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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcacagcgcgatctatctcaacgctggatctctgtttcacttgccgcgagccatgtatggttcagggcctgctcgcgtgttccggatcctgattaccggtgccaaattgctgcttgatccagGCTAACCTGCGGATCCTGGTCACTGGTGGGGCGGGCTTCATCGGCTCGCACCTCGTGGACAGGCTCATGGAGAACGAGAAACACGAG

Basic information

species Zea mays
transcript GRMZM2G044027_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044027_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g16980.4 (Oryza sativa), 3'ss of exon 2
gtcacagcgcgatctatctcaacgctggatctctgtttcacttgccgcgagccatgtatggttcagggcctgctcgcgtgttccggatcctgattaccggtgccaaattgctgcttgatccagGCTAACCTGCGGATCCTGGTCACTGGTGGGGCGGGCTTCATCGGCTCGCACCTCGTGGACAGGCTCATGGAGAACGAGAAACACGAG
        | ||| | |  |       |||| |||  || |         ||| | || |      |||| | ||||  |  | ||   ||||||    |||     |||    |   | ||||| |||||| ||||||| ||||| || || || ||||||||||||||||||||||| |||| |||||||||||||||||| ||||||
--------gtgattt-tgccgggatccgatcgctggatctc---------gccgtatacgt-----ggcccgatcgctcgacctgg--tctgattgttcgtgggtgtttgtgtgtgtgtgcagGCGAACCTGAGGATCCTCGTCACCGGCGGAGCTGGCTTCATCGGCTCGCACCTCGTCGACAAGCTCATGGAGAACGAGAAGCACGAG
















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|6637013|gb|AW261285.1|AW261285
EST:     CCCGCCCGCCGCCGACCCCGTCGCCCCTCCGCTTCTCCAAGTTCTTCCAG                         GCTAACCTGCGGATCCTGGTCACTGGTGGGGCGGGCTTCATCGGCTCGCAC
genomic: CCCGCCCGCCGCCGACCCCGTCGCCCCTCCGCTTCTCCAAGTTCTTCCAGgtcacagcgc ... cttgatccagGCTAACCTGCGGATCCTGGTCACTGGTGGGGCGGGCTTCATCGGCTCGCAC
EST: gi|149097834|gb|EE183762.2|EE183762
EST:     CCCGCCCGCCGCCGACCCCGTCGCCCCTCCGCTTCTCCAAGTTCTTCCAG                         GCTAACCTGCGGATCCTGGTCACTGGTGGGGCGGGCTTCATCGGCTCGCAC
genomic: CCCGCCCGCCGCCGACCCCGTCGCCCCTCCGCTTCTCCAAGTTCTTCCAGgtcacagcgc ... cttgatccagGCTAACCTGCGGATCCTGGTCACTGGTGGGGCGGGCTTCATCGGCTCGCAC
EST: gi|6020952|gb|AW065880.1|AW065880
EST:     CCCGCCCGGCGCCGACCCCGTCGCCCCTCCGCTTCTCCAAGTTCTTCCAG                         GCTAACCTGCGGATCCTGGTCACTGGTGGGGCGGGCTTCATCGGCTCTCTA
genomic: CCCGCCCGCCGCCGACCCCGTCGCCCCTCCGCTTCTCCAAGTTCTTCCAGgtcacagcgc ... cttgatccagGCTAACCTGCGGATCCTGGTCACTGGTGGGGCGGGCTTCATCGGCTCGC-A
EST: gi|60672298|gb|DN475062.1|DN475062
EST:     CCCGCCCGCCGCCGACCCCGTCGCCCCTCCGCTTCTCCAAGTTCTTCCAG                         GCTAACCTGCGGATCCTGGTCACTGGTGGGGCGGGCTTCATCGGCTCGCAC
genomic: CCCGCCCGCCGCCGACCCCGTCGCCCCTCCGCTTCTCCAAGTTCTTCCAGgtcacagcgc ... cttgatccagGCTAACCTGCGGATCCTGGTCACTGGTGGGGCGGGCTTCATCGGCTCGCAC
EST: gi|40334152|gb|CK368222.1|CK368222
EST:     CCCGCCCGCCGCCGACCCCGTCGCCCCTTCGCTTCTCCAAGTTCTTCCAG                         GCTAACCTGCGGATCCTGGTCACTGGTGGGGCGGGCTTCATCGGCTCGCAC
genomic: CCCGCCCGCCGCCGACCCCGTCGCCCCTCCGCTTCTCCAAGTTCTTCCAGgtcacagcgc ... cttgatccagGCTAACCTGCGGATCCTGGTCACTGGTGGGGCGGGCTTCATCGGCTCGCAC
EST: gi|22473192|gb|BU037672.1|BU037672
EST:     CCCGCCCGCCGCCGACCCCGTCGCCCCTCCGCTTCTCCAAGTTCTTCCAG                         GCTAACCTGCGGATCCTGGTCACTGGTGGGGCGGGCTTCATCGGCTCGCAC
genomic: CCCGCCCGCCGCCGACCCCGTCGCCCCTCCGCTTCTCCAAGTTCTTCCAGgtcacagcgc ... cttgatccagGCTAACCTGCGGATCCTGGTCACTGGTGGGGCGGGCTTCATCGGCTCGCAC
EST: gi|26558105|gb|CA830340.1|CA830340
EST:     CCCGCCCGCCGCCGACCCCGTCGCCCCTCCGCTTCTCCAAGGTCTTCCAG                         GGTAAACCCTGCGGATCCTGGTCACTGGTGGGGCGGGCTTCATCGGCTCGC
genomic: CCCGCCCGCCGCCGACCCCGTCGCCCCTCCGCTTCTCCAAGTTCTTCCAGgtcacagcgc ... cttgatccagGCT-AA-CCTGCGGATCCTGGTCACTGGTGGGGCGGGCTTCATCGGCTCGC
EST: gi|148945878|gb|EC891170.2|EC891170
EST:     CCCGCCCGCCGCCGACCCCGTCGCCCCTCCGCTTCTCCAAGTTCTTCCAG                         GCTAACCTGCGGATCCTGGTCACTGGTGGGGCGGGCTTCATCGGCTCGCAC
genomic: CCCGCCCGCCGCCGACCCCGTCGCCCCTCCGCTTCTCCAAGTTCTTCCAGgtcacagcgc ... cttgatccagGCTAACCTGCGGATCCTGGTCACTGGTGGGGCGGGCTTCATCGGCTCGCAC
EST: gi|67016223|gb|CO444972.1|CO444972
EST:     CCCGCCCGCCGCCGACCCCGTCGCCCCTCCGCTTCTCCAAGTTCTTCCAG                         GCTAACCTGCGGATCCTGGTCACTGGTGGGGCGGGCTTCATCGGCTCGCAC
genomic: CCCGCCCGCCGCCGACCCCGTCGCCCCTCCGCTTCTCCAAGTTCTTCCAGgtcacagcgc ... cttgatccagGCTAACCTGCGGATCCTGGTCACTGGTGGGGCGGGCTTCATCGGCTCGCAC
EST: gi|21987903|gb|BQ779431.1|BQ779431
EST:     CCCGCCCGCCGCCGACCCCGTCGCCCCTCCGCTTCTCCAAGTTCTTCCAG                         GCTAACCTGCGGATCCTGGTCACTGGTGGGGCGGGCTTCATCGGCTCGCAC
genomic: CCCGCCCGCCGCCGACCCCGTCGCCCCTCCGCTTCTCCAAGTTCTTCCAGgtcacagcgc ... cttgatccagGCTAACCTGCGGATCCTGGTCACTGGTGGGGCGGGCTTCATCGGCTCGCAC
EST: gi|148951041|gb|EC896695.2|EC896695
EST:     CCCGCCCGCCGCCGACCCCGTCGCCCCTCCGCTTCTCCAAGTTCTTCCAG                         GCTAACCTGCGGATCCTGGTCACTGGTGGGGCGGGCTTCATCGGCTCGCAC
genomic: CCCGCCCGCCGCCGACCCCGTCGCCCCTCCGCTTCTCCAAGTTCTTCCAGgtcacagcgc ... cttgatccagGCTAACCTGCGGATCCTGGTCACTGGTGGGGCGGGCTTCATCGGCTCGCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctgctcgcgtgttccggatcctgattaccggtgccaaattgctgcttgatccagGCTAACCTGCGGATCCTGGTCACTGGTGGGGCGGGCTTCATCGGCTCGCACCTCGTGGACAGGCTCATGGAGAACGAGAAACACGAG
                                    aaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcacagcgcgatctatctcaacgctggatctctgtttcacttgccgcgagccatgtatggttcagggcctgctcgcgtgttccggatcctgattaccggtgccaaattgctgcttgatccagGCTAACCTGCGGATCCTGGTCACTGGTGGGGCGGGCTTCATCGGCTCGCACCTCGTGGACAGGCTCATGGAGAACGAGAAACACGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA