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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTGCTTTTATGGATCAAATCTGTAATTGAGGAAACTGGGAGTGGTGTTACCACAGATCAACTCAAAGACTATGTCTGGAAGACACTAAAGAGTGGAAAGgtatgtcagttcgcagaggtttagtgtttgtgatcatgctcgaacaaggttgtttcccacaagaaagctatatcgattcactgaattttgaatgatgtgc...

Basic information

species Zea mays
transcript GRMZM2G063851_T01
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G063851_T05 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os11g33240.2 (Oryza sativa), 5'ss of exon 15
AGTGCTTTTATGGATCAAATCTGTAATTGAGGAAACTGGGAGTGGTGTTACCACAGATCAACTCAAAGACTATGTCTGGAAGACACTAAAGAGTGGAAAGgtatgtcagttcgcagaggtttagtgtttgtgatcatgctcgaacaaggttgtttcccacaagaaagctatatcgattcactgaattttgaatgatgtgc-
|||||| || ||||||||||||||||| |  || || || |||| |||||| || |||||||||||||| ||||| |||||||||||||| ||||||||||||  | |  || | |   | |    ||  |||  | |  |  | | | | || |   |   | ||  | |||    ||    | |||  |||||      
AGTGCTGTTGTGGATCAAATCTGTAATAGGTGAGACAGGTAGTGATGTTACAACTGATCAACTCAAAGAGTATGTGTGGAAGACACTAAAAAGTGGAAAGgtagcttatctcactgttatatctatttgatgaggaagtgcatatatgatcgtgttttaactgcaaatt-tattttctcgggaagtttgaaatgaaaactc

upper sequence: GRMZM2G063851_T05 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os02g10070.1 (Oryza sativa), 5'ss of exon 15
AGTGCTTTTATGGATCAAATCTGTAATTGAGGAAACTGGGAGTGGTGTTACCACAGATCAACTCAAAGACTATGTCTGGAAGACACTAAAGAGTGGAAAGgtatgtcagttc-gcagaggtttagtgtttg-tgatcatgctcgaacaaggttgtttcccacaagaaagctatatcgattcactgaattttgaatgatgtgc
|||| | || ||||||||||||||||| |  || ||||| ||||  ||||| || |||||||||||||| ||||| |||||||||||||| ||||||||||||  | |  || |       ||  | |||| |||  | |  |  |  |   |||||   ||   || |  |  || | |  ||||   || | || |  | 
AGTGTTGTTGTGGATCAAATCTGTAATAGGTGAGACTGGTAGTGACGTTACAACTGATCAACTCAAAGAGTATGTGTGGAAGACACTAAAAAGTGGAAAGgtagcttatctccgtgttatatttctatttgatgaggaagtgcatatcatcatgtttta-actgaaatgaaaactcaactttctgagagttcattgctaag-
















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|40335071|gb|CK369141.1|CK369141
EST:     AGAGTGGAAAG                         GTTGTTCCTGGGTTTGGTCATGGAGTTCTGCGTAAGACCGACCCACGGTAT
genomic: AGAGTGGAAAGgtatgtcagt ... tcaatcatagGTTGTTCCTGGGTTTGGTCATGGAGTTCTGCGTAAGACCGACCCACGGTAT
EST: gi|5901109|gb|AW042209.1|AW042209
EST:     CCACAGATCAACTCAAAGACTATGTCTGGAAGACACTAAAGAGTGGAAAG                         GTTGTTCCTGGGTTTGGTCATGGAGTTCTGCGTAAGACCGACCCACGGTAT
genomic: CCACAGATCAACTCAAAGACTATGTCTGGAAGACACTAAAGAGTGGAAAGgtatgtcagt ... tcaatcatagGTTGTTCCTGGGTTTGGTCATGGAGTTCTGCGTAAGACCGACCCACGGTAT
EST: gi|116813560|gb|EC856011.1|EC856011
EST:     CCACAGATCAACTCAAAGACTATGTCTGGAAGACACTAAAGAGTGGAAAG                         GTTGTTCCTGGGTTTGGTCATGGAGTTCTGCGTAAGACCGACCCACGGTAT
genomic: CCACAGATCAACTCAAAGACTATGTCTGGAAGACACTAAAGAGTGGAAAGgtatgtcagt ... tcaatcatagGTTGTTCCTGGGTTTGGTCATGGAGTTCTGCGTAAGACCGACCCACGGTAT
EST: gi|78179069|gb|DV549442.1|DV549442
EST:     CCACAGATCAACTCAAAGACTATGTCTGGAAGACACTAAAGAGTGGAAAG                         GTTGTTCCTGGGTTTGGTCATGGAGTTCTGCGTAAGACCGACCCACGGTAT
genomic: CCACAGATCAACTCAAAGACTATGTCTGGAAGACACTAAAGAGTGGAAAGgtatgtcagt ... tcaatcatagGTTGTTCCTGGGTTTGGTCATGGAGTTCTGCGTAAGACCGACCCACGGTAT
EST: gi|31364242|gb|CD448597.1|CD448597
EST:     CCACAGATCAACTCAAAGACTATGTCTGGAAGACACTAAAGAGTGGAAAG                         GTTGTTCCTGGGTTTGGTCATGGAGTTCTGCGTAAGACCGACCCACGGTAT
genomic: CCACAGATCAACTCAAAGACTATGTCTGGAAGACACTAAAGAGTGGAAAGgtatgtcagt ... tcaatcatagGTTGTTCCTGGGTTTGGTCATGGAGTTCTGCGTAAGACCGACCCACGGTAT
EST: gi|148929642|gb|EC876096.2|EC876096
EST:     CCACAGATCAACTCAAAGACTATGTCTGGAAGACACTAAAGAGTGGAAAG                         GTTGTTCCTGGGTTTGGTCATGGAGTTCTGCGTAAGACCGACCCACGGTAT
genomic: CCACAGATCAACTCAAAGACTATGTCTGGAAGACACTAAAGAGTGGAAAGgtatgtcagt ... tcaatcatagGTTGTTCCTGGGTTTGGTCATGGAGTTCTGCGTAAGACCGACCCACGGTAT
EST: gi|76010584|gb|DT937754.1|DT937754
EST:     CCACAGATCAATTCAAAGACTATGTCTGGAAGACACTAAAGAGTGGAAAG                         GTTGTTCCTGGGTTTGGTCATGGAGTTCTGCGTAAGACCGACCCACGGTAT
genomic: CCACAGATCAACTCAAAGACTATGTCTGGAAGACACTAAAGAGTGGAAAGgtatgtcagt ... tcaatcatagGTTGTTCCTGGGTTTGGTCATGGAGTTCTGCGTAAGACCGACCCACGGTAT
EST: gi|31363851|gb|CD448206.1|CD448206
EST:     AAAGAGTGGAAAG                         G-TGTTTCCTGGGTTTGGTCATGGAGTTCTGCGTAAGACCGACCCACGGTA
genomic: AAAGAGTGGAAAGgtatgtcagt ... tcaatcatagGTTG-TTCCTGGGTTTGGTCATGGAGTTCTGCGTAAGACCGACCCACGGTA
EST: gi|6964715|gb|AW433408.1|AW433408
EST:     CCACAGATCAACTCAAAGACTATGTCTGGAAGACACTAAAGAGTGGAAAG                         GTTGTTCCTGGGTTTGGTCATGGAGTTCTGCGTAAGACCGACCCACGGTAT
genomic: CCACAGATCAACTCAAAGACTATGTCTGGAAGACACTAAAGAGTGGAAAGgtatgtcagt ... tcaatcatagGTTGTTCCTGGGTTTGGTCATGGAGTTCTGCGTAAGACCGACCCACGGTAT
EST: gi|76010585|gb|DT937755.1|DT937755
EST:     CCACAGATCAACTCAAAGACTATGTCTGGAAGACACTAAAGAGTGGAAAG                         GTTGTTCCTGGGTTTGGTCATGGAGTTCTGCGTAAGACCGACCCACGGTAT
genomic: CCACAGATCAACTCAAAGACTATGTCTGGAAGACACTAAAGAGTGGAAAGgtatgtcagt ... tcaatcatagGTTGTTCCTGGGTTTGGTCATGGAGTTCTGCGTAAGACCGACCCACGGTAT
EST: gi|7145414|gb|AW506895.1|AW506895
EST:     CCACAGATCAACTCAAAGACTATGTCTGGAAGACACTAAAGAGTGGAAAG                         GTTGTTCCTGGGTTTGGTCATGGAGTTCTGCGTAAGACCGACCCACGGTAT
genomic: CCACAGATCAACTCAAAGACTATGTCTGGAAGACACTAAAGAGTGGAAAGgtatgtcagt ... tcaatcatagGTTGTTCCTGGGTTTGGTCATGGAGTTCTGCGTAAGACCGACCCACGGTAT
EST: gi|116825307|gb|EC869024.1|EC869024
EST:     CCACAGATCAACTCAAAGACTATGTCTGGAAGACACTACAGAGTGGAAAG                         GTTGTTCCTGGGTTTGGTCATGGAGTTCTGCGTAAGACCGACCCACGGTAT
genomic: CCACAGATCAACTCAAAGACTATGTCTGGAAGACACTAAAGAGTGGAAAGgtatgtcagt ... tcaatcatagGTTGTTCCTGGGTTTGGTCATGGAGTTCTGCGTAAGACCGACCCACGGTAT
EST: gi|60395299|gb|DN228168.1|DN228168
EST:     CCACAGATCAACTCAAAGACTATGTCTGGAAGACACTAAAGAGTGGAAAG                         GTTGTTCCTGGGTTTGGTCATGGAGTTCTGCGTAAGACCGACCCACGGTAT
genomic: CCACAGATCAACTCAAAGACTATGTCTGGAAGACACTAAAGAGTGGAAAGgtatgtcagt ... tcaatcatagGTTGTTCCTGGGTTTGGTCATGGAGTTCTGCGTAAGACCGACCCACGGTAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTGCTTTTATGGATCAAATCTGTAATTGAGGAAACTGGGAGTGGTGTTACCACAGATCAACTCAAAGACTATGTCTGGAAGACACTAAAGAGTGGAAAGgtatgtcagttcgcagaggtttagtgtttgtgatcatgctcgaacaaggttgtttcccacaagaaagctatatcgattcactgaattttgaatgatgtgc

- - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acaagaaa