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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTTGTGTCAGTGAGCCATCTTTTTATTGGAGTACTATACTGCCTTATTGGCTGGAGCTTCGGCATCCCAAAGCGCGCGgtatagtcaacacctccatgatctttttcttttttgatagataacagcctatctaactcacagttaagcgttttcagtgacatttatgagcagggtgtgc...

Basic information

species Zea mays
transcript GRMZM2G083344_T03
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G083344_T03 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os05g15160.1 (Oryza sativa), 5'ss of exon 4
TTTTGTGTCAGTGAGCCATCTTTTTATTGGAGTACTATACTGCCTTATTGGCTGGAGCTTCGGCATCCCAAAGCGCGCGgtatagtca-------acacctccatgatctttttcttttttgatagataacagcctatctaactcacagttaagcgttttcagt-gacatttatgagcagggtgtgc
||||||||| ||||||||||||||  | |||||  | ||||||||| | |||||||| || ||  ||||||||||||||||||  |||        | | ||    | | |  |   |||  |||   | ||    ||  |    |   ||| | ||| |  ||  |||| ||| |           
TTTTGTGTCGGTGAGCCATCTTTTGGTAGGAGTCTTGTACTGCCTTGTCGGCTGGAGTTTTGGTCTCCCAAAGCGCGCGgtattctcatgcccatgcccttcttcaaccatgattcctttcaataatgagca-tgaatacacaaaattattaggggttgttggtcaacatatatcattgc-------
















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|78105001|gb|DV523419.1|DV523419
EST:     GAGTACTATACTGCCTTATTGGCTGGAGCTTCGGCATCCCAAAGCGCGCG                         CAAATCAACTCAACACTTCTGA
genomic: GAGTACTATACTGCCTTATTGGCTGGAGCTTCGGCATCCCAAAGCGCGCGgtatagtcaa ... acttctgtagCCAATCAACTCAACACTTCTGA
EST: gi|78104083|gb|DV522501.1|DV522501
EST:     GAGTACTATACTGCCTTATTGGCTGGAGCTTCGGCATCCCAAAGCGCGCG                         CCAATCAACTCAACACTTCTGAAGCAGCTTGTTCCAGTTGCGGTTTGCCAT
genomic: GAGTACTATACTGCCTTATTGGCTGGAGCTTCGGCATCCCAAAGCGCGCGgtatagtcaa ... acttctgtagCCAATCAACTCAACACTTCTGAAGCAGCTTGTTCCAGTTGCGGTTTGCCAT
EST: gi|149009525|gb|EE041508.2|EE041508
EST:     GAGTACTATACTGCCTTATTGGCTGGAGCTTCGGCATCCCAAAGCGCGCG                         CCAATCAACTCAACACTTCTGAAGCAGCTTGTTCCAGTTGCGGTTTGCCAT
genomic: GAGTACTATACTGCCTTATTGGCTGGAGCTTCGGCATCCCAAAGCGCGCGgtatagtcaa ... acttctgtagCCAATCAACTCAACACTTCTGAAGCAGCTTGTTCCAGTTGCGGTTTGCCAT
EST: gi|71439302|gb|DR820352.1|DR820352
EST:     GAGTACTATACTGCCTTATTGGCTGGAGCTTCGGCATCCCAAAGCGCGCG                         CCAATCAACTCAACACTTCTGAAGCAGCTTGTTCCAGTTGCGGTTTGCCAT
genomic: GAGTACTATACTGCCTTATTGGCTGGAGCTTCGGCATCCCAAAGCGCGCGgtatagtcaa ... acttctgtagCCAATCAACTCAACACTTCTGAAGCAGCTTGTTCCAGTTGCGGTTTGCCAT
EST: gi|78087779|gb|DV516172.1|DV516172
EST:     GAGTACTATACTGCCTTATTGGCTGGAGCTTCGGCATCCCAAAGCGCGCG                         CCAATCAACTCAACACTTCTGAAGCAGCTTGTTCCAGTTGCGGTTTGCCAT
genomic: GAGTACTATACTGCCTTATTGGCTGGAGCTTCGGCATCCCAAAGCGCGCGgtatagtcaa ... acttctgtagCCAATCAACTCAACACTTCTGAAGCAGCTTGTTCCAGTTGCGGTTTGCCAT
EST: gi|148961156|gb|EE011865.2|EE011865
EST:     GAGTACTATACTGCCTTATTGGCTGGAGCTTCGGCATCCCAAAGCGCGCG                         CCAATCAACTCAACACTTCTGAAGCAGCTTGTTCCAGTTGCGGTTTGCCAT
genomic: GAGTACTATACTGCCTTATTGGCTGGAGCTTCGGCATCCCAAAGCGCGCGgtatagtcaa ... acttctgtagCCAATCAACTCAACACTTCTGAAGCAGCTTGTTCCAGTTGCGGTTTGCCAT
EST: gi|28931223|gb|CB334584.1|CB334584
EST:     GAGTACTATACTGGCTTATTGGCTGGAGCTTCGGCATCCCAAAGCGCGCG                         CCAATCAACTCAACACTTCTGA
genomic: GAGTACTATACTGCCTTATTGGCTGGAGCTTCGGCATCCCAAAGCGCGCGgtatagtcaa ... acttctgtagCCAATCAACTCAACACTTCTGA
EST: gi|71768356|gb|DR966293.1|DR966293
EST:     GAGTACTATACTGCCTTATTGGCTGGAGCTTCGGCATCCCAAAGCGCGCG                         CCAATCAACTCAACACTTCTGAAGCAGCTTGTTCCAGTTGCGGTTTGCCAT
genomic: GAGTACTATACTGCCTTATTGGCTGGAGCTTCGGCATCCCAAAGCGCGCGgtatagtcaa ... acttctgtagCCAATCAACTCAACACTTCTGAAGCAGCTTGTTCCAGTTGCGGTTTGCCAT
EST: gi|211525181|gb|FL202007.1|FL202007
EST:     GAGTACTATACTGCCTTATTGGCTGGAGCTCCGGCATCCCAAAGCGCGCG                         CCAATCAACTCAACACTTCTG
genomic: GAGTACTATACTGCCTTATTGGCTGGAGCTTCGGCATCCCAAAGCGCGCGgtatagtcaa ... acttctgtagCCAATCAACTCAACACTTCTG
EST: gi|61119701|gb|DN560662.1|DN560662
EST:     GAGTACTATACTGCCTTATTGGCTGGAGCTTCGGCATCCCAAAGCGCGCG                         CCAATCAACTCAACACTTCTGAAGCAGCTTGTTCCAGTTGCGGTTTGCCAT
genomic: GAGTACTATACTGCCTTATTGGCTGGAGCTTCGGCATCCCAAAGCGCGCGgtatagtcaa ... acttctgtagCCAATCAACTCAACACTTCTGAAGCAGCTTGTTCCAGTTGCGGTTTGCCAT
EST: gi|91055754|gb|EB166172.1|EB166172
EST:     GAGTACTATACTGCCTTATTGGCTGGAGCTTCGGCATCCCAAAGCGCGCG                         CCAATCAACTCAACACTTCTGAAGCAGCTTGTTCCAGTTGCGGTTTGCCAT
genomic: GAGTACTATACTGCCTTATTGGCTGGAGCTTCGGCATCCCAAAGCGCGCGgtatagtcaa ... acttctgtagCCAATCAACTCAACACTTCTGAAGCAGCTTGTTCCAGTTGCGGTTTGCCAT
EST: gi|76930051|gb|DV172256.1|DV172256
EST:     GAGTACTATACTGCCTTATTGGCTGGAGCTTCGGCATCCCAAAGCGCGCG                         CCAATCAACTCAACACTTCTGAAGCAGCTTGTTCCAGTTGCGGTTTGCCAT
genomic: GAGTACTATACTGCCTTATTGGCTGGAGCTTCGGCATCCCAAAGCGCGCGgtatagtcaa ... acttctgtagCCAATCAACTCAACACTTCTGAAGCAGCTTGTTCCAGTTGCGGTTTGCCAT
EST: gi|94477389|gb|EB706347.1|EB706347
EST:     GAGTACTATACTGCCTTATTGGCTGGAGCTTCGGCATCCCAAAGCGCGCG                         CCAATCAACTCAACACTTCTGAAGCAGCTTGTTCCAGTTGCGGTTTGCCAT
genomic: GAGTACTATACTGCCTTATTGGCTGGAGCTTCGGCATCCCAAAGCGCGCGgtatagtcaa ... acttctgtagCCAATCAACTCAACACTTCTGAAGCAGCTTGTTCCAGTTGCGGTTTGCCAT
EST: gi|149095075|gb|EE180680.2|EE180680
EST:     GAGTACTATACTGCCTTATTGGCTGGAGCTTCGGCATCCCAAAGCGCGCG                         CCAATCAACTCAACACTTCTGAAGCAGCTTGTTCCAGTTGCGGTTTGCCAT
genomic: GAGTACTATACTGCCTTATTGGCTGGAGCTTCGGCATCCCAAAGCGCGCGgtatagtcaa ... acttctgtagCCAATCAACTCAACACTTCTGAAGCAGCTTGTTCCAGTTGCGGTTTGCCAT
EST: gi|28390338|gb|CB250166.1|CB250166
EST:     GAGTACTATACTGCCTTATTGGCTGGAGCTTCGGCATCCCAAAGCGCGCG                         CCAATCAACTCAACACTTCTGAAGCAGCTTGTTCCAGTTGCG
genomic: GAGTACTATACTGCCTTATTGGCTGGAGCTTCGGCATCCCAAAGCGCGCGgtatagtcaa ... acttctgtagCCAATCAACTCAACACTTCTGAAGCAGCTTGTTCCAGTTGCG
EST: gi|148962629|gb|EE013519.2|EE013519
EST:     GAGTACTATACTGCCTTATTGGCTGGAGCTTCGGCATCCCAAAGCGCGCG                         CCAATCAACTCAACACTTCTGAAGCAGCTTGTTCCAGTTGCGGTTTGCCAT
genomic: GAGTACTATACTGCCTTATTGGCTGGAGCTTCGGCATCCCAAAGCGCGCGgtatagtcaa ... acttctgtagCCAATCAACTCAACACTTCTGAAGCAGCTTGTTCCAGTTGCGGTTTGCCAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTTGTGTCAGTGAGCCATCTTTTTATTGGAGTACTATACTGCCTTATTGGCTGGAGCTTCGGCATCCCAAAGCGCGCGgtatagtcaacacctccatgatctttttcttttttgatagataacagcctatctaactcacagttaagcgttttcagtgacatttatgagcagggtgtgc

- - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT