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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGATGTCATGTGCTCGGCCTGTCAGATGGCTGTCGTGTGGATAGAGAACCAGCTCCGCGAAAACAAGACCAAGGAGCTCATACTGCAGTACGCTAACCAGgtaaccaaactaacgatttactctgcatcttttttttcttcttcttctttggccaatttcttggatcgtatctgttgtatatatataataaccggtgacaggattctgcctgtgttcttgcatgcaccag

Basic information

species Zea mays
transcript GRMZM2G123029_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G123029_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os05g04630.6 (Oryza sativa), 5'ss of exon 8
AGATGTCATGTGCTCGGCCTGTCAGATGGCTGTCGTGTGGATAGAGAACCAGCTCCGCGAAAACAAGACCAAGGAGCTCATACTGCAGTACGCTAACCAGgtaaccaaactaacgatttactctgcatcttttttttcttcttcttctttggccaatttcttggatcgtatctgttgtatatatataataaccggtgacaggattctgcctgtgttcttgcatgcaccag
 ||||  ||||| || |  ||| |||||||||| |||||||||||||||||||| |||||||| || || |||||||| ||| || | || ||||| ||||| || |       | |  || || |   ||| | |  ||||     | ||   |||| ||   |  || | ||   |  || |  |                                           
TGATGCTATGTGTTCAGTTTGTGAGATGGCTGTTGTGTGGATAGAGAACCAGCTACGCGAAAATAAAACGAAGGAGCTGATATTGAATTATGCTAATCAGgttactatcactgtg-tccacactac---tttctatgattctcaaattatg--taattgctgacaaggt-tttgccttgcat-tccag------------------------------------------
















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|211417811|gb|FL246180.1|FL246180
EST:     AGCTCCGCGAAAACAAGACCAAGGAGCTCATACTGCAGTACGCTAACCAG                         CTGTGTGAGCGTCTGCCGAGCCCCAACGGAGAATCAACAGTCAGCTGCCAG
genomic: AGCTCCGCGAAAACAAGACCAAGGAGCTCATACTGCAGTACGCTAACCAGgtaaccaaac ... catgcaccagCTGTGTGAGCGTCTGCCGAGCCCCAACGGAGAGTCAACAGTCAGCTGCCAG
EST: gi|149100422|gb|EE186497.2|EE186497
EST:     AGCTCCGCGAAAACAAGACCAAGGAGCTCATACTGCAGTACGCTAACCAG                         CTGTGTGAGCGTCTGCCGAGCCCCAACGGAGAGTCAACAGTCAGCTGCCAG
genomic: AGCTCCGCGAAAACAAGACCAAGGAGCTCATACTGCAGTACGCTAACCAGgtaaccaaac ... catgcaccagCTGTGTGAGCGTCTGCCGAGCCCCAACGGAGAGTCAACAGTCAGCTGCCAG
EST: gi|110208372|gb|EC890269.1|EC890269
EST:     AGCTCCGCGAAAACAAGACCAAGGAGCTCATACTGCAGTACGCTAACCAG                         CTGTGTGAGCGTCTGCCGAGCCCCAACGGAGAGTCAACAGTCAGCTGCCAG
genomic: AGCTCCGCGAAAACAAGACCAAGGAGCTCATACTGCAGTACGCTAACCAGgtaaccaaac ... catgcaccagCTGTGTGAGCGTCTGCCGAGCCCCAACGGAGAGTCAACAGTCAGCTGCCAG
EST: gi|148999547|gb|EE036519.2|EE036519
EST:     AACAAGACCAAGGAGCTCATACTGCAGTACGCTAACCAG                         CTGTGTGAGCGTCTGCCGAGCCCCAACGGAGAGTCAACAGTCAGCTGCCAG
genomic: AACAAGACCAAGGAGCTCATACTGCAGTACGCTAACCAGgtaaccaaac ... catgcaccagCTGTGTGAGCGTCTGCCGAGCCCCAACGGAGAGTCAACAGTCAGCTGCCAG
EST: gi|211114340|gb|FL479352.1|FL479352
EST:     AG-TCCGCGAAAACAAGACCAAGGAGYTCATACTGCAGTACGCTAACCAG                         CTGTGTGAGCGTCTGCCGAGCCCCAACGGAGAGTCAACAGTCAGCTGCCAG
genomic: AGCTCCGCGAAAACAAGACCAAGGAGCTCATACTGCAGTACGCTAACCAGgtaaccaaac ... catgcaccagCTGTGTGAGCGTCTGCCGAGCCCCAACGGAGAGTCAACAGTCAGCTGCCAG
EST: gi|32913325|gb|CF018137.1|CF018137
EST:     AGCTCCGCGAAAACAAGACCAAGGAGCTCATACTGCAGTACGCTAACCAG                         CTGTGTGAGCGTCTGCCGAGCCCCAACGGAGAGTCAACAGTCAGCTGCCAG
genomic: AGCTCCGCGAAAACAAGACCAAGGAGCTCATACTGCAGTACGCTAACCAGgtaaccaaac ... catgcaccagCTGTGTGAGCGTCTGCCGAGCCCCAACGGAGAGTCAACAGTCAGCTGCCAG
EST: gi|7204603|gb|AW559186.1|AW559186
EST:     AGCTCCGCGAAAACAAGACCAAGGAGCTCATACTGCAGTACGCTAACCAG                         CTGTGTGAGCGTCTGCCGAGCCCCAACGGAGAGTCAACAGTCAGCTGCCAG
genomic: AGCTCCGCGAAAACAAGACCAAGGAGCTCATACTGCAGTACGCTAACCAGgtaaccaaac ... catgcaccagCTGTGTGAGCGTCTGCCGAGCCCCAACGGAGAGTCAACAGTCAGCTGCCAG
EST: gi|149078277|gb|EE167036.2|EE167036
EST:     AGCTCCGCGAAAACAAGACCAAGGAGCTCATACTGCAGTACGCTAACCAG                         CTGTGTGAGCGTCTGCCGAGCCCCAACGGAGAGTCAACAGTCAGCTGCCAG
genomic: AGCTCCGCGAAAACAAGACCAAGGAGCTCATACTGCAGTACGCTAACCAGgtaaccaaac ... catgcaccagCTGTGTGAGCGTCTGCCGAGCCCCAACGGAGAGTCAACAGTCAGCTGCCAG
EST: gi|211417815|gb|FL246184.1|FL246184
EST:     GGAGCTCATACTGCAGTACGCTAACCAG                         CTGTGTGAGCGTCTGCCGAGCCCCAACGGAGAGTCAACAGTCAGCTGCCAG
genomic: GGAGCTCATACTGCAGTACGCTAACCAGgtaaccaaac ... catgcaccagCTGTGTGAGCGTCTGCCGAGCCCCAACGGAGAGTCAACAGTCAGCTGCCAG
EST: gi|93012558|gb|EB638078.1|EB638078
EST:     AGCTCCGCGAAAACAAGACCAAGGAGCTCATACTGCAGTACGCTAACCAG                         CTGTGTGAGCGTCTGCCGAGCCCCAACGGAGAGTCAACAGTCAGCTGCCAG
genomic: AGCTCCGCGAAAACAAGACCAAGGAGCTCATACTGCAGTACGCTAACCAGgtaaccaaac ... catgcaccagCTGTGTGAGCGTCTGCCGAGCCCCAACGGAGAGTCAACAGTCAGCTGCCAG
EST: gi|211453148|gb|FL447178.1|FL447178
EST:     AGCTCCGCGAAAACAAGACCAAGGAGCTCATACTGCAGTACGCTAACCAG                         CTGTGTGAGCGTCTGCCGAGCCCCAACGGAGAGTCAACAGTCAGCTGCCAG
genomic: AGCTCCGCGAAAACAAGACCAAGGAGCTCATACTGCAGTACGCTAACCAGgtaaccaaac ... catgcaccagCTGTGTGAGCGTCTGCCGAGCCCCAACGGAGAGTCAACAGTCAGCTGCCAG
EST: gi|6827002|gb|AW330645.1|AW330645
EST:     AGCTCCGCGAAAACAAGACCAAGGAGCTCATACTGCAGTACGCTAACCAG                         CTGTGTGAGCGNCTGCCGAGCCCCAACGGAGAGTCAACAGTCAGCTGCCAG
genomic: AGCTCCGCGAAAACAAGACCAAGGAGCTCATACTGCAGTACGCTAACCAGgtaaccaaac ... catgcaccagCTGTGTGAGCGTCTGCCGAGCCCCAACGGAGAGTCAACAGTCAGCTGCCAG
EST: gi|45567994|gb|CK985848.1|CK985848
EST:     AGCTCCGCGAAAACAAGACCAAGGAGCTCATACTGCAGTACGCTAACCAG                         CTGTGTGAGCGTCTGCCGAGCCCCAACGGAGAGTCAACAGTCAGCTGCCAG
genomic: AGCTCCGCGAAAACAAGACCAAGGAGCTCATACTGCAGTACGCTAACCAGgtaaccaaac ... catgcaccagCTGTGTGAGCGTCTGCCGAGCCCCAACGGAGAGTCAACAGTCAGCTGCCAG
EST: gi|78109241|gb|DV527657.1|DV527657
EST:     AGCTCCGCGAAAACAAGACCAAGGAGCTCATACTGCAGTACGCTAACCAG                         CTGTGTGAGGGTCTGCCGAGCCCCAACGGAGAGTCAACAGTCAGTTGCCAG
genomic: AGCTCCGCGAAAACAAGACCAAGGAGCTCATACTGCAGTACGCTAACCAGgtaaccaaac ... catgcaccagCTGTGTGAGCGTCTGCCGAGCCCCAACGGAGAGTCAACAGTCAGCTGCCAG
EST: gi|149097402|gb|EE183255.2|EE183255
EST:     AGCTCCGCGAAAACAAGACCAAGGAGCTCATACTGCAGTACGCTAACCAG                         CTGTGTGAGCGTCTGCCGAGCCCCAACGGAGAGTCAACAGTCAGCTGCCAG
genomic: AGCTCCGCGAAAACAAGACCAAGGAGCTCATACTGCAGTACGCTAACCAGgtaaccaaac ... catgcaccagCTGTGTGAGCGTCTGCCGAGCCCCAACGGAGAGTCAACAGTCAGCTGCCAG
EST: gi|40303709|gb|CK348096.1|CK348096
EST:     AGCTCCGCGAAAACAAGACCAAGGAGCTCATACTGCAGTACGCTAACCAG                         CTGTGTGAGCGTCTGCCGAGCCCCAACGGAGAGTCAACAGTCAGCTGCCAG
genomic: AGCTCCGCGAAAACAAGACCAAGGAGCTCATACTGCAGTACGCTAACCAGgtaaccaaac ... catgcaccagCTGTGTGAGCGTCTGCCGAGCCCCAACGGAGAGTCAACAGTCAGCTGCCAG
EST: gi|6993891|gb|AW453105.1|AW453105
EST:     GCTCCGCGAAAACAAGACCAAGGAGCTCATACTGCAGTACGCTAACCAG                         CTGTGTGAGCGTCTGCCGAGCCCCAACGGAGAGTCAACAGTCAGCTGCCAG
genomic: GCTCCGCGAAAACAAGACCAAGGAGCTCATACTGCAGTACGCTAACCAGgtaaccaaac ... catgcaccagCTGTGTGAGCGTCTGCCGAGCCCCAACGGAGAGTCAACAGTCAGCTGCCAG
EST: gi|148980773|gb|EE027343.2|EE027343
EST:     AGCTCCGCGAAAACAAGACCAAGGAGCTCATACTGCAGTACGCTAACCAG                         CTGTGTGAGCGTCTGCCGAGCCCCAACGGAGAGTCAACAGTCAGCTGCCAG
genomic: AGCTCCGCGAAAACAAGACCAAGGAGCTCATACTGCAGTACGCTAACCAGgtaaccaaac ... catgcaccagCTGTGTGAGCGTCTGCCGAGCCCCAACGGAGAGTCAACAGTCAGCTGCCAG
EST: gi|18180292|gb|BM381502.1|BM381502
EST:     GCGAAAACAAGACCAAGGAGCTCATACTGCAGTACGCTAACCAG                         CTGTGTGAGCGTCTGCCGAGCCCCAACGGAGAGTCAACAGTCAGCTGCCAG
genomic: GCGAAAACAAGACCAAGGAGCTCATACTGCAGTACGCTAACCAGgtaaccaaac ... catgcaccagCTGTGTGAGCGTCTGCCGAGCCCCAACGGAGAGTCAACAGTCAGCTGCCAG
EST: gi|211489971|gb|FL475496.1|FL475496
EST:     AACAAGACCAAGGAGCTCATACTGCAGTACGCTACCCAG                         CTGTGTGAGCGTCTGCCGAGCCCCAACGGAGAGTCAACAGTCAGCTGCCAG
genomic: AACAAGACCAAGGAGCTCATACTGCAGTACGCTAACCAGgtaaccaaac ... catgcaccagCTGTGTGAGCGTCTGCCGAGCCCCAACGGAGAGTCAACAGTCAGCTGCCAG
EST: gi|149066691|gb|EE286828.2|EE286828
EST:     AGCTCCGCGAAAACAAGACCAAGGAGCTCATACTGCAGTACGCTAACCAG                         CTGTGTGAGCGTCTGCCGAGCCCCAACGGAGAGTCAACAGTCAGCTGCCAG
genomic: AGCTCCGCGAAAACAAGACCAAGGAGCTCATACTGCAGTACGCTAACCAGgtaaccaaac ... catgcaccagCTGTGTGAGCGTCTGCCGAGCCCCAACGGAGAGTCAACAGTCAGCTGCCAG
EST: gi|110520668|gb|EE024852.1|EE024852
EST:     AGCTCCGCGAAAACAAGACCAAGGAGCTCATACTGCAGTACGCTAACCAG                         CTGTGTGAGCGTCTGCCGAGCCCCAACGGAGAGTCAACAGTCAGCTGCCAG
genomic: AGCTCCGCGAAAACAAGACCAAGGAGCTCATACTGCAGTACGCTAACCAGgtaaccaaac ... catgcaccagCTGTGTGAGCGTCTGCCGAGCCCCAACGGAGAGTCAACAGTCAGCTGCCAG
EST: gi|211453149|gb|FL447179.1|FL447179
EST:     CAAGGAGCTCATACTGCAGTACGCTAACCAG                         CTGTGTGAGCGTCTGCCGAGCCCCAACGGAGAGTCAACAGTCAGCTGCCAG
genomic: CAAGGAGCTCATACTGCAGTACGCTAACCAGgtaaccaaac ... catgcaccagCTGTGTGAGCGTCTGCCGAGCCCCAACGGAGAGTCAACAGTCAGCTGCCAG
EST: gi|211401889|gb|FL450336.1|FL450336
EST:     AGCTCCGCGAAAACAAGACCAAGGAGCTCATACTGCAGTACGCTAACCAG                         CTGTGTGAGCGTCTGCCGAGCCCCAACGGAGAGTCAACAGTCAGCTGCCAG
genomic: AGCTCCGCGAAAACAAGACCAAGGAGCTCATACTGCAGTACGCTAACCAGgtaaccaaac ... catgcaccagCTGTGTGAGCGTCTGCCGAGCCCCAACGGAGAGTCAACAGTCAGCTGCCAG
EST: gi|60358971|gb|DN225944.1|DN225944
EST:     AGCTCCGCGAAAACAAGACCAAGGAGCTCATACTGCAGTACGCTAACCAG                         CTGTGTGAGCGTCTGCCGAGCCCCAACGGAGAGTCAACAGTCAGCTGCCAG
genomic: AGCTCCGCGAAAACAAGACCAAGGAGCTCATACTGCAGTACGCTAACCAGgtaaccaaac ... catgcaccagCTGTGTGAGCGTCTGCCGAGCCCCAACGGAGAGTCAACAGTCAGCTGCCAG
EST: gi|6695716|gb|AW288794.1|AW288794
EST:     AGCTCCGCGAAAACAAGACCAAGGAGCTCATACTGCAGTACGCTAACCAG                         CTGTGTGAGCGTCTGCCGAGCCCCAACGGAGAGTCAACAGTCAGCTGCCAG
genomic: AGCTCCGCGAAAACAAGACCAAGGAGCTCATACTGCAGTACGCTAACCAGgtaaccaaac ... catgcaccagCTGTGTGAGCGTCTGCCGAGCCCCAACGGAGAGTCAACAGTCAGCTGCCAG
EST: gi|5510772|gb|AI857156.1|AI857156
EST:     AGCTCCGCGAAACCAAGACCAAGGAGCTCATACTGCAGTACGCTAACCAG                         CTGTGTGAGCGTCTGCCGAGCCCCAACGGAGAGTCAACAGTCAGCTGCCAG
genomic: AGCTCCGCGAAAACAAGACCAAGGAGCTCATACTGCAGTACGCTAACCAGgtaaccaaac ... catgcaccagCTGTGTGAGCGTCTGCCGAGCCCCAACGGAGAGTCAACAGTCAGCTGCCAG
EST: gi|91876727|gb|EB406684.1|EB406684
EST:     AGCTCCGCGAAAACAAGACCAAGGAGCTCATACTGCAGTACGCTAACCAG                         CTGTGTGAGCGTCTGCCGAGCCCCAACGGAGAGTCAACAGTCAGCTGCCAG
genomic: AGCTCCGCGAAAACAAGACCAAGGAGCTCATACTGCAGTACGCTAACCAGgtaaccaaac ... catgcaccagCTGTGTGAGCGTCTGCCGAGCCCCAACGGAGAGTCAACAGTCAGCTGCCAG
EST: gi|91876845|gb|EB406802.1|EB406802
EST:     AGCTCCGCGAAAACAAGACCAAGGAGCTCATACTGCAGTACGCTAACCAG                         CTGTGTGAGCGTCTGCCGAGCCCCAACGGAGAGTCAACAGTCAGCTGCCAG
genomic: AGCTCCGCGAAAACAAGACCAAGGAGCTCATACTGCAGTACGCTAACCAGgtaaccaaac ... catgcaccagCTGTGTGAGCGTCTGCCGAGCCCCAACGGAGAGTCAACAGTCAGCTGCCAG
EST: gi|148987680|gb|EE031561.2|EE031561
EST:     AGCTCCGCGAAAACAAGACCAAGGAGCTCATACTGCAGTACGCTAACCAG                         CTGTGTGAGCGTCTGCCGAGCCCCAACGGAGAGTCAACAGTCAGCTGCCAG
genomic: AGCTCCGCGAAAACAAGACCAAGGAGCTCATACTGCAGTACGCTAACCAGgtaaccaaac ... catgcaccagCTGTGTGAGCGTCTGCCGAGCCCCAACGGAGAGTCAACAGTCAGCTGCCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGATGTCATGTGCTCGGCCTGTCAGATGGCTGTCGTGTGGATAGAGAACCAGCTCCGCGAAAACAAGACCAAGGAGCTCATACTGCAGTACGCTAACCAGgtaaccaaactaacgatttactctgcatcttttttttcttcttcttctttggccaatttcttggatcgtatctgttgtatatatataataaccggtgacaggattctgcctgtgttcttgcatgcaccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG