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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcaagatcaaactatgcacatctttagtttttttttcctcgtgactttgtgctagttgagaggagaacaaggtttacatgttcaaggacattttacttccactgaaatcagtgatgatggcatctttatataattatgcagGTGAAACATGGAGTGGGCGTGGAGGGGATCGTGAACCATATTCTGCAGGCGTGGGAGATCGCGACTGGTAATAAGCGGCGATAAGATCTCACGACTTGGG

Basic information

species Zea mays
transcript GRMZM2G413652_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G413652_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os05g49050.1 (Oryza sativa), 3'ss of exon 6
gttcaagatcaaactatgcacatctttagtttttttttcctcgtgactttgtgctagttgagaggagaacaaggtttacatgttcaaggacattttacttccactgaaatcagtgatgatggcatctttatataattatgcagGTGAAACATGGAGTGGGCGTGGAGGGGATCGTGAACCATATTCTGCAGGCGTGGGAGATCGCGACTGGTAATAAGCGGCGATAAGATCTCACGACTTGGG-
|||||  || |||| || ||||| |   |||  |||||   || |       |  | || | || ||   | | |    ||    | ||||||   |  ||||     |    || | ||      |||| |    | | ||||||||||||||||| ||||||||||  || |||||||| || ||||| || ||||||||||| || || || ||||| ||||| |    || || |   | 
gttcagtattaaaccatacacattt---gttccttttttagcgggg------gaaaattaacagaagctgatgata---attgcaagggacat---agctccatatttacacatgcttat------tttacactgct-tccagGTGAAACATGGAGTCGGCGTGGAGGAAATTGTGAACCACATCCTGCAAGCTTGGGAGATCGCCACCGGCAACAAGCGTCGATA-GCCTGCAGGATTCTTGG
















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|26557997|gb|CA830232.1|CA830232
EST:     AGCGAGACGCACTTCGCATGCGCGAAGGAGGGCCCTTTGTGTTTGCACAG                         GTGAAACATGGAGTGGGCGTGGAGGGGATCGTGAACCATATTCTGCAGGCG
genomic: AGCGAGACGCACTTCGCATGCGCGAAGGAGGGCCCTTTGTGTTTGCACAGgttcaagatc ... aattatgcagGTGAAACATGGAGTGGGCGTGGAGGGGATCGTGAACCATATTCTGCAGGCG
EST: gi|40336418|gb|CK370488.1|CK370488
EST:     AGCGAGACGCACTTCGCATGCGCGAAGGAGGGCCCTTTGTGTTTGCACAG                         GTGAAACATGGAGTGGGCGTGGAGGGGATCGTGAACCATATTCTGCAGGCG
genomic: AGCGAGACGCACTTCGCATGCGCGAAGGAGGGCCCTTTGTGTTTGCACAGgttcaagatc ... aattatgcagGTGAAACATGGAGTGGGCGTGGAGGGGATCGTGAACCATATTCTGCAGGCG
EST: gi|37389805|gb|CF632125.1|CF632125
EST:     AGCGAGACGCACTTCGCATGCGCGAAGGAGGGCCCTTTGTGTTTGCACAG                         GTGAAACATGGAGTGGGCGTGGAGGGGATCGTGAACCATATTCTGCAGGCG
genomic: AGCGAGACGCACTTCGCATGCGCGAAGGAGGGCCCTTTGTGTTTGCACAGgttcaagatc ... aattatgcagGTGAAACATGGAGTGGGCGTGGAGGGGATCGTGAACCATATTCTGCAGGCG
EST: gi|32928124|gb|CF032936.1|CF032936
EST:     AGCGAGACGCACCTCGCATGCGCGAAGGAGGGCCCTTTGTGTTTGCACAG                         GTGAAACATGGAGTGGGCGTGGAGGGGATCGTGAACCATATTCTGCAGGCG
genomic: AGCGAGACGCACTTCGCATGCGCGAAGGAGGGCCCTTTGTGTTTGCACAGgttcaagatc ... aattatgcagGTGAAACATGGAGTGGGCGTGGAGGGGATCGTGAACCATATTCTGCAGGCG
EST: gi|78179335|gb|DV549708.1|DV549708
EST:     AGCGAGACGCACTTCGCATGCGCGAAGGAGGGCCCTTTGTGTTTGCACAG                         GTGAAACATGGAGTGGGCGTGGAGGGGATCGTGAACCATATTCTGCAGGCG
genomic: AGCGAGACGCACTTCGCATGCGCGAAGGAGGGCCCTTTGTGTTTGCACAGgttcaagatc ... aattatgcagGTGAAACATGGAGTGGGCGTGGAGGGGATCGTGAACCATATTCTGCAGGCG
EST: gi|21891681|gb|BQ744894.1|BQ744894
EST:     GCGAGACGCACTTTCGCATGCGCGAAGGAGGGCCCTTTGTGTTTGCACAG                         GTGAAACATGGAGTGGGCGTGGAGGGGATCGTGAACCATATTCTGCAGGCG
genomic: GCGAGACGCAC-TTCGCATGCGCGAAGGAGGGCCCTTTGTGTTTGCACAGgttcaagatc ... aattatgcagGTGAAACATGGAGTGGGCGTGGAGGGGATCGTGAACCATATTCTGCAGGCG
EST: gi|166459428|gb|EG288282.1|EG288282
EST:     CGAGACGCACTTCGCATGCGCGAAGGAGGGCCCTTTGTGTTTGCACAG                         GTGAAACATGGAGTGGGCGTGGAGGGGATCGTGAACCATATTCTGCAGGCG
genomic: CGAGACGCACTTCGCATGCGCGAAGGAGGGCCCTTTGTGTTTGCACAGgttcaagatc ... aattatgcagGTGAAACATGGAGTGGGCGTGGAGGGGATCGTGAACCATATTCTGCAGGCG
EST: gi|161407584|gb|DW042408.1|DW042408
EST:     AGCGAGACGCACTTCGCATGCGCGAAGGAGGGCCCTTTGTGTTTGCACAG                         GTGAAACATGGAGTGGGCGTGGAGGGGATCGTGAACCATATTCTGCAGGCG
genomic: AGCGAGACGCACTTCGCATGCGCGAAGGAGGGCCCTTTGTGTTTGCACAGgttcaagatc ... aattatgcagGTGAAACATGGAGTGGGCGTGGAGGGGATCGTGAACCATATTCTGCAGGCG
EST: gi|211452606|gb|FL416418.1|FL416418
EST:     AGCGAGACGCACTTCGCATGCGCGAAGGAGGGCCCTTTGTGTTTGCACAG                         GTGAAACATGGAGTGGGCGTGGAGGGGATCGTGAACCATATTCTGCAGGCG
genomic: AGCGAGACGCACTTCGCATGCGCGAAGGAGGGCCCTTTGTGTTTGCACAGgttcaagatc ... aattatgcagGTGAAACATGGAGTGGGCGTGGAGGGGATCGTGAACCATATTCTGCAGGCG
EST: gi|60358340|gb|DN225313.1|DN225313
EST:     AGCGAGACGCACTTCGCATGCGCGAAGGAGGGCCCTTTGTGTTTGCACAG                         GTGAAACATGGAGTGGGCGTGGAGGGGATCGTGAACCATATTCTGCAGGCG
genomic: AGCGAGACGCACTTCGCATGCGCGAAGGAGGGCCCTTTGTGTTTGCACAGgttcaagatc ... aattatgcagGTGAAACATGGAGTGGGCGTGGAGGGGATCGTGAACCATATTCTGCAGGCG
EST: gi|8577258|gb|BE129895.1|BE129895
EST:     AGCGAGACGCACTTCGCATGCGCGAAGGAGGGCCCCTTGTGTTTGCACAG                         GTGAAACATGGAGTGGGCGTGGAGGGGATCGTGAACCATATTCTGCAGGCG
genomic: AGCGAGACGCACTTCGCATGCGCGAAGGAGGGCCCTTTGTGTTTGCACAGgttcaagatc ... aattatgcagGTGAAACATGGAGTGGGCGTGGAGGGGATCGTGAACCATATTCTGCAGGCG
EST: gi|94473481|gb|EB702439.1|EB702439
EST:     AGCGAGACGCACTTCGCATGCGCGAAGGAGGGCCCTTTGTGTTTGCACAG                         GTGAAACATGGAGTGGGCGTGGAGGGGATCGTGAACCATATTCTGCAGGCG
genomic: AGCGAGACGCACTTCGCATGCGCGAAGGAGGGCCCTTTGTGTTTGCACAGgttcaagatc ... aattatgcagGTGAAACATGGAGTGGGCGTGGAGGGGATCGTGAACCATATTCTGCAGGCG
EST: gi|12047268|gb|BF729407.1|BF729407
EST:     AGCGAGACGCACTTCGCATGCGCGAAGGAGGGCCCTTTGTGTTTGCACAG                         GTGAAACATGGAGTGGGCGTGGAGGGGATCGTGAACCATATTCTGCAGGCG
genomic: AGCGAGACGCACTTCGCATGCGCGAAGGAGGGCCCTTTGTGTTTGCACAGgttcaagatc ... aattatgcagGTGAAACATGGAGTGGGCGTGGAGGGGATCGTGAACCATATTCTGCAGGCG
EST: gi|32856963|gb|CD996644.1|CD996644
EST:     AGCGAGACGCACTTCGCATGCGCGAAGGAGGGCCCTTTGTGTTTGCACAG                         GTGAAACATGGAGTGGGCGTGGAGGGGATCGTGAACCATATTCTGCAGGCG
genomic: AGCGAGACGCACTTCGCATGCGCGAAGGAGGGCCCTTTGTGTTTGCACAGgttcaagatc ... aattatgcagGTGAAACATGGAGTGGGCGTGGAGGGGATCGTGAACCATATTCTGCAGGCG
EST: gi|21891682|gb|BQ744895.1|BQ744895
EST:     AGCGAGACGCACTTCGCATGCGCGAAGGAGGGCCCTTTGTGTTTGCACAG                         GTGAAACATGGAGTGGGCGTGGAGGGGATCGTGAACCATATTCTGCAGGCG
genomic: AGCGAGACGCACTTCGCATGCGCGAAGGAGGGCCCTTTGTGTTTGCACAGgttcaagatc ... aattatgcagGTGAAACATGGAGTGGGCGTGGAGGGGATCGTGAACCATATTCTGCAGGCG
EST: gi|18173278|gb|BM348666.1|BM348666
EST:     AGCGAGACGCACTTCGCATGCGCGAAGGAGGGCCCTTTGTGTTTGCACAG                         GTGAAACATGGAGTGGGCGTGGAGGGGATCGTGAACCATATTCTGCAGGCG
genomic: AGCGAGACGCACTTCGCATGCGCGAAGGAGGGCCCTTTGTGTTTGCACAGgttcaagatc ... aattatgcagGTGAAACATGGAGTGGGCGTGGAGGGGATCGTGAACCATATTCTGCAGGCG
EST: gi|87156249|gb|DY401038.1|DY401038
EST:     AGCGAGACGCACTTCGCATGCGCGAAGGAGGGCCCTTTGTGTTTGCACAG                         GTGAAACATGGAGTGGGCGTGGAGGGGATCGTGAACCATATTCTGCAGGCG
genomic: AGCGAGACGCACTTCGCATGCGCGAAGGAGGGCCCTTTGTGTTTGCACAGgttcaagatc ... aattatgcagGTGAAACATGGAGTGGGCGTGGAGGGGATCGTGAACCATATTCTGCAGGCG
EST: gi|21843537|gb|BQ704118.1|BQ704118
EST:     AGCGAGACGCACTTCGCATGCGCGAAGGAGGGCCCTTTGTGTTTGCACAG                         GTGAAACATGGAGTGGGCGTGGAGGGGATCGTGAACCATATTCTGCAGGCG
genomic: AGCGAGACGCACTTCGCATGCGCGAAGGAGGGCCCTTTGTGTTTGCACAGgttcaagatc ... aattatgcagGTGAAACATGGAGTGGGCGTGGAGGGGATCGTGAACCATATTCTGCAGGCG
EST: gi|32910302|gb|CF015114.1|CF015114
EST:     AGCGAGACGCACTTCGCATGCGCGAAGGAGGGCCCTTTGTGTTTGCACAG                         GTGAAACATGGAGTGGGCGTGGAGGGGATCGTGAACCATATTCTGCAGGCG
genomic: AGCGAGACGCACTTCGCATGCGCGAAGGAGGGCCCTTTGTGTTTGCACAGgttcaagatc ... aattatgcagGTGAAACATGGAGTGGGCGTGGAGGGGATCGTGAACCATATTCTGCAGGCG
EST: gi|20300761|gb|BQ163704.1|BQ163704
EST:     AGCGAGACGCGCTTCGCATGCGCGAAGGAGGGCCCTTTGTGTTTGCACAG                         GTGAAACATGGAGTGGGCGTGGAGGGGATCGTGAACCATATTCTGCAGGCG
genomic: AGCGAGACGCACTTCGCATGCGCGAAGGAGGGCCCTTTGTGTTTGCACAGgttcaagatc ... aattatgcagGTGAAACATGGAGTGGGCGTGGAGGGGATCGTGAACCATATTCTGCAGGCG
EST: gi|101386125|gb|EB815103.1|EB815103
EST:     AGCGAGACGCACTTCGCATGCGCGAAGGAGGGCCCTTTGTGTTTGCACAG                         GTGAAACATGGAGTGGGCGTGGAGGGGATCGTGAACCATATTCTGCAGGCG
genomic: AGCGAGACGCACTTCGCATGCGCGAAGGAGGGCCCTTTGTGTTTGCACAGgttcaagatc ... aattatgcagGTGAAACATGGAGTGGGCGTGGAGGGGATCGTGAACCATATTCTGCAGGCG
EST: gi|20300389|gb|BQ163332.1|BQ163332
EST:     AGCGAGACGCGCTTCGCATGCGCGAAGGAGGGCCCTTTGTGTTTGCACAG                         GTGAAACATGGAGTGGGCGTGGAGGGGATCGTGAACCATATTCTGCAGGCG
genomic: AGCGAGACGCACTTCGCATGCGCGAAGGAGGGCCCTTTGTGTTTGCACAGgttcaagatc ... aattatgcagGTGAAACATGGAGTGGGCGTGGAGGGGATCGTGAACCATATTCTGCAGGCG
EST: gi|50326358|gb|CO521484.1|CO521484
EST:     AGCGAGACGCACTTCGCATGCGCGAAGGAGGGCCCTTTGTGTTTGCACAG                         GTGAAACATGGAGTGGGCGTGGAGGGGATCGTGAACCATATTCTGCAGGCG
genomic: AGCGAGACGCACTTCGCATGCGCGAAGGAGGGCCCTTTGTGTTTGCACAGgttcaagatc ... aattatgcagGTGAAACATGGAGTGGGCGTGGAGGGGATCGTGAACCATATTCTGCAGGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gacattttacttccactgaaatcagtgatgatggcatctttatataattatgcagGTGAAACATGGAGTGGGCGTGGAGGGGATCGTGAACCATATTCTGCAGGCGTGGGAGATCGCGACTGGTAATAAGCGGCGATAAGATCTCACGACTTGGG
                                   atctttatataattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcaagatcaaactatgcacatctttagtttttttttcctcgtgactttgtgctagttgagaggagaacaaggtttacatgttcaaggacattttacttccactgaaatcagtgatgatggcatctttatataattatgcagGTGAAACATGGAGTGGGCGTGGAGGGGATCGTGAACCATATTCTGCAGGCGTGGGAGATCGCGACTGGTAATAAGCGGCGATAAGATCTCACGACTTGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC