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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgtaacagtcgtatacgaacttggtgagaacgatcttatctcgaacttttgatctcattttctgggatacttcttctgccattccaatcttagtattttctctctctatatatatatatctttcggtgaacagAGCATTGCAGAAGCAGTTGGAGACTGGTTCTTTGACAGAAGAGAGGTGAAGGAGATAGATTGCGAATACCCCTGCAACCCGACGTGCCACAACTTGGTCT

Basic information

species Zea mays
transcript GRMZM2G141873_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G141873_T07 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os05g02120.1 (Oryza sativa), 3'ss of exon 11
gtactgtaacagtcgtatacgaacttggtgagaacgatcttatctcgaacttttgatctcattttctgggatacttcttctgccattccaatcttagtattttctctctctatatatatatatctttcggtgaacagAGCATTGCAGAAGCAGTTGGAGACTGGTTCTTTGACAGAAGAGAGGTGAAGGAGATAGATTGCGAATACCCCTGCAACCCGACGTGCCACAACTTGGTCT
                      ||||  ||||      || | |  |||  | | |     |  ||     | |||  | | |   | |||| ||     || |||    | ||    |  ||||   | |||| ||| ||||||||| || |||||||| ||||||||||||||||||||||||||||| || ||||| ||||| |||||||||||||| |||||||||||||| |
----------------------acttactgag------ctaaccatgaaggtgtcagtat-tcctccaatcttcttggtttacttcttcaatatt-----ttgctcgtggtctaacgttgaatct---gctgaatagACCATTGCAGAGGCGGTTGGAGATTGGTTCTTTGACAGAAGAGAGGTGAAGGAAATTGATTGTGAATATCCCTGCAACCCGACTTGCCACAACTTGGTTT
















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|149011848|gb|EE042455.2|EE042455
EST:     TGAACTCGTTGACTTGGCACTCTCCAACTTCCCCCAGAGTCAACAATAAG                         AGCATTGCAGAAGCAGTTGGAGACTGGTTCTTTGACAGAAGAGAGGTGAAG
genomic: TGAACTCGTTGACTTGGCACTCTCCAACTTCCCCCAGAGTCAACAATAAGgtactgtaac ... cggtgaacagAGCATTGCAGAAGCAGTTGGAGACTGGTTCTTTGACAGAAGAGAGGTGAAG
EST: gi|71423226|gb|DR805987.1|DR805987
EST:     TGAACTCGTTGACTTGGCACTCTCCAACTTCCCCCAGAGTCAACAATAAG                         AGCATTGCAGAAGCAGTTGGAGACTGGTTCTTTGACAGAAGAGAGGTGAAG
genomic: TGAACTCGTTGACTTGGCACTCTCCAACTTCCCCCAGAGTCAACAATAAGgtactgtaac ... cggtgaacagAGCATTGCAGAAGCAGTTGGAGACTGGTTCTTTGACAGAAGAGAGGTGAAG
EST: gi|71417999|gb|DR804277.1|DR804277
EST:     TGAACTCGTTGACTTGGCACTCTCCAACTTCCCCCAGAGTCAACAATAAG                         AGCATTGCAGAAGCAGTTGGAGACTGGTTCTTTGACAGAAGAGAGGTGAAG
genomic: TGAACTCGTTGACTTGGCACTCTCCAACTTCCCCCAGAGTCAACAATAAGgtactgtaac ... cggtgaacagAGCATTGCAGAAGCAGTTGGAGACTGGTTCTTTGACAGAAGAGAGGTGAAG
EST: gi|78087078|gb|DV515471.1|DV515471
EST:     TGAACTCGTTGACTTGGCACTCTCCAACTTCCCCCAGAGTCAACAATAAG                         AGCATTGCAGAAGCAGTTGGAGACTGGTTCTTTGACAGAAGAGAGGTGAAG
genomic: TGAACTCGTTGACTTGGCACTCTCCAACTTCCCCCAGAGTCAACAATAAGgtactgtaac ... cggtgaacagAGCATTGCAGAAGCAGTTGGAGACTGGTTCTTTGACAGAAGAGAGGTGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccattccaatcttagtattttctctctctatatatatatatctttcggtgaacagAGCATTGCAGAAGCAGTTGGAGACTGGTTCTTTGACAGAAGAGAGGTGAAGGAGATAGATTGCGAATACCCCTGCAACCCGACGTGCCACAACTTGGTCT
                                      tatctttc  CT-rich tract
                        tctctatatatatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactgtaacagtcgtatacgaacttggtgagaacgatcttatctcgaacttttgatctcattttctgggatacttcttctgccattccaatcttagtattttctctctctatatatatatatctttcggtgaacagAGCATTGCAGAAGCAGTTGGAGACTGGTTCTTTGACAGAAGAGAGGTGAAGGAGATAGATTGCGAATACCCCTGCAACCCGACGTGCCACAACTTGGTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT