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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattgttttcaggtttgttaaatcatttgtcactgttggcttcttattgacagaaagttccctcttgtaactcagGAGTCAGCCACAATGATGAAGTTGATACTGTTGCTATTGCTCCTTTTGTAAAG

Basic information

species Zea mays
transcript GRMZM2G077299_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G077299_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os12g03470.5 (Oryza sativa), 3'ss of exon 9
gtaattgttttcaggtttgttaaatcat--ttgtcactgttggcttctt--attgacagaaagttccctcttgtaactcagGAGTCAGCCACAATGATGAAGTTGATACTGTTGCTATTGCTCCTTTTGTAAAG
|||||  ||  ||  ||| ||| ||| |  | | ||| | || | || |  ||||  |  ||  ||  |  | ||  |||||| ||||||| ||||||||||||||||||| ||| ||||||||||||||||| 
gtaataattgccatattttttatatctttatcgccacagctgacctccttaattgctactaaactcttttatata--tcagGAATCAGCCATAATGATGAAGTTGATACTGCTGCAATTGCTCCTTTTGTAAAA

upper sequence: GRMZM2G077299_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os11g03730.2 (Oryza sativa), 3'ss of exon 9
gtaattgttttcaggtttgttaaatcat--ttgtcactgttggcttctt--attgacagaaagttccctcttgtaactcagGAGTCAGCCACAATGATGAAGTTGATACTGTTGCTATTGCTCCTTTTGTAAAG
|||||  ||  ||  ||| ||| ||| |  |   ||| | || | || |  || ||||  ||  ||    ||  |  |||||| ||||||| ||||||||||||||||||| ||| ||||||||||||||||| 
gtaataattgccatattttttatatcttgatcaccacagctgacctcctgaatcgacactaaactct---ttaaatatcagGAATCAGCCATAATGATGAAGTTGATACTGCTGCGATTGCTCCTTTTGTAAAA
















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|32847594|gb|CD987275.1|CD987275
EST:     ACTGAACCAATCTGGGTATTCAACAATG                         GAGTCAGCCACAATGATGAAGTTGATACTGTTGCTATTGCTCCTTTTGTAA
genomic: ACTGAACCAATCTGGGTATTCAACAATGgtaattgttt ... tgtaactcagGAGTCAGCCACAATGATGAAGTTGATACTGTTGCTATTGCTCCTTTTGTAA
EST: gi|12045517|gb|BF727656.1|BF727656
EST:     CTTGCGGAGGACCTGGGTACTGAACCAATCTGGGTATTCAACAATG                         GAGTCAGCCACAATGATGAAGTTGATACTGTTGCTATTGCTCCTTTTGTAA
genomic: CTTGCGGAGGACCTGGGTACTGAACCAATCTGGGTATTCAACAATGgtaattgttt ... tgtaactcagGAGTCAGCCACAATGATGAAGTTGATACTGTTGCTATTGCTCCTTTTGTAA
EST: gi|32846175|gb|CD985856.1|CD985856
EST:     ACTGAACCAATCTGGGTATTCAACAATG                         GAGTCAGCCACAATGATGAAGTTGATACTGTTGCTATTGCTCCTTTTGTAA
genomic: ACTGAACCAATCTGGGTATTCAACAATGgtaattgttt ... tgtaactcagGAGTCAGCCACAATGATGAAGTTGATACTGTTGCTATTGCTCCTTTTGTAA
EST: gi|6095297|gb|AW119964.1|AW119964
EST:     CTTGCGGAGGACCTGGGTACTGAACCAATCTGGGTATTCAACAATG                         GAGTCAGCCACAATGATGAAGTTGATACTGTTGCTATTGCTCCTTTTGTAA
genomic: CTTGCGGAGGACCTGGGTACTGAACCAATCTGGGTATTCAACAATGgtaattgttt ... tgtaactcagGAGTCAGCCACAATGATGAAGTTGATACTGTTGCTATTGCTCCTTTTGTAA
EST: gi|211082959|gb|FL420012.1|FL420012
EST:     CTTGCGGAGGACCTGGGTACTGAACCAATCTGGGTATTCAACAATG                         GAGTCAGCCACAATGATGAAGTTGATACTGTTGCTATTGCTCCTTTTGTAA
genomic: CTTGCGGAGGACCTGGGTACTGAACCAATCTGGGTATTCAACAATGgtaattgttt ... tgtaactcagGAGTCAGCCACAATGATGAAGTTGATACTGTTGCTATTGCTCCTTTTGTAA
EST: gi|32865761|gb|CF005443.1|CF005443
EST:     GGGTACTGAACCAATCTGGGTATTCAACAATG                         GAGTCAGCCACAATGATGAAGTTGATACTGTTGCTATTGCTCCTTTTGTAA
genomic: GGGTACTGAACCAATCTGGGTATTCAACAATGgtaattgttt ... tgtaactcagGAGTCAGCCACAATGATGAAGTTGATACTGTTGCTATTGCTCCTTTTGTAA
EST: gi|78179997|gb|DV550370.1|DV550370
EST:     CTTGCGGAGGACCTGGGTACTGAACCAATCTGGGTATTCAACAATG                         GAGTCAGCCACAATGATGAAGTTGATACTGTTGCTATTGCTCCTTTTGTAA
genomic: CTTGCGGAGGACCTGGGTACTGAACCAATCTGGGTATTCAACAATGgtaattgttt ... tgtaactcagGAGTCAGCCACAATGATGAAGTTGATACTGTTGCTATTGCTCCTTTTGTAA
EST: gi|211043015|gb|FL421679.1|FL421679
EST:     CTTGCGGAGGACCTGGGTACTGAACCAATCTGGGTATTCAACAATG                         GAGTCAGCCACAATGATGAAGTTGATACTGTTGCTATTGCTCCTTTTGTAA
genomic: CTTGCGGAGGACCTGGGTACTGAACCAATCTGGGTATTCAACAATGgtaattgttt ... tgtaactcagGAGTCAGCCACAATGATGAAGTTGATACTGTTGCTATTGCTCCTTTTGTAA
EST: gi|32846927|gb|CD986608.1|CD986608
EST:     ACTGAACCAATCTGGGTATTCAACAATG                         GAGTCAGCCACAATGATGAAGTTGATACTGTTGCTATTGCTCCTTTTGTAA
genomic: ACTGAACCAATCTGGGTATTCAACAATGgtaattgttt ... tgtaactcagGAGTCAGCCACAATGATGAAGTTGATACTGTTGCTATTGCTCCTTTTGTAA
EST: gi|32835529|gb|CD975207.1|CD975207
EST:     GGTACTGAACCAATCTGGGTATTCAACAATG                         GAGTCAGCCACAATGATGAAGTTGATACTGTTGCTATTGCTCCTTTTGTAA
genomic: GGTACTGAACCAATCTGGGTATTCAACAATGgtaattgttt ... tgtaactcagGAGTCAGCCACAATGATGAAGTTGATACTGTTGCTATTGCTCCTTTTGTAA
EST: gi|71441725|gb|DR822775.1|DR822775
EST:     CTTGCGGAGGACCTGGGTACTGAACCAATCTGGGTATTCAACAATG                         GAGTCAGCCACAATGATGAAGTTGATACTGTTGCTATTGCTCCTTTTGTAA
genomic: CTTGCGGAGGACCTGGGTACTGAACCAATCTGGGTATTCAACAATGgtaattgttt ... tgtaactcagGAGTCAGCCACAATGATGAAGTTGATACTGTTGCTATTGCTCCTTTTGTAA
EST: gi|32846588|gb|CD986269.1|CD986269
EST:     GGTACTGAACCAATCTGGGTATTCAACAATG                         GAGTCAGCCACAATGATGAAGTTGATACTGTTGCTATTGCTCCTTTTGTAA
genomic: GGTACTGAACCAATCTGGGTATTCAACAATGgtaattgttt ... tgtaactcagGAGTCAGCCACAATGATGAAGTTGATACTGTTGCTATTGCTCCTTTTGTAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatcatttgtcactgttggcttcttattgacagaaagttccctcttgtaactcagGAGTCAGCCACAATGATGAAGTTGATACTGTTGCTATTGCTCCTTTTGTAAAG
                                            ttgtaac  putative branch site (score: 2)
                                     ttccctcttgt  CT-rich tract
                    ttcttatt  TA-rich tract