGATCAAAAGGTGGTCAAGgttgtttatc ... gcttttgtagGGGAGCGGTGAGCCAAAACGCAAGGTCATCAAGCATAGCAAGCTTGAGAAGGACAAAGAGTTATTTCAACTAGCCCAGCAATACCACAAAGTGGTTGCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 24

GTGAAGGATCCTTGAAGGAAAATCGTGCATCAGAGCAAGTGGGCGCTCCAAGTGATCAAAAGGTGGTCAAGgttgtttatc ... gcttttgtagGGGAGCGGTGAGCCAAAACGCAAGGTCATCAAGCATAGCAAGCTTGAGAAGGACAAAGAGTTATTTCAACTAGCCCAGCAATACCACAAAGTGGTTGCAG


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 50

GTGAAGGATCCTTGAAGGAAAATCGTGCATCAGAGCAAGTGGGCGCTCCAAGTGATCAAAAGGTGGTCAAGgttgtttatc ... gcttttgtagGGGAGCGGTGAGCCAAAACGCAAGGTCATCAAGCATAGCAAGCTTGAGAAGGACAAAGAGTTATTTCAACTAGCCCAGCAATACCACAAAGTGGTTGCAG


Block sizes: 42 (upstream exon), 49 (downstream exon)
Score: 24

GTGAAGGATCCTTGAAGGAAAATCGTGCATCAGAGCAAGTGGGCGCTCCAAGTGATCAAAAGGTGGTCAAGgttgtttatc ... gcttttgtagGGGAGCGGTGAGCCAAAACGCAAGGTCATCAAGCATAGCAAGCTTGAGAAGGACAAAGAGTTATTTCAACTAGCCCAGCAATACCACAAAGTGGTTGCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttgcaagaagaattagtctttgcgagatgggattgatttgcttgcttttgtagGGGAGCGGTGAGCCAAAACGCAAGGTCATCAAGCATAGCAAGCTTGAGAAGGACAAAGAGTTATTTCAACTAGCCCAGCAATACCACAAAGTGGTTGCAG
                                gattgat  putative branch site (score: 24)
                                          cttgctttt  putative PPT
         aagaatta  TA-rich tract