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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCCTTCCTACTAGGAgtgtgagttacttgatctcttttacctatcctgtaaatttataaccgatgatttttttgggtgcaagtttaacagtacacatgtgcatgtcaataccttc...

Basic information

species Zea mays
transcript GRMZM2G087144_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G087144_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os09g35960.1 (Oryza sativa), 5'ss of exon 3
GGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCCTTCCTACTAGGAgtgtgagttacttgatctcttttacctatcctgtaaatttataaccgatgatttttttgggtgcaagtttaacagtacacatgtgcatgtcaataccttc-----
||||||||| || | || ||||||||||||||||||||||| |||||||||||||||  || ||||||| ||   |||  |||| || |||| |  |  ||| ||||    ||||||| |     ||  |    |     | || | |     
GGCATTGAACCAGGAATCAGGGCTGAAGTTTGGCCCTTCCTGCTAGGAGTgtgagttttttaatctcttctatgcatctagtaa-ttcataagctttcgtttctttgac--caagtttgaggtcgcaactacatacacgtagacttcctatag
















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|148981030|gb|EE027393.2|EE027393
EST:     GGCATTGAAGCCAGCATTAGGGCTGAAGTTTGGCCCTTCCTACTAGGA                         GTCCATGATTTGAATAGCTCTGAAGAGGAA
genomic: GGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCCTTCCTACTAGGAgtgtgagtta ... gtatctgcagCT--ATGATTTGAATAGCTCTGAAGAGGAA
EST: gi|149106092|gb|EE291756.2|EE291756
EST:     GGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCCTTCCTACTAGGA                         G
genomic: GGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCCTTCCTACTAGGAgtgtgagtta ... gtatctgcag-
EST: gi|149106092|gb|EE291756.2|EE291756
EST:     GGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCCTTCCTACTAGGA                         G
genomic: GGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCCTTCCTACTAGGAgtgtgagtta ... gtatctgcag-
EST: gi|149106092|gb|EE291756.2|EE291756
EST:     GGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCCTTCCTACTAGGA                         G
genomic: GGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCCTTCCTACTAGGAgtgtgagtta ... gtatctgcag-
EST: gi|148939166|gb|EC883612.2|EC883612
EST:     GGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCCTTCCTACTAGGA                         G
genomic: GGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCCTTCCTACTAGGAgtgtgagtta ... gtatctgcag-
EST: gi|148939166|gb|EC883612.2|EC883612
EST:     GGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCCTTCCTACTAGGA                         G
genomic: GGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCCTTCCTACTAGGAgtgtgagtta ... gtatctgcag-
EST: gi|148939166|gb|EC883612.2|EC883612
EST:     GGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCCTTCCTACTAGGA                         G
genomic: GGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCCTTCCTACTAGGAgtgtgagtta ... gtatctgcag-
EST: gi|50332287|gb|CO527413.1|CO527413
EST:     GGCATTGAAGCAAGCATTACGGCTGAAGTTTGGCCCTTCCTACTAGGA                         G
genomic: GGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCCTTCCTACTAGGAgtgtgagtta ... gtatctgcag-
EST: gi|50332287|gb|CO527413.1|CO527413
EST:     GGCATTGAAGCAAGCATTACGGCTGAAGTTTGGCCCTTCCTACTAGGA                         G
genomic: GGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCCTTCCTACTAGGAgtgtgagtta ... gtatctgcag-
EST: gi|50332287|gb|CO527413.1|CO527413
EST:     GGCATTGAAGCAAGCATTACGGCTGAAGTTTGGCCCTTCCTACTAGGA                         G
genomic: GGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCCTTCCTACTAGGAgtgtgagtta ... gtatctgcag-
EST: gi|211328212|gb|FL409834.1|FL409834
EST:     GGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCCTTCCTACTAGGA                         G
genomic: GGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCCTTCCTACTAGGAgtgtgagtta ... gtatctgcag-
EST: gi|211328212|gb|FL409834.1|FL409834
EST:     GGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCCTTCCTACTAGGA                         G
genomic: GGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCCTTCCTACTAGGAgtgtgagtta ... gtatctgcag-
EST: gi|211328212|gb|FL409834.1|FL409834
EST:     GGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCCTTCCTACTAGGA                         G
genomic: GGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCCTTCCTACTAGGAgtgtgagtta ... gtatctgcag-
EST: gi|211240372|gb|FL028808.1|FL028808
EST:     GGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCCTTCCTACTAGGA                         G
genomic: GGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCCTTCCTACTAGGAgtgtgagtta ... gtatctgcag-
EST: gi|211240372|gb|FL028808.1|FL028808
EST:     GGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCCTTCCTACTAGGA                         G
genomic: GGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCCTTCCTACTAGGAgtgtgagtta ... gtatctgcag-
EST: gi|211240372|gb|FL028808.1|FL028808
EST:     GGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCCTTCCTACTAGGA                         G
genomic: GGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCCTTCCTACTAGGAgtgtgagtta ... gtatctgcag-
EST: gi|211240371|gb|FL028807.1|FL028807
EST:     GGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCCTTCCTACTAGGA                         G
genomic: GGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCCTTCCTACTAGGAgtgtgagtta ... gtatctgcag-
EST: gi|211240371|gb|FL028807.1|FL028807
EST:     GGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCCTTCCTACTAGGA                         G
genomic: GGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCCTTCCTACTAGGAgtgtgagtta ... gtatctgcag-
EST: gi|211240371|gb|FL028807.1|FL028807
EST:     GGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCCTTCCTACTAGGA                         G
genomic: GGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCCTTCCTACTAGGAgtgtgagtta ... gtatctgcag-
EST: gi|50325323|gb|CO520449.1|CO520449
EST:     GGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCCTTCCTACTAGGA                         G
genomic: GGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCCTTCCTACTAGGAgtgtgagtta ... gtatctgcag-
EST: gi|50325323|gb|CO520449.1|CO520449
EST:     GGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCCTTCCTACTAGGA                         G
genomic: GGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCCTTCCTACTAGGAgtgtgagtta ... gtatctgcag-
EST: gi|50325323|gb|CO520449.1|CO520449
EST:     GGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCCTTCCTACTAGGA                         G
genomic: GGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCCTTCCTACTAGGAgtgtgagtta ... gtatctgcag-
EST: gi|148959376|gb|EC905424.2|EC905424
EST:     GGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCCCTTCCTACTAGGA                         G
genomic: GGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCC-TTCCTACTAGGAgtgtgagtta ... gtatctgcag-
EST: gi|148959376|gb|EC905424.2|EC905424
EST:     GGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCCCTTCCTACTAGGA                         G
genomic: GGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCC-TTCCTACTAGGAgtgtgagtta ... gtatctgcag-
EST: gi|148959376|gb|EC905424.2|EC905424
EST:     GGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCCCTTCCTACTAGGA                         G
genomic: GGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCC-TTCCTACTAGGAgtgtgagtta ... gtatctgcag-
EST: gi|148964953|gb|EE015802.2|EE015802
EST:     GGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCCTTCCTACTAGGA                         G
genomic: GGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCCTTCCTACTAGGAgtgtgagtta ... gtatctgcag-
EST: gi|148964953|gb|EE015802.2|EE015802
EST:     GGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCCTTCCTACTAGGA                         G
genomic: GGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCCTTCCTACTAGGAgtgtgagtta ... gtatctgcag-
EST: gi|148964953|gb|EE015802.2|EE015802
EST:     GGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCCTTCCTACTAGGA                         G
genomic: GGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCCTTCCTACTAGGAgtgtgagtta ... gtatctgcag-

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCCTTCCTACTAGGAgtgtgagttacttgatctcttttacctatcctgtaaatttataaccgatgatttttttgggtgcaagtttaacagtacacatgtgcatgtcaataccttc

- - TTGAAG
- -  TGAAGC
- - -  AAGCAA
- - - - AGCAAG
- - - - - - - - - - - CTGAAG