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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATATCTATTTATGGGAGGAAGAAAAGCGAATGGGACCAAATGGCAAGTTGGATAGTGAACAATGAATTATATAGCGAGAATGTTGTTTGGTTAATTCAGgttgatagccctgtcccccttcttttgttcaagtgtgttcaataaccaaatgtgaaactctggctagcccacaatgtaacaagagtataatttctgtgctttattatttgtttcattttttgtcttcag

Basic information

species Zea mays
transcript GRMZM2G134396_T03
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G134396_T03 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os07g49270.1 (Oryza sativa), 5'ss of exon 12
GATATCTATTTATGGGAGGAAGAAAAGCGAATGGGACCAAATGGCAAGTTGGATAGTGAACAATGAATTATATAGCGAGAATGTTGTTTGGTTAATTCAGgtt---------------gatagccctgtcccccttc--------ttttgttcaagtgtgttcaataacca---aatgtgaaactctggctagcccacaatgtaacaag--agtataatttctgtgctttattatttgtttcattttttgtcttcag-----------------------------------
 |||||||| |||||||| |||||||| || ||||| || |||||||| ||||||||||| |||||||| || ||||||||||||||||||||||||||||||               |||  |   |||  | |          |||| |   ||| | ||   ||| ||   | |    || |||           ||   |||||   |||||| | | ||    | | |||||  ||  | ||||| |                                        
AATATCTATCTATGGGAGAAAGAAAAGTGAGTGGGATCAGATGGCAAGCTGGATAGTGAATAATGAATTGTACAGCGAGAATGTTGTTTGGTTAATTCAGgttatgacactctctgttgatgtcgtcgtctgcttctagtcataattttatctgagttttttttctaaacattcagtaatcaattcttaaactttgtaaaccaaacaaactagtatactctgtgcaggtaactattttatttttattttgccagagtagatttactgaaacattgtttaattttatctgcag

upper sequence: GRMZM2G134396_T03 (Zea mays), 5'ss of exon 11
lower sequence: PP1S168_82V6.1 (Physcomitrella patens), 5'ss of exon 11
GATATCTATTTATGGGAGGAAGAAAAGCGAATGGGACCAAATGGCAAGTTGGATAGTGAACAATGAATTATATAGCGAGAATGTTGTTTGGTTAATTCAGgttgatagccctgtcccccttcttttgttcaagtgtgttcaataaccaaatgtgaaactctggctagcccacaatgtaacaagagtataatttctgtgctttattatttgtttcattttttgtcttcag
|||||| ||||| || |||||||| ||||| ||||| ||  ||||||||||||||||  |||||    | || || || || ||   |||| | || ||||||  |     | |     | ||| |    ||   | ||         |   |   | | ||   |    |     | |  ||   || |||||  |   |  || |                      
GATATCAATTTACGGAAGGAAGAAGAGCGAGTGGGATCAGTTGGCAAGTTGGATAGTTGACAATCGGCTGTACAGTGAAAACGTCACTTGGCTTATCCAGgttcttt-taatttgtttgtccttatacgaaacattatttgg-----gagcattttattgtgataaagggattgactgaggagga-atgatttcaatatatagttgt----------------------
















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|21987227|gb|BQ778755.1|BQ778755
EST:     GGATAGTGAACAATGAATTATATAGCGAGAATGTTGTCTGGTTAATTCAG                         ATTCCTCGGATATACAATGTATACAGGGAGATGGGCACAATCAATTCTTTC
genomic: GGATAGTGAACAATGAATTATATAGCGAGAATGTTGTTTGGTTAATTCAGgttgatagcc ... ttgtcttcagATTCCTCGGATATACAATGTATACAGGGAGATGGGCACAATCAATTCTTTC
EST: gi|26557914|gb|CA830149.1|CA830149
EST:     GATAG-GAACAATGAATTATATAGCGAGAATGTTGTCTTGGTTAATTCAG                         ATTCCTCGGATATACAATGTATACAGGGAGATGGGCACAATCAATTCTTTC
genomic: GATAGTGAACAATGAATTATATAGCGAGAATGTTGT-TTGGTTAATTCAGgttgatagcc ... ttgtcttcagATTCCTCGGATATACAATGTATACAGGGAGATGGGCACAATCAATTCTTTC
EST: gi|74237693|gb|DT645607.1|DT645607
EST:     GGATAGTGAACAATGAATTATATAGCGAGAATGTTGTTTGGTTAATTCAG                         ATTCCTCGGATATACAATGTATACAGGGAGATGGGCACAATCAATTCTTTC
genomic: GGATAGTGAACAATGAATTATATAGCGAGAATGTTGTTTGGTTAATTCAGgttgatagcc ... ttgtcttcagATTCCTCGGATATACAATGTATACAGGGAGATGGGCACAATCAATTCTTTC
EST: gi|71299098|gb|DR785546.1|DR785546
EST:     GGATAGTGAACAATGAATTATATAGCGAGAATGTTGTTTGGTTAATTCAG                         ATTCCTCGGATATACAATGTATACAGGGAGATGGGCACAATCAATTCTTTC
genomic: GGATAGTGAACAATGAATTATATAGCGAGAATGTTGTTTGGTTAATTCAGgttgatagcc ... ttgtcttcagATTCCTCGGATATACAATGTATACAGGGAGATGGGCACAATCAATTCTTTC
EST: gi|32835884|gb|CD975562.1|CD975562
EST:     GGATAGTGACCAATGAATTATATAGCGAGAATGTTGTTTGGTTAATTCAG                         ATTCCTCGGATATACAATGTATACAGGGAGATGGGCACAATCAATTCTTTC
genomic: GGATAGTGAACAATGAATTATATAGCGAGAATGTTGTTTGGTTAATTCAGgttgatagcc ... ttgtcttcagATTCCTCGGATATACAATGTATACAGGGAGATGGGCACAATCAATTCTTTC
EST: gi|32863100|gb|CF002782.1|CF002782
EST:     GGATAGTGAACAATGAATTATATAGCGAGAATGTTGTTTGGTTAATTCAG                         ATTCCTCGGATATACAATGTATACAGGGAGATGGGCACAATCAATTCTTTC
genomic: GGATAGTGAACAATGAATTATATAGCGAGAATGTTGTTTGGTTAATTCAGgttgatagcc ... ttgtcttcagATTCCTCGGATATACAATGTATACAGGGAGATGGGCACAATCAATTCTTTC

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), 47 (downstream exon)
Score: 194

GATATCTATTTATGGGAGGAAGAAAAGCGAATGGGACCAAATGGCAAGTTGGATAGTGAACAATGAATTATATAGCGAGAATGTTGTTTGGTTAATTCAGgttgatagcc ... ttgtcttcagATTCCTCGGATATACAATGTATACAGGGAGATGGGCACAATCAATTCTTTCCAAAACCTCCTTGACAATATTTTTCTCCCTCTTTATGAAGTAACTGTTG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 157

GATATCTATTTATGGGAGGAAGAAAAGCGAATGGGACCAAATGGCAAGTTGGATAGTGAACAATGAATTATATAGCGAGAATGTTGTTTGGTTAATTCAGgttgatagcc ... ttgtcttcagATTCCTCGGATATACAATGTATACAGGGAGATGGGCACAATCAATTCTTTCCAAAACCTCCTTGACAATATTTTTCTCCCTCTTTATGAAGTAACTGTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 269

GATATCTATTTATGGGAGGAAGAAAAGCGAATGGGACCAAATGGCAAGTTGGATAGTGAACAATGAATTATATAGCGAGAATGTTGTTTGGTTAATTCAGgttgatagcc ... ttgtcttcagATTCCTCGGATATACAATGTATACAGGGAGATGGGCACAATCAATTCTTTCCAAAACCTCCTTGACAATATTTTTCTCCCTCTTTATGAAGTAACTGTTG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 126

GATATCTATTTATGGGAGGAAGAAAAGCGAATGGGACCAAATGGCAAGTTGGATAGTGAACAATGAATTATATAGCGAGAATGTTGTTTGGTTAATTCAGgttgatagcc ... ttgtcttcagATTCCTCGGATATACAATGTATACAGGGAGATGGGCACAATCAATTCTTTCCAAAACCTCCTTGACAATATTTTTCTCCCTCTTTATGAAGTAACTGTTG