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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTCCAAGGTTCAGTTTCTACGATGCTGACAAACCAATGTATACATCACGGAGAAACCTACCACCATCTATGGTCAACAATAGTAAGgtgttatgccgtctatctgtactaaaatgagtcatcacattgtccttttttgcactatattatattatttatttcacgtttgttattaattattagtaccatggttccctgcctttgcttacttattttgatacttggggcattcatttatcctatctggttaatgtgtccccttctaacacgttggtgtcactgcag

Basic information

species Zea mays
transcript GRMZM2G391936_T02
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G391936_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os03g52460.1 (Oryza sativa), 5'ss of exon 11
CCTCCAAGGTTCAGTTTCTACGATGCTGACAAACCAATGTATACATCACGGAGAAACCTACCACCATCTATGGTCAACAATAGTAAGgtgttatgccgtctatctgtactaaaatgagtcatcacattgtccttttttgcactatattatattatttatttcacgtttgttattaattattagt-accatggttccctgcctttgcttacttattttgatacttggggcattcatttatcctatctggttaatgtgtccccttctaacacgttggtgtcactgcag
|| || || ||||| || || |||||| | ||||||||||| ||||||||||||||| |||| ||||||||| |||| ||||||||||| |        ||||||| ||||  |||  ||  |    |||  | ||||       |  |||||  |||| |||| || |       |    | | | ||                                                                                                 
CCACCGAGATTCAGCTTTTATGATGCTAATAAACCAATGTACACATCACGGAGAAACTTACCGCCATCTATGATCAATAATAGTAAGgtatgtgataccctatctgaactagcatgtatc-cctttctgtgatattttagttcccaa-atattccttatgtcactttcgacgcatgtatccaattagca-------------------------------------------------------------------------------------------------

upper sequence: GRMZM2G391936_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA07G38820.2 (Glycine max), 5'ss of exon 11
CCTCCAAGGTTCAGTTTCTACGATGCTGACAAACCAATGTATACATCACGGAGAAACCTACCACCATCTATGGTCAACAATAGTAAGgt--gttatgccgtctatctgtactaaaatgagtcatcacattgtccttttttgcactatattatattatttatttcacgtttgttattaattattagtaccatggttccctgcctttgcttacttattttgatacttggggcattcatttatcctatctggttaatgtgtccccttctaacacgttggtgtcactgcag
|| || ||||| || || || ||||| | |||||||||||||||||||||||||||| |||||||||| | | |  ||||||| |||||  ||  | |   ||  ||    | |||    |  | |  |  | |    | | | ||    |   |  ||| ||   |   | |     | ||| ||                                                                                                     
CCACCCAGGTTTAGCTTTTATGATGCAGCCAAACCAATGTATACATCACGGAGAAACTTACCACCATCAAAGATTGACAATAGCAAGgtcagtccttcaaacttgctcctgtgaaaaactttgttaagtaattcacactagaagtaccaaagccttattacttggggaaggatgaacttaatttgtt----------------------------------------------------------------------------------------------------

upper sequence: GRMZM2G391936_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA17G01900.1 (Glycine max), 5'ss of exon 11
CCTCCAAGGTTCAGTTTCTACGATGCTGACAAACCAATGTATACATCACGGAGAAACCTACCACCATCTATGGTCAACAATAGTAAGgtgttatgccgtctatctgtactaaaatgagtcatcacattgtccttttttgcactatattatattatttatttcacgtttgttattaatt--attagtaccatggttccctgcctttgcttacttattttgatacttggggcattcatttatcctatctggttaatgtgtccccttctaacacgttggtgtcactgcag
|| |||||||| || || |||||||| |  |||||||||||||||||| |||||||| |||||||||| | | |  ||||||| ||||  | |   | || | || | ||    ||||  ||            ||||  | ||| | | | ||    |  ||      |||||  ||     |||   |   | ||     | | ||| |  || |  |            | | || ||||   |  |  |                                  
CCACCAAGGTTTAGCTTTTACGATGCAGCAAAACCAATGTATACATCAAGGAGAAACTTACCACCATCAAAGATTGACAATAGCAAGg--tcagttcttcaaact-tgctcctgtgagaaat------------tttttaagtatttcacactagaagtaccaaagcc-ttattgctttgggaagtgtgaacttacctcttttctactttcaaatctcaaactacaacattgttacttgtccttctttatgcag---------------------------------

upper sequence: GRMZM2G391936_T01 (Zea mays), 5'ss of exon 7
lower sequence: AT5G19220.1 (Arabidopsis thaliana), 5'ss of exon 11
CCTCCAAGGTTCAGTTTCTACGATGCTGACAAACCAATGTATACATCACGGAGAAACCTACCACCATCTATGGTCAACAATAGTAAGgtgttatgccgtctatctgtactaaaatgagtcatcacattgtccttttttgcactatattatattatttatttcacgtttgttattaattattagtaccatggttccctgcctttgcttacttattttgatacttggggcattcatttatcctatctggttaatgtgtccccttctaacacgttggtgtcactgcag
|||      || ||||||||||| || |  |||||||| ||||||||| |||||||||| |||||||| |   |  ||||   ||||||                  | |||||  || ||| | |||  | |||  | |  | |||| |  | ||  |    | |||  | || |  ||||   |    |||   | | | ||                                                                                 
CCTGGGGCATTTAGTTTCTACGACGCGGCAAAACCAATATATACATCAAGGAGAAACCTGCCACCATCAAAAATAGACAACTCTAAGgta-----------------agtaaaaccagccatgatatttccttttagttctatgtattttggtgttggtc---cattt--tcttcaggattaactcttaagtttattacatgtgaag------------------------------------------------------------------------------

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|71757054|gb|DR954991.1|DR954991
EST:     TGTATACATCACGGAGAAACCTACCACCATCTATGGTCAACAATAGTAAG                         ATCACTGATTCAATCATTTCCCACGGATGTTTCTTGGATAACTGCAGGATA
genomic: TGTATACATCACGGAGAAACCTACCACCATCTATGGTCAACAATAGTAAGgtgttatgcc ... gtcactgcagATCACTGATTCAATCATTTCCCACGGATGTTTCTTGGATAACTGCAGGATA
EST: gi|71324302|gb|DR798853.1|DR798853
EST:     GGAGAAACCTACCACCATCTATGGTCAACAATAGTAAG                         ATCACTGATTCAATCATTTCCCACGGATGTTTCTTGGATAACTGCAGGATA
genomic: GGAGAAACCTACCACCATCTATGGTCAACAATAGTAAGgtgttatgcc ... gtcactgcagATCACTGATTCAATCATTTCCCACGGATGTTTCTTGGATAACTGCAGGATA
EST: gi|24763417|gb|CA398592.1|CA398592
EST:     TCTATGGTCAACAATAGTAAG                         ATCACTGATTCAATCATTTCCCACGGATGTTTCTTGGATAACTGCAGGATA
genomic: TCTATGGTCAACAATAGTAAGgtgttatgcc ... gtcactgcagATCACTGATTCAATCATTTCCCACGGATGTTTCTTGGATAACTGCAGGATA
EST: gi|211232745|gb|FL322840.1|FL322840
EST:     TGTATACATCACGGAGAAACCTACCACCATCTATGGTCAACAATAGTAAG                         ATCACTGATTCAATCATTTCCCACGGATGTTTCTTGGATAACTGCAGGATA
genomic: TGTATACATCACGGAGAAACCTACCACCATCTATGGTCAACAATAGTAAGgtgttatgcc ... gtcactgcagATCACTGATTCAATCATTTCCCACGGATGTTTCTTGGATAACTGCAGGATA
EST: gi|110195335|gb|EC877232.1|EC877232
EST:     TGTATACATCACGGAGAAACCTACCACCATCTATGGTCAACAATAGTAAG                         ATCACTGATTCAATCATTTCCCACGGATGTTTCTTGGATAACTGCAGGATA
genomic: TGTATACATCACGGAGAAACCTACCACCATCTATGGTCAACAATAGTAAGgtgttatgcc ... gtcactgcagATCACTGATTCAATCATTTCCCACGGATGTTTCTTGGATAACTGCAGGATA
EST: gi|18178292|gb|BM379502.1|BM379502
EST:     GGAGAAACCTACCACCATCTATGGTCAACAATAGTAAG                         ATCACTGATTCAATCATTTCCCACGGATGTTTCTTGGATAACTGCAGGATA
genomic: GGAGAAACCTACCACCATCTATGGTCAACAATAGTAAGgtgttatgcc ... gtcactgcagATCACTGATTCAATCATTTCCCACGGATGTTTCTTGGATAACTGCAGGATA
EST: gi|71429962|gb|DR811012.1|DR811012
EST:     TGTATACATCACGGAGAAACCTACCACCATCTATGGTCAACAATAGTAAG                         ATCACTGATTCAATCATTTCCCACGGATGTTTCTTGGATAACTGCAGGATA
genomic: TGTATACATCACGGAGAAACCTACCACCATCTATGGTCAACAATAGTAAGgtgttatgcc ... gtcactgcagATCACTGATTCAATCATTTCCCACGGATGTTTCTTGGATAACTGCAGGATA
EST: gi|93281647|gb|EB673911.1|EB673911
EST:     GGTCAACAATAGTAAG                         ATCACTGATTCAATCATTTCCCACGGATGTTTCTTGGATAACTGCAGGATA
genomic: GGTCAACAATAGTAAGgtgttatgcc ... gtcactgcagATCACTGATTCAATCATTTCCCACGGATGTTTCTTGGATAACTGCAGGATA
EST: gi|71323466|gb|DR798382.1|DR798382
EST:     TGTATACATCACGGAGAAACCTACCACCATCTATGGTCAACAATAGTAAG                         ATCACTGATTCAATCATTTCCCACGGATGTTTCTTGGATAACTGCAGGATA
genomic: TGTATACATCACGGAGAAACCTACCACCATCTATGGTCAACAATAGTAAGgtgttatgcc ... gtcactgcagATCACTGATTCAATCATTTCCCACGGATGTTTCTTGGATAACTGCAGGATA
EST: gi|32850355|gb|CD990036.1|CD990036
EST:     TGTATACATCACGGAGAAACCTACCACCATCTATGGTCAACAATAGTAAG                         ATCACTGATTCAATCATTTCCCACGGATGTTTCTTGGATAACTGCAGGATA
genomic: TGTATACATCACGGAGAAACCTACCACCATCTATGGTCAACAATAGTAAGgtgttatgcc ... gtcactgcagATCACTGATTCAATCATTTCCCACGGATGTTTCTTGGATAACTGCAGGATA
EST: gi|31348918|gb|CD433275.1|CD433275
EST:     CCACCATCTATGGTCAACAATAGTAAG                         ATCACTGATTCTATCATTTCCCACGGATGTTTCTTGGATAACTGCAGGATA
genomic: CCACCATCTATGGTCAACAATAGTAAGgtgttatgcc ... gtcactgcagATCACTGATTCAATCATTTCCCACGGATGTTTCTTGGATAACTGCAGGATA
EST: gi|50335821|gb|CO530947.1|CO530947
EST:     TGTATACATCACGGAGAAACCTACCACCATCTATGGTCAACAATAGTAAG                         ATCACTGATTCAATCATTTCCCACGGATGTTTCTTGGATAACTGCAGGATA
genomic: TGTATACATCACGGAGAAACCTACCACCATCTATGGTCAACAATAGTAAGgtgttatgcc ... gtcactgcagATCACTGATTCAATCATTTCCCACGGATGTTTCTTGGATAACTGCAGGATA
EST: gi|31362917|gb|CD447274.1|CD447274
EST:     TGTATACATCACGGAGAAACCTACCACCATCTATGGTCAACAATAGTAAG                         ATCACTGATTCAATCATTTCCCACGGATGTTTCTTGGATAACTGCAGGATA
genomic: TGTATACATCACGGAGAAACCTACCACCATCTATGGTCAACAATAGTAAGgtgttatgcc ... gtcactgcagATCACTGATTCAATCATTTCCCACGGATGTTTCTTGGATAACTGCAGGATA
EST: gi|78103575|gb|DV522003.1|DV522003
EST:     TGTATACATCACGGAGAAACCTACCACCATCTATGGTCAACAATAGTAAG                         ATCACTGATTCAATCATTGCCCACGGATGTTTCTTGGATAACTGCAGGATA
genomic: TGTATACATCACGGAGAAACCTACCACCATCTATGGTCAACAATAGTAAGgtgttatgcc ... gtcactgcagATCACTGATTCAATCATTTCCCACGGATGTTTCTTGGATAACTGCAGGATA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTCCAAGGTTCAGTTTCTACGATGCTGACAAACCAATGTATACATCACGGAGAAACCTACCACCATCTATGGTCAACAATAGTAAGgtgttatgccgtctatctgtactaaaatgagtcatcacattgtccttttttgcactatattatattatttatttcacgtttgttattaattattagtaccatggttccctgcctttgcttacttattttgatacttggggcattcatttatcctatctggttaatgtgtccccttctaacacgttggtgtcactgcag

- - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA