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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTGATGGGTTCATTGACCTTGATGCATATGATACAATAGCAATGAAGATCAAAGGGGATGGAAGATGCTACATATCTACAgtgtgttttctcacacaagactcactcttgaatattaaatgtccagtcagtattgttcttcagaatctgaaatcttaataagtacag

Basic information

species Zea mays
transcript GRMZM2G144716_T02
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G144716_T02 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os01g52720.1 (Oryza sativa), 5'ss of exon 6
TTTGATGGGTTCATTGACCTTGATGCATATGATACAATAGCAATGAAGATCAAAGGGGATGGAAGATGCTACATATCTACAgtgtgttttctcacacaagactcactcttgaatattaaatgtccagtcagtattgttcttcagaatctgaaatcttaataagtacag
||| |||| |||||||| ||||||||||||||||| ||||| |||||  ||| ||||||||||||||||||||||||||| || ||| | ||||  |  ||  || | |||||| |   || || ||| | ||   | ||  | |||||||| ||||||| |  ||||
TTTAATGGTTTCATTGATCTTGATGCATATGATACTATAGCGATGAAACTCAGAGGGGATGGAAGATGCTACATATCTACTgtatgtatcctcatcct-gagacagtattgaatgtgcgatatcaagttaatacgttgctatataatctgaa-tcttaattaa-acag
















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|89248889|gb|DY620675.1|DY620675
EST:     ATACAATAGCAATGAAGATCAAAGGGGATGGAAGATGCTACATATCTACA                         ATATACACGGAGAATTGGGTGAATTCACCCGGGCAACAAGAAGACAACTCG
genomic: ATACAATAGCAATGAAGATCAAAGGGGATGGAAGATGCTACATATCTACAgtgtgttttc ... ataagtacagATATACACGGAGAATTGGGTGAATTCACCCGGGCAACAAGAAGACAACTCG
EST: gi|12046177|gb|BF728316.1|BF728316
EST:     ATACAATAGCAATGAAGATCAAAGGGGATGGAAGATGCTACATATCTACA                         ATATACACGGAGAATTGGGTGAATTCACCCGGGCAACAAGAAGACAACTCG
genomic: ATACAATAGCAATGAAGATCAAAGGGGATGGAAGATGCTACATATCTACAgtgtgttttc ... ataagtacagATATACACGGAGAATTGGGTGAATTCACCCGGGCAACAAGAAGACAACTCG
EST: gi|71429695|gb|DR810745.1|DR810745
EST:     ATACAATAGCAATGAAGATCAAAGGGGATGGAAGATGCTACATATCTACA                         ATATACACGGAGAATTGGGTGAATTCACCCGGGCAACAAGAAGACAACTCG
genomic: ATACAATAGCAATGAAGATCAAAGGGGATGGAAGATGCTACATATCTACAgtgtgttttc ... ataagtacagATATACACGGAGAATTGGGTGAATTCACCCGGGCAACAAGAAGACAACTCG
EST: gi|78179752|gb|DV550125.1|DV550125
EST:     ATACAATAGCAATGAAGATCAAAGGGGATGGAAGATGCTACATATCTACA                         ATATACACGGAGAATTGGGTGAATTCACCCGGGCAACAAGAAGACAACTCG
genomic: ATACAATAGCAATGAAGATCAAAGGGGATGGAAGATGCTACATATCTACAgtgtgttttc ... ataagtacagATATACACGGAGAATTGGGTGAATTCACCCGGGCAACAAGAAGACAACTCG
EST: gi|6636927|gb|AW261199.1|AW261199
EST:     ATACAATAGCAATGAAGATCAAAGGGGATGGAAGATGCTACATATCTACA                         ATATACACGGAGAACTGGGTGAATTCACCCGGGCAACAAGAAGACAACT
genomic: ATACAATAGCAATGAAGATCAAAGGGGATGGAAGATGCTACATATCTACAgtgtgttttc ... ataagtacagATATACACGGAGAATTGGGTGAATTCACCCGGGCAACAAGAAGACAACT
EST: gi|78081290|gb|DV509702.1|DV509702
EST:     ATACAATAGCAATGAAGATCAAAGGGGATGGAAGATGCTACATATCTACA                         ATATACACGGAGAATTGGGTGAATTCACCCGGGCAACAAGAAGACAACTCG
genomic: ATACAATAGCAATGAAGATCAAAGGGGATGGAAGATGCTACATATCTACAgtgtgttttc ... ataagtacagATATACACGGAGAATTGGGTGAATTCACCCGGGCAACAAGAAGACAACTCG
EST: gi|78081291|gb|DV509703.1|DV509703
EST:     ATACAATAGCAATGAAGATCAAAGGGGATGGAAGATGCTACATATCTACA                         ATATACACGGAGAATTGGGTGAATTCACCCGGGCAACAAGAAGACAACTCG
genomic: ATACAATAGCAATGAAGATCAAAGGGGATGGAAGATGCTACATATCTACAgtgtgttttc ... ataagtacagATATACACGGAGAATTGGGTGAATTCACCCGGGCAACAAGAAGACAACTCG
EST: gi|32838973|gb|CD978654.1|CD978654
EST:     ATACAATAGCAATGAAGATCAAAGGGGATGGAAGATGCTACATATCTACA                         ATATACACGGAGAATTGGGTGAATTCACCCGGGCAACAAGAAGACAACTCA
genomic: ATACAATAGCAATGAAGATCAAAGGGGATGGAAGATGCTACATATCTACAgtgtgttttc ... ataagtacagATATACACGGAGAATTGGGTGAATTCACCCGGGCAACAAGAAGACAACTCG
EST: gi|60340500|gb|DN207473.1|DN207473
EST:     ATACAATAGCAATGAAGATCAAAGGGGATGGAAGATGCTACATATCTACA                         ATATACACGGAGAATTGGGTGAATTCACCCGGGCAACAAGAAGACAACTCG
genomic: ATACAATAGCAATGAAGATCAAAGGGGATGGAAGATGCTACATATCTACAgtgtgttttc ... ataagtacagATATACACGGAGAATTGGGTGAATTCACCCGGGCAACAAGAAGACAACTCG
EST: gi|76917524|gb|DV166879.1|DV166879
EST:     ATACAATAGCAATGAAGATCAAAGGGGATGGAAGATGCTACATATCTACA                         ATATACACGGAGAATTGGGTGAATTCACCCGGGCAACAAGAAGACAACTCG
genomic: ATACAATAGCAATGAAGATCAAAGGGGATGGAAGATGCTACATATCTACAgtgtgttttc ... ataagtacagATATACACGGAGAATTGGGTGAATTCACCCGGGCAACAAGAAGACAACTCG
EST: gi|71429835|gb|DR810885.1|DR810885
EST:     ATACAATAGCAATGAAGATCAAAGGGGATGGAAGATGCTACATATCTACA                         ATATACACGGAGAATTGGGTGAATTCACCCGGGCAACAAGAAGACAACTCG
genomic: ATACAATAGCAATGAAGATCAAAGGGGATGGAAGATGCTACATATCTACAgtgtgttttc ... ataagtacagATATACACGGAGAATTGGGTGAATTCACCCGGGCAACAAGAAGACAACTCG
EST: gi|6827615|gb|AW331258.1|AW331258
EST:     ATACAATAGCAATGAAGATCAAAGGGGATGGAAGATGCTACATATCTACA                         ATATACACGGAGAATTGGGTGAATTCACCCGGGCAACAAGAAGACAACTCG
genomic: ATACAATAGCAATGAAGATCAAAGGGGATGGAAGATGCTACATATCTACAgtgtgttttc ... ataagtacagATATACACGGAGAATTGGGTGAATTCACCCGGGCAACAAGAAGACAACTCG
EST: gi|148957873|gb|EC904027.2|EC904027
EST:     ATACAATAGCAATGAAGATCAAAGGGGATGGAAGATGCTACATATCTACA                         ATATACACGGAGAATTGGGTGAATTCACCCGGGCAACAAGAAGACAACTCG
genomic: ATACAATAGCAATGAAGATCAAAGGGGATGGAAGATGCTACATATCTACAgtgtgttttc ... ataagtacagATATACACGGAGAATTGGGTGAATTCACCCGGGCAACAAGAAGACAACTCG
EST: gi|211417239|gb|FL450863.1|FL450863
EST:     ATACAATAGCAATGAAGATCAAAGGGGATGGAAGATGCTACATATCTACA                         ATATACACGGAGAATTGGGTGAATTCACCCGGGCAACAAGAAGACAACTCG
genomic: ATACAATAGCAATGAAGATCAAAGGGGATGGAAGATGCTACATATCTACAgtgtgttttc ... ataagtacagATATACACGGAGAATTGGGTGAATTCACCCGGGCAACAAGAAGACAACTCG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTGATGGGTTCATTGACCTTGATGCATATGATACAATAGCAATGAAGATCAAAGGGGATGGAAGATGCTACATATCTACAgtgtgttttctcacacaagactcactcttgaatattaaatgtccagtcagtattgttcttcagaatctgaaatcttaataagtacag

- - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG