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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTACTGCAAATCGCTTGCTAGCATCGAAACAGACCATTCCTCATTACTACTTGACAGTAGATGCACGTGTTGACAAACTTGTCCAgtatgtttctaacctaatttgtgatctacaagccctttttgttggtgaacagcactgattcctttattacttctaactatgagttccttgtgtcactctctaatcaacag

Basic information

species Zea mays
transcript GRMZM2G015132_T01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G015132_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os02g01500.1 (Oryza sativa), 5'ss of exon 12
GTTACTGCAAATCGCTTGCTAGCATCGAAACAGACCATTCCTCATTACTACTTGACAGTAGATGCACGTGTTGACAAACTTGTCCAgtatgtttctaacctaatttgtgatcta---caagccctttttgt-tggtgaaca---gcactgattcctttat-tacttctaactatg-agttccttgtgtcactctctaatcaacag---------
||||||||||| ||| |||||   || ||||| || ||||||||||| ||||||||||| || || |||||||| || ||| || ||||||||     |    ||||| || ||   ||| ||  | ||   | |  |||    | | ||||||  ||   |||| ||   | || || |  ||     | |   | ||    |          
GTTACTGCAAACCGCCTGCTAAGCTCTAAACAAACTATTCCTCATTATTACTTGACAGTTGACGCCCGTGTTGATAATCTTATCAAgtatgttgaagcctagctttgtaatttaaagcaatcctatattacataggaaacctatgtaatgattcaattccatactgctggttttgtagctttttaaaatagttctttatttcaatctaatccag

upper sequence: GRMZM2G015132_T01 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA07G03930.2 (Glycine max), 5'ss of exon 12
GTTACTGCAAATCGCTTGCTAGCATCGAAACAGACCATTCCTCATTACTACTTGACAGTAGATGCACGTGTTGACAAACTTGTCCAgtatgtttctaacctaatttgtgatctacaagcc--ctttttgttggtgaacagcactgattcctttattacttctaactatgagttccttgtgtcactctctaatcaacag
|| || ||    ||  | |||  ||| ||||| || |||||||||||||| || ||||||||| || |||||||||||||      ||| || |||    | |  | |  || ||| |    | | |  ||    |  |   |||||  |   |   | | || ||||                              
GTCACAGCTTCACGGCTACTATTATCAAAACAAACTATTCCTCATTACTATTTAACAGTAGATACATGTGTTGACAAACTCACGAGgtaagtctctgttatcaaatat--tcgacaggtttacctgtcattacatattatttctgataacgcgaactcct-tatctatag----------------------------

upper sequence: GRMZM2G015132_T01 (Zea mays), 5'ss of exon 11
lower sequence: Vv09s0002g01800.t01 (Vitis vinifera), 5'ss of exon 13
GTTACTGCAAATCGCTTGCTAGCATCGAAACAGACCATTCCTCATTACTACTTGACAGTAGATGCACGTGTTGACAAACTTGTCCAgtatgtttctaacctaatttgtgatctacaagc---cctttttgttggtgaacagcactgattcctttattacttctaactatgagttccttgtgtcactctctaatcaacag
 | || ||    ||| |  ||  |||||| ||||| ||||| ||||| || |||||||| ||| || |||||||||||||| |  |||  |  | ||      |   |  | || ||     ||    | |   |   | |   ||||  ||    |  | ||  || |    ||  | | || ||||||   ||    
ATCACAGCTTCACGCCTATTATTATCGAAGCAGACTATTCCCCATTATTATTTGACAGTGGATACATGTGTTGACAAACTTATGGAgtgagcat-tagttccttccatcttttaaaaaataacccacgtttcaatcttctgtgatgat--ctaagctgttgctctctct---ctctctctctctctctctctgcag---

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|32789248|gb|CD941484.1|CD941484
EST:     ATTCCTCATTACTACTTGACAGTAGATGCACGTGTTGACAAACTTGTCCA                         GTTGCGAGGTGAACTGAACCCACTGCAGGATGCTTCTGGTGGAAAGAAAAT
genomic: ATTCCTCATTACTACTTGACAGTAGATGCACGTGTTGACAAACTTGTCCAgtatgtttct ... taatcaacagGTTGCGAGGTGAACTGAACCCACTGCAGGATGCTTCTGGTGGAAAGAAAAT
EST: gi|74235054|gb|DT642968.1|DT642968
EST:     ATTCCTCATTACTACTTGACAGTAGATGCACGTGTTGACAAACTTGTCCA                         GTTGCGAGGTGAACTGAACCCACTGCAGGATGCTTCTGGTGGAAAGAAAAT
genomic: ATTCCTCATTACTACTTGACAGTAGATGCACGTGTTGACAAACTTGTCCAgtatgtttct ... taatcaacagGTTGCGAGGTGAACTGAACCCACTGCAGGATGCTTCTGGTGGAAAGAAAAT
EST: gi|32840355|gb|CD980036.1|CD980036
EST:     ATTCCTCATTACTACTTGACAGTAGATGCACGTGTTGACAAACTTGTCCA                         GTTGCGAGGTGAACTGAACCCACTGCAGGATGCTTCTGGTGGAAAGAAAAT
genomic: ATTCCTCATTACTACTTGACAGTAGATGCACGTGTTGACAAACTTGTCCAgtatgtttct ... taatcaacagGTTGCGAGGTGAACTGAACCCACTGCAGGATGCTTCTGGTGGAAAGAAAAT
EST: gi|32938642|gb|CF043461.1|CF043461
EST:     ATTCCTCATTACTACTTGACAGTAGATGCACGTGTTGACAAACTTGTCCA                         GTTGCGAGGTGAACTGAACCCACTGCAGGATGCTTCTGGTG-AAAGAAAAT
genomic: ATTCCTCATTACTACTTGACAGTAGATGCACGTGTTGACAAACTTGTCCAgtatgtttct ... taatcaacagGTTGCGAGGTGAACTGAACCCACTGCAGGATGCTTCTGGTGGAAAGAAAAT
EST: gi|32932311|gb|CF037123.1|CF037123
EST:     ATTCCTCATTACTACTTGACAGTAGATGCACGTGTTGACAAACTTGTCCA                         GTTGCGAGGTGAACTGAACCCACTGCAGGATGCTTCTGGTGGAAAGAAAAT
genomic: ATTCCTCATTACTACTTGACAGTAGATGCACGTGTTGACAAACTTGTCCAgtatgtttct ... taatcaacagGTTGCGAGGTGAACTGAACCCACTGCAGGATGCTTCTGGTGGAAAGAAAAT

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: 271

GTTACTGCAAATCGCTTGCTAGCATCGAAACAGACCATTCCTCATTACTACTTGACAGTAGATGCACGTGTTGACAAACTTGTCCAgtatgtttct ... taatcaacagGTTGCGAGGTGAACTGAACCCACTGCAGGATGCTTCTGGTGGAAAGAAAATATCAATTAATGATCTTGTCATCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 521

GTTACTGCAAATCGCTTGCTAGCATCGAAACAGACCATTCCTCATTACTACTTGACAGTAGATGCACGTGTTGACAAACTTGTCCAgtatgtttct ... taatcaacagGTTGCGAGGTGAACTGAACCCACTGCAGGATGCTTCTGGTGGAAAGAAAATATCAATTAATGATCTTGTCATCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 357

GTTACTGCAAATCGCTTGCTAGCATCGAAACAGACCATTCCTCATTACTACTTGACAGTAGATGCACGTGTTGACAAACTTGTCCAgtatgtttct ... taatcaacagGTTGCGAGGTGAACTGAACCCACTGCAGGATGCTTCTGGTGGAAAGAAAATATCAATTAATGATCTTGTCATCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 568

GTTACTGCAAATCGCTTGCTAGCATCGAAACAGACCATTCCTCATTACTACTTGACAGTAGATGCACGTGTTGACAAACTTGTCCAgtatgtttct ... taatcaacagGTTGCGAGGTGAACTGAACCCACTGCAGGATGCTTCTGGTGGAAAGAAAATATCAATTAATGATCTTGTCATCAAG