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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacagttggaaaaagatgattaagttggtatttaccatttctctcacagcctgccattgttcttagctaagttttgctaagagtgtagtaactgattttttttctatcccttcttgcacaaattcctatgcacagGTCAGCGGTTGATCAAGAATATCCGCCCACTTTTTGATGGAGCGGTTATTGAGCCATGCTTGCTTCATGGTGATCTGTGGAGCGGAAACATAAGCTCTGA

Basic information

species Zea mays
transcript GRMZM2G030299_T03
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G030299_T03 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os03g02640.1 (Oryza sativa), 3'ss of exon 6
gtacagttggaaaaagatgattaagttggtatttaccatttctctcacagcctgc-cattgttcttagctaagttttgctaagagtgtagtaactgattttttttctatcccttcttgcacaaattcct-atgcacagGTCAGCGGTTGATCAAGAATATCCGCCCACTTTTTGATGGAGCGGTTATTGAGCCATGCTTGCTTCATGGTGATCTGTGGAGCGGAAACATAAGCTCTGA
|| | || || ||| ||  |   |      |   |||  |  |||||     ||       | ||    || | || || |    | |  |   |  |  |  ||| |||  | |   |  |   |||| | | ||||||||||| |||||| ||||||| |  ||||||||||| || || ||||| |||||||||||||||||||| ||||| ||||| ||||||||||| |||||
gtgc-gtggggaaaggacaacatataaatcaagcacccgtgttctcatcttttgtatgagatactctaatatgctt-gccatttttctgttggttcgtggtccttc-atctttgccaacttatgctccttaagtacagGTCAGCGATTGATCGAGAATATGCATCCACTTTTTGAAGGCGCTGTTATGGAGCCATGCTTGCTTCATGGGGATCTATGGAGTGGAAACATAAGTTCTGA
















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|60337252|gb|DN204225.1|DN204225
EST:     GTTGGAGTTGGCATCGAGACGATATGGAGATTCGGCCATACTCGAAAAAG                         GTCAGCGGTTGATCAAGAATATCCGCCCACTTTTTGATGGAGCGGTTATTG
genomic: GTTGGAGTTGGCATCGAGACGATATGGAGATTCGGCCATACTCGAAAAAGgtacagttgg ... ctatgcacagGTCAGCGGTTGATCAAGAATATCCGCCCACTTTTTGATGGAGCGGTTATTG
EST: gi|76283912|gb|DV023480.1|DV023480
EST:     CGGCCATACTCGAAAAAG                         GTCAGCGGTTGATCAAGAATATCCGCCCACTTTTTGATGGAGCGGTTATTG
genomic: CGGCCATACTCGAAAAAGgtacagttgg ... ctatgcacagGTCAGCGGTTGATCAAGAATATCCGCCCACTTTTTGATGGAGCGGTTATTG
EST: gi|149108778|gb|EE189830.2|EE189830
EST:     GTTGGAGTTGGCATCGAGACGATATGGAGATTCGGCCATACTCGAAAAAG                         GTCAGCGGTTGATCAAGAATATCCGCCCACTTTTTGATGGAGCGGTTATTG
genomic: GTTGGAGTTGGCATCGAGACGATATGGAGATTCGGCCATACTCGAAAAAGgtacagttgg ... ctatgcacagGTCAGCGGTTGATCAAGAATATCCGCCCACTTTTTGATGGAGCGGTTATTG
EST: gi|60348350|gb|DN215323.1|DN215323
EST:     GTTGGAGTTGGCATCGAGACGATATGGAGATTCGGCCATACTCGAAAAAG                         GTCAGCGGTTGATCAAGAATATCCGCCCACTTTTTGATGGAGCGGTTATTG
genomic: GTTGGAGTTGGCATCGAGACGATATGGAGATTCGGCCATACTCGAAAAAGgtacagttgg ... ctatgcacagGTCAGCGGTTGATCAAGAATATCCGCCCACTTTTTGATGGAGCGGTTATTG
EST: gi|76288116|gb|DV027684.1|DV027684
EST:     GTTGGAGTTGGCATCGAGACGATATGGAGATTCGGCCATACTCGAAAAAG                         GTCAGCGGTTGATCAAGAATATCCGCCCACTTTTTGATGGAGCGGTTATTG
genomic: GTTGGAGTTGGCATCGAGACGATATGGAGATTCGGCCATACTCGAAAAAGgtacagttgg ... ctatgcacagGTCAGCGGTTGATCAAGAATATCCGCCCACTTTTTGATGGAGCGGTTATTG
EST: gi|78544199|gb|DV621697.1|DV621697
EST:     GTTGGAGTTGGCATCGAGACGATATGGAGATTCGGCCATACTCGAAAAAG                         GTCAGCGGTTGATCAAGAATATCCGCCCACTTTTTGATGGAGCGGTTATTG
genomic: GTTGGAGTTGGCATCGAGACGATATGGAGATTCGGCCATACTCGAAAAAGgtacagttgg ... ctatgcacagGTCAGCGGTTGATCAAGAATATCCGCCCACTTTTTGATGGAGCGGTTATTG
EST: gi|211523349|gb|FL468083.1|FL468083
EST:     GTTGGAGTTGGCATCGAGACGATATGGAGATTCGGCCATACTCGAAAAAG                         GTCAGCGGTTGATCAAGAATATCCGCCCACTTTTTGATGGAGCGGTTATTG
genomic: GTTGGAGTTGGCATCGAGACGATATGGAGATTCGGCCATACTCGAAAAAGgtacagttgg ... ctatgcacagGTCAGCGGTTGATCAAGAATATCCGCCCACTTTTTGATGGAGCGGTTATTG
EST: gi|76283911|gb|DV023479.1|DV023479
EST:     CGGCCATACTCGAAAAAG                         GTCAGCGGTTGATCAAGAATATCCGCCCACTTTTTGATGGAGCGGTTATTG
genomic: CGGCCATACTCGAAAAAGgtacagttgg ... ctatgcacagGTCAGCGGTTGATCAAGAATATCCGCCCACTTTTTGATGGAGCGGTTATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagtgtagtaactgattttttttctatcccttcttgcacaaattcctatgcacagGTCAGCGGTTGATCAAGAATATCCGCCCACTTTTTGATGGAGCGGTTATTGAGCCATGCTTGCTTCATGGTGATCTGTGGAGCGGAAACATAAGCTCTGA
                                          ttcctat  CT-rich tract
        taactgatttttttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacagttggaaaaagatgattaagttggtatttaccatttctctcacagcctgccattgttcttagctaagttttgctaagagtgtagtaactgattttttttctatcccttcttgcacaaattcctatgcacagGTCAGCGGTTGATCAAGAATATCCGCCCACTTTTTGATGGAGCGGTTATTGAGCCATGCTTGCTTCATGGTGATCTGTGGAGCGGAAACATAAGCTCTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG