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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATTTCTTCACCGTTGGAATTGGTTGGGTGCTATTTGGTGGACTTCCTTTTGATCTTgtaagttttgggtcttgtttctatgccacttatctttgtataatctcccagtgaatactgaacccaaagttttcgtgtgcag

Basic information

species Zea mays
transcript GRMZM2G133226_T03
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G133226_T04 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os02g40030.2 (Oryza sativa), 5'ss of exon 7
-------------------------------------------GATTTCTTCACCGTTGGAATTGGTTGGGTGCTATTTGGTGGACTTCCTTTTGATCTTgtaagttttgggtcttgtttct-----atgccacttatctttgtataatctccca---gtgaatactgaac--ccaaa--gttttcgtgtgcag------
                                           |||||||||||||| |||||||| ||||| || |||||||| |||||||||||||| || ||||    ||  ||||| |     |||  |   |  ||||| |  | | |||   |||  | | ||||  | |||  || |   | |  |       
AAGTTGTTTTTTAGTGTCCTTTCATATTTACCTTTTTCTGCAGGATTTCTTCACCGTCGGAATTGGCTGGGTTCTGTTTGGTGGGCTTCCTTTTGATCTGgtgagttaaatgtagtgtttgtttaggatggaaagaagatttgtctccttttccacgcgtgctttccgaactactaaatggtatgattttataaaatttc

upper sequence: GRMZM2G133226_T04 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os02g40030.1 (Oryza sativa), 5'ss of exon 9
GATTTCTTCACCGTTGGAATTGGTTGGGTGCTATTTGGTGGACTTCCTTTTGATCTTgtaagttttgggtcttgtttct-----atgccacttatctttgtataatctccca---gtgaatactgaac--ccaaa--gttttcgtgtgcag------
|||||||||||||| |||||||| ||||| || |||||||| |||||||||||||| || ||||    ||  ||||| |     |||  |   |  ||||| |  | | |||   |||  | | ||||  | |||  || |   | |  |       
GATTTCTTCACCGTCGGAATTGGCTGGGTTCTGTTTGGTGGGCTTCCTTTTGATCTGgtgagttaaatgtagtgtttgtttaggatggaaagaagatttgtctccttttccacgcgtgctttccgaactactaaatggtatgattttataaaatttc
















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|71440135|gb|DR821185.1|DR821185
EST:     TCACCGTTGGAATTGGTTGGGTGCTATTTGGTGGACTTCCTTTTGATCTT                         CTTAATGTTATAGGACAAGGACTAGGCTTTCTGGGCTCTGGATTGTATGCC
genomic: TCACCGTTGGAATTGGTTGGGTGCTATTTGGTGGACTTCCTTTTGATCTTgtaagttttg ... tcgtgtgcagCTTAATGTTATAGGACAAGGACTAGGCTTTCTGGGCTCTGGATTGTATGCC
EST: gi|148933234|gb|EC876885.2|EC876885
EST:     TCCCCGTTGGAATTGGTTGGGTGCTATTTGGTGGACTTCCTTTTGATCTT                         TTTAATGTTATAGGACAAGGACTAGGCTTTCTGGGCTCTGGATTGTATGCC
genomic: TCACCGTTGGAATTGGTTGGGTGCTATTTGGTGGACTTCCTTTTGATCTTgtaagttttg ... tcgtgtgcagCTTAATGTTATAGGACAAGGACTAGGCTTTCTGGGCTCTGGATTGTATGCC
EST: gi|166442891|gb|EG164741.1|EG164741
EST:     TCACCGTTGGAATTGGTTGGGTGCTATTTGGTGGACTTCCTTTTGATCTT                         CTTAATGTTATAGGACAGGGACTAGGCTTTCTGGGCTCTGGATTGTATGCC
genomic: TCACCGTTGGAATTGGTTGGGTGCTATTTGGTGGACTTCCTTTTGATCTTgtaagttttg ... tcgtgtgcagCTTAATGTTATAGGACAAGGACTAGGCTTTCTGGGCTCTGGATTGTATGCC
EST: gi|149103657|gb|EE289061.2|EE289061
EST:     TCCCCGTTGGAATTGGTTGGGTGCTATTTGGTGGACTTCCTTTTGATCTT                         TTTAATGTTATAGGACAAGGACTAGGCTTTTTGGGCTTTGGATTGTATGCC
genomic: TCACCGTTGGAATTGGTTGGGTGCTATTTGGTGGACTTCCTTTTGATCTTgtaagttttg ... tcgtgtgcagCTTAATGTTATAGGACAAGGACTAGGCTTTCTGGGCTCTGGATTGTATGCC
EST: gi|148947033|gb|EC892330.2|EC892330
EST:     TCACCGTTGGAATTGGTTGGGTGCTATTTGGTGGACTTCCTTTTGATCTT                         CTTAATGTTATAGGACAAGGACTAGGCTTTCTGGGCTCTGGATTGTATGCC
genomic: TCACCGTTGGAATTGGTTGGGTGCTATTTGGTGGACTTCCTTTTGATCTTgtaagttttg ... tcgtgtgcagCTTAATGTTATAGGACAAGGACTAGGCTTTCTGGGCTCTGGATTGTATGCC
EST: gi|91054598|gb|EB165016.1|EB165016
EST:     TCACCGTTGGAATTGGTTGGGTGCTATTTGGTGGACTTCCTTTTGATCTT                         CTTAATGTTATAGGACAAGGACTAGGCTTTCTGGGCTCTGGATTGTATGCC
genomic: TCACCGTTGGAATTGGTTGGGTGCTATTTGGTGGACTTCCTTTTGATCTTgtaagttttg ... tcgtgtgcagCTTAATGTTATAGGACAAGGACTAGGCTTTCTGGGCTCTGGATTGTATGCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATTTCTTCACCGTTGGAATTGGTTGGGTGCTATTTGGTGGACTTCCTTTTGATCTTgtaagttttgggtcttgtttctatgccacttatctttgtataatctcccagtgaatactgaacccaaagttttcgtgtgcag

- - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - GGTGGA