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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCCAGAGAAGGCTCGCGCAGAACAGAGAGGCTGCTCGGAAGAGTCGCCTGCGGAAGAAGgtggacacaagatcttcaccattcttgtggtgttagtgttacaaattacaatcatgtttgtggtgttacaattctgttaccttgttcaacag

Basic information

species Zea mays
transcript GRMZM2G445575_T02
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G445575_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os04g54474.2 (Oryza sativa), 5'ss of exon 5
GCCCAGAGAAGGCTCGCGCAGAACAGAGAGGCTGCTCGGAAGAGTCGCCTGCGGAAGAAGgtggac--acaagatcttcaccattcttgtggtgttagtgttacaaattacaat-----catgtttgtggtgttacaattctgttaccttgttcaacag------------
| ||  ||||| || || || |||||||||||||| ||||| || ||||||||||| |||||  |   |||||  ||| || | |    || ||| |   |   | |||  |       ||| ||||       | |      ||| |    | |  |             
GTCCTCAGAAGACTTGCACAAAACAGAGAGGCTGCACGGAAAAGCCGCCTGCGGAAAAAGgtaaaatgacaagtacttaactactaacatgctgtcaccatgctagattgtagctttcccatttttgaaaaacaaaatcctcattatcggcatgattatggtgttccatag
















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|94477975|gb|EB706933.1|EB706933
EST:     GGCTCGCGCAGAACAGAGAGGCTGCTCGGAAGAGTCGCCTGCGGAAGAAG                         GCCTACATCCAGCAGCTAGAGACAAGCCGCATGAAGCTGTCGCAGCTAGAG
genomic: GGCTCGCGCAGAACAGAGAGGCTGCTCGGAAGAGTCGCCTGCGGAAGAAGgtggacacaa ... tgttcaacagGCCTACATCCAGCAGCTAGAGACAAGCCGCATGAAGCTGTCGCAGCTAGAG
EST: gi|148955465|gb|EC901061.2|EC901061
EST:     GGCTCGCGCAGAACAGAGAGGCTGCTCGGAAGAGTCGCCTGCGGAAGAAG                         GCCTACATCCAGCAGCTAGAGACAAGCCGCATGAAGCTGTCGCAGCTAGAG
genomic: GGCTCGCGCAGAACAGAGAGGCTGCTCGGAAGAGTCGCCTGCGGAAGAAGgtggacacaa ... tgttcaacagGCCTACATCCAGCAGCTAGAGACAAGCCGCATGAAGCTGTCGCAGCTAGAG
EST: gi|148999148|gb|EE036061.2|EE036061
EST:     GGCTCGCGCAGAACAGAGAGGCTGCTCGGAAGAGTCGCCTGCGGAAGAAG                         GCCTACATCCAGCAGCTAGAGACAAGCCGCATGAAGCTGTCGCAGCTAGAG
genomic: GGCTCGCGCAGAACAGAGAGGCTGCTCGGAAGAGTCGCCTGCGGAAGAAGgtggacacaa ... tgttcaacagGCCTACATCCAGCAGCTAGAGACAAGCCGCATGAAGCTGTCGCAGCTAGAG
EST: gi|149079352|gb|EE168328.2|EE168328
EST:     GGCTCGCGCAGAACAGAGAGGCTGCTCGGAAGAGTCGCCTGCGGAAGAAG                         GCCTACATCCAGCAGCTAGAGACAAGCCGCATGAAGCTGTCGCAGCTAGAG
genomic: GGCTCGCGCAGAACAGAGAGGCTGCTCGGAAGAGTCGCCTGCGGAAGAAGgtggacacaa ... tgttcaacagGCCTACATCCAGCAGCTAGAGACAAGCCGCATGAAGCTGTCGCAGCTAGAG
EST: gi|148933922|gb|EC877905.2|EC877905
EST:     GGCTCGCGCAGAACAGAGAGGCTGCTCGGAAGAGTCGCCTGCGGAAGAAG                         GCCTACATCCAGCAGCTAGAGACAAGCCGCATGAAGCTGTCGCAGCTAGAG
genomic: GGCTCGCGCAGAACAGAGAGGCTGCTCGGAAGAGTCGCCTGCGGAAGAAGgtggacacaa ... tgttcaacagGCCTACATCCAGCAGCTAGAGACAAGCCGCATGAAGCTGTCGCAGCTAGAG
EST: gi|148969929|gb|EE020834.2|EE020834
EST:     GGCTCGCGCAGAACAGAGAGGCTGCTCGGAAGAGTCGCCTGCGGAAGAAG                         GCCTACATCCAGCAGCTAGAGACAAGCCGCATGAAGCTGTCGCAGCTAGAG
genomic: GGCTCGCGCAGAACAGAGAGGCTGCTCGGAAGAGTCGCCTGCGGAAGAAGgtggacacaa ... tgttcaacagGCCTACATCCAGCAGCTAGAGACAAGCCGCATGAAGCTGTCGCAGCTAGAG
EST: gi|74235598|gb|DT643512.1|DT643512
EST:     GGCTCGCGCAGAACAGAGAGGCTGCTCGGAAGAGTCGCCTGCGGAAGAAG                         GCCTACATCCAGCAGCTAGAGACAAGCCGCATGAAGCTGTCGCAGCTAGAG
genomic: GGCTCGCGCAGAACAGAGAGGCTGCTCGGAAGAGTCGCCTGCGGAAGAAGgtggacacaa ... tgttcaacagGCCTACATCCAGCAGCTAGAGACAAGCCGCATGAAGCTGTCGCAGCTAGAG
EST: gi|149000175|gb|EE037312.2|EE037312
EST:     GGCTCGCGCAGAACAGAGAGGCTGCTCGGAAGAGTCGCCTGCGGAAGAAG                         GCCTACATCCAGCAGCTAGAGACAAGCCGCATGAAGCTGTCGCAGCTAGAG
genomic: GGCTCGCGCAGAACAGAGAGGCTGCTCGGAAGAGTCGCCTGCGGAAGAAGgtggacacaa ... tgttcaacagGCCTACATCCAGCAGCTAGAGACAAGCCGCATGAAGCTGTCGCAGCTAGAG

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCCAGAGAAGGCTCGCGCAGAACAGAGAGGCTGCTCGGAAGAGTCGCCTGCGGAAGAAGgtggacacaagatcttcaccattcttgtggtgttagtgttacaaattacaatcatgtttgtggtgttacaattctgttaccttgttcaacag

- - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG