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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaccataccctgctagctcgcatctttgctgagatatatgatctatgccttttccccccttttgatgattcctttgtggctttgctgcctttttatctgaaacagGGGAGAGGCTGGGAAGAAGGATAGCCACGGATGCTATCACCACGCCGGTAGTGAACACGTCGGCCTACTGGTTCAACAACTCGCAAGAGCTAATCGACTT

Basic information

species Zea mays
transcript GRMZM2G075153_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G075153_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g25940.4 (Oryza sativa), 3'ss of exon 2
gtaccataccctgctagctcgcatctttgctgagatatatgatctatgccttttccccccttttgatgattcctttgtggc---tttgctgcctt---tttatctgaaacagGGGAGAGGCTGGGAAGAAGGATAGCCACGGATGCTATCACCACGCCGGTAGTGAACACGTCGGCCTACTGGTTCAACAACTCGCAAGAGCTAATCGACTT
                |    ||   |   |    | |  |||||||  | || |||||  |     | ||  ||| ||     |||  ||| ||   | || ||     ||| ||||||||||| |||||||| ||||| || || ||||||||||| ||||||||||| |||||||||||||||||||||||||| ||||| || |||||
----------------gtaatcacgatcaatcccctctcagatctatcgccttccccccgctgcttcggtttttttctgatccatttcgtgcttttgatatacctatcgaagGCGAGAGGCTGGGCAGAAGGATCGCCACAGACGCGATCACCACGCCAGTAGTGAACACCTCGGCCTACTGGTTCAACAACTCGCAGGAGCTCATTGACTT
















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|30705385|gb|CD058765.1|CD058765
EST:     GGCCGAGCGTAACCTGCTCGGCTCCGACGCCAGCCTCGCCGTCCACGCGG                         GGGAGAGGCTGGGAAGAAGGATAGCCACGGATGCTATCACCACGCCGGTAG
genomic: GGCCGAGCGTAACCTGCTCGGCTCCGACGCCAGCCTCGCCGTCCACGCGGgtaccatacc ... tctgaaacagGGGAGAGGCTGGGAAGAAGGATAGCCACGGATGCTATCACCACGCCGGTAG
EST: gi|149094739|gb|EE180295.2|EE180295
EST:     GGCCGAGCGTAACCTGCTCGGCTCCGACGCCAGCCTCGCCGTCCACGCGG                         GGGAGAGGCTGGGAAGAAGGATAGCCACGGATGCTATCACCACGCCGGTAG
genomic: GGCCGAGCGTAACCTGCTCGGCTCCGACGCCAGCCTCGCCGTCCACGCGGgtaccatacc ... tctgaaacagGGGAGAGGCTGGGAAGAAGGATAGCCACGGATGCTATCACCACGCCGGTAG
EST: gi|71419168|gb|DR804676.1|DR804676
EST:     GGCCGAGCGTAACCTGCTCGGCTCCGACGCCAGCCTCGCCGTCCACGCGG                         GGGAGAGGCTGGGAAGAAGGATAGCCACGGATGCTATCACCACGCCGGTAG
genomic: GGCCGAGCGTAACCTGCTCGGCTCCGACGCCAGCCTCGCCGTCCACGCGGgtaccatacc ... tctgaaacagGGGAGAGGCTGGGAAGAAGGATAGCCACGGATGCTATCACCACGCCGGTAG
EST: gi|76284198|gb|DV023766.1|DV023766
EST:     GGCCGAGCGTAACCTGCTCGGCTCCGACGCCAGCCTCGCCGTCCACGCGG                         GGGAGAGGCTGGGAAGAAGGATAGCCACGGATGCTATCACCACGCCGGTAG
genomic: GGCCGAGCGTAACCTGCTCGGCTCCGACGCCAGCCTCGCCGTCCACGCGGgtaccatacc ... tctgaaacagGGGAGAGGCTGGGAAGAAGGATAGCCACGGATGCTATCACCACGCCGGTAG
EST: gi|78111688|gb|DV530085.1|DV530085
EST:     GGCCGAGCGTAACCTGCTCGGCTCCGACGCCAGCCTCGCCGTCCACGCGG                         GGGAGAGGCTGGGAAGAAGGATAGCCACGGATGCTATCACCACGCCGGTAG
genomic: GGCCGAGCGTAACCTGCTCGGCTCCGACGCCAGCCTCGCCGTCCACGCGGgtaccatacc ... tctgaaacagGGGAGAGGCTGGGAAGAAGGATAGCCACGGATGCTATCACCACGCCGGTAG
EST: gi|76291942|gb|DV031510.1|DV031510
EST:     GGCCGAGCGTAACCTGCTCGGCTCCGACGCCAGCCTCGCCGTCCACGCGG                         GGGAGAGGCTGGGAAGAAGGATAGCCACGGATGCTATCACCACGCCGGTAG
genomic: GGCCGAGCGTAACCTGCTCGGCTCCGACGCCAGCCTCGCCGTCCACGCGGgtaccatacc ... tctgaaacagGGGAGAGGCTGGGAAGAAGGATAGCCACGGATGCTATCACCACGCCGGTAG
EST: gi|148948278|gb|EC893795.2|EC893795
EST:     GGCCGAGCGTAACCTGCTCGGCTCCGACGCCAGCCTCGCCGTCCACGCGG                         GGGAGAGGCTGGGAAGAAGGATAGCCACGGATGCTATCACCACGCCGGTAG
genomic: GGCCGAGCGTAACCTGCTCGGCTCCGACGCCAGCCTCGCCGTCCACGCGGgtaccatacc ... tctgaaacagGGGAGAGGCTGGGAAGAAGGATAGCCACGGATGCTATCACCACGCCGGTAG
EST: gi|149074757|gb|EE163186.2|EE163186
EST:     GGCCGAGCGTAACCTGCTCGGCTCCGACGCCAGCCTCGCCGTCCACGCGG                         GGGAGAGGCTGGGAAGAAGGATAGCCACGGATGCTATCACCACGCCGGTAG
genomic: GGCCGAGCGTAACCTGCTCGGCTCCGACGCCAGCCTCGCCGTCCACGCGGgtaccatacc ... tctgaaacagGGGAGAGGCTGGGAAGAAGGATAGCCACGGATGCTATCACCACGCCGGTAG
EST: gi|74245810|gb|DT653724.1|DT653724
EST:     GGCCGAGCGTAACCTGCTCGGCTCCGACGCCAGCCTCGCCGTCCACGCGG                         GGGAGAGGCTGGGAAGAAGGATAGCCACGGATGCTATCACCACGCCGGTAG
genomic: GGCCGAGCGTAACCTGCTCGGCTCCGACGCCAGCCTCGCCGTCCACGCGGgtaccatacc ... tctgaaacagGGGAGAGGCTGGGAAGAAGGATAGCCACGGATGCTATCACCACGCCGGTAG
EST: gi|76933173|gb|DV173352.1|DV173352
EST:     GGCCGAGCGTAACCTGCTCGGCTCCGACGCCAGCCTCGCCGTCCACGCGG                         GGGAGAGGCTGGGAAGAAGGATAGCCACGGATGCTATCACCACGCCGGTAG
genomic: GGCCGAGCGTAACCTGCTCGGCTCCGACGCCAGCCTCGCCGTCCACGCGGgtaccatacc ... tctgaaacagGGGAGAGGCTGGGAAGAAGGATAGCCACGGATGCTATCACCACGCCGGTAG
EST: gi|149108488|gb|EE189677.2|EE189677
EST:     GGCCGAGCGTAACCTGCTCGGCTCCGACGCCAGCCTCGCCGTCCACGCGG                         GGGAGAGGCTGGGAAGAAGGATAGCCACGGATGCTATCACCACGCCGGTAG
genomic: GGCCGAGCGTAACCTGCTCGGCTCCGACGCCAGCCTCGCCGTCCACGCGGgtaccatacc ... tctgaaacagGGGAGAGGCTGGGAAGAAGGATAGCCACGGATGCTATCACCACGCCGGTAG
EST: gi|38229609|gb|CF919922.1|CF919922
EST:     GGCCGAGCGTAACCTGCTCGGCTCCGACGCCAGCCTCGCCGTCCACGCGG                         GGGAGAGGCTGGGAAGAAGGATAGCCACGGATGCTATCACCACGCCGGTAG
genomic: GGCCGAGCGTAACCTGCTCGGCTCCGACGCCAGCCTCGCCGTCCACGCGGgtaccatacc ... tctgaaacagGGGAGAGGCTGGGAAGAAGGATAGCCACGGATGCTATCACCACGCCGGTAG
EST: gi|91873684|gb|EB403641.1|EB403641
EST:     GGCCGAGCGTAACCTGCTCGGCTCCGACGCCAGCCTCGCCGTCCACGCGG                         GGGAGAGGCTGGGAAGAAGGATACCCACGGATGCTATCACCACGCCGGTAG
genomic: GGCCGAGCGTAACCTGCTCGGCTCCGACGCCAGCCTCGCCGTCCACGCGGgtaccatacc ... tctgaaacagGGGAGAGGCTGGGAAGAAGGATAGCCACGGATGCTATCACCACGCCGGTAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttccccccttttgatgattcctttgtggctttgctgcctttttatctgaaacagGGGAGAGGCTGGGAAGAAGGATAGCCACGGATGCTATCACCACGCCGGTAGTGAACACGTCGGCCTACTGGTTCAACAACTCGCAAGAGCTAATCGACTT
         ttttgat  putative branch site (score: 4)
                                  ctgcctttttatct  putative PPT
                                       tttttatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaccataccctgctagctcgcatctttgctgagatatatgatctatgccttttccccccttttgatgattcctttgtggctttgctgcctttttatctgaaacagGGGAGAGGCTGGGAAGAAGGATAGCCACGGATGCTATCACCACGCCGGTAGTGAACACGTCGGCCTACTGGTTCAACAACTCGCAAGAGCTAATCGACTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT