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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcaaattgctctgaactcttatttctgcaggtcttgatataaacttttgttgatgatatctcatgttgaagctacttctttggcagATTTTTAGAACACTTGGCACACCTAGCGAGAAGATTTGGCCTGGCTATGCTAAATTACCAGGCGTGAAAGTAAATTTTGTCAAACAACC

Basic information

species Zea mays
transcript GRMZM2G139038_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G139038_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os04g41100.2 (Oryza sativa), 3'ss of exon 3
-----------------------------------------------------------gtatgcaaattgctctgaactctt----atttctgcaggtcttgatataaacttttgttgatgatatctcatgttgaagctacttctttggcagATTTTTAGAACACTTGGCACACCTAGCGAGAAGATTTGGCCTGGCTATGCTAAATTACCAGGCGTGAAAGTAAATTTTGTCAAACAACC
                                                             |||     |   ||   || ||    ||  ||  |   ||||||||| | | |  ||||| |||||||||| ||||||||||| | | |||||| |||||||||||||||||||||| ||||||||| |||||||||||||| ||||| || || || ||||| |||||||||||||||||
gtatttcgtttgacttgtgattttgcatccttgcaattactatatttttttcagaggtctcatgttggatttcctttcctgttgcagatacctataaaccttgatatatattatatttgatcatatctcatggtgaagctacttttattgcagATATTTAGAACACTTGGCACACCTAACGAGAAGATATGGCCTGGCTATGCCAAATTGCCGGGTGTAAAAGTCAATTTTGTCAAACAACC

upper sequence: GRMZM2G139038_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv01s0010g02550.t01 (Vitis vinifera), 3'ss of exon 2
-------------------------------gtatgcaaattgct-ctgaactcttatt-tctgcaggt-----cttgatataaacttttgttgatgatatctcatgttg---aagctacttctttg---gcagATTTTTAGAACACTTGGCACACCTAGCGAGAAGATTTGGCCTGGCTATGCTAAATTACCAGGCGTGAAAGTAAATTTTGTCAAACAACC
                                 ||    |||  | |||  | | || |  ||  | |      |||||||||   |  | |  |   ||  ||||  ||    ||  |  ||| ||   ||||||||||||||| ||||||||||| || ||||  ||||||||||| | | | ||||| || || || || || || || ||||| || | 
gtaacttaactagttagcttctgcttgtgatacattaccattattgctgcccccctactgcctatatgattctacttgatatatggtgatttccagtttaattcattctgtatgaggaatatctatgattgcagATTTTTAGAACCCTTGGCACACCAAGTGAGACAATTTGGCCTGGGTTTTCCAAATTGCCTGGAGTCAAGGTTAACTTCGTCAAGCATCA
















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|67025976|gb|CO454725.1|CO454725
EST:     CCAAAGAACCATTATTTAATGGAAAAACAGAGTTTGAACAGCTAGATAAG                         ATTTTTAGAACACTTGGCACACCTAGCGAGAAGATTTGGCCTGGCTATGCT
genomic: CCAAAGAACCATTATTTAATGGAAAAACAGAGTTTGAACAGCTAGATAAGgtatgcaaat ... tctttggcagATTTTTAGAACACTTGGCACACCTAGCGAGAAGATTTGGCCTGGCTATGCT
EST: gi|13388885|gb|BG462452.1|BG462452
EST:     GTTTGAACAGCTAGATAAG                         ATTTTTAGAACACTTGGCACACCTAGCGAGAAGATTTGGCCTGGCTATGCT
genomic: GTTTGAACAGCTAGATAAGgtatgcaaat ... tctttggcagATTTTTAGAACACTTGGCACACCTAGCGAGAAGATTTGGCCTGGCTATGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttgatataaacttttgttgatgatatctcatgttgaagctacttctttggcagATTTTTAGAACACTTGGCACACCTAGCGAGAAGATTTGGCCTGGCTATGCTAAATTACCAGGCGTGAAAGTAAATTTTGTCAAACAACC
                tgttgat  putative branch site (score: 4)
                                        ctacttcttt  putative PPT
     atataaacttttgtt  TA-rich tract