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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agcaatgaacttgcacactggtacatggttctgtttatcttgctgtttctgtcaatgtctcagtcttacctaggtttccattgattggcctatcaaacagCGCACTGGAGTTTCTATCAACATGCAAGATTGCAAATCTGACTATTAGAGCAGAACTCGGATGCTGCTTGCTGCATCGAGGCGGTAGATTGACCATCCAG

Basic information

species Zea mays
transcript GRMZM2G009021_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G009021_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os07g46555.1 (Oryza sativa), 3'ss of exon 4
agcaatgaacttgcacactggtaca-tggttct--gtttatcttgctgtttctgtcaatgtctcagtcttacctaggtttccattgattggcctatc-aaacagCGCACTGGAGTTTCTATCAACATGCAAGATTGCAAATCTGACTATTAGAGCAGAACTCGGATGCTGCTTGCTGCATCGAGGCGGTAGATTGACCATCCAG
    ||| | ||     |||   || ||||| |  |||  |  |  |||||| ||||| |   || |  |    |   | || |  | | |||| ||  | ||| ||  ||||||| |  || || ||||||||||||||||| |||||||||||||| || || || || ||||| |||||| | |||||||| || ||  ||
--gtatgcatttttcttctgtggcaatggttttttgttctttctaatgtttc-gtcaaagcggcaatgattttaa---taccttccacttgcctgtctgagcagTGCGTTGGAGTTCCATTCCACCTGCAAGATTGCAAATCTCACTATTAGAGCAGAGCTTGGGTGTTGTTTGCTTCATCGAAGTGGTAGATTAACTATTGAG
















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|211342145|gb|FL091793.1|FL091793
EST:     GGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGCTTCGACAA                         CGCACTGGAGTTTCTATCAACATG
genomic: GGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGTTTCGACAAgtaagctctt ... tatcaaacagCGCACTGGAGTTTCTATCAACATG
EST: gi|211342151|gb|FL091799.1|FL091799
EST:     GGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGTTTCGACAA                         CGCACTGGAGTTTCTATCAACATGCAAGATTGCAAATCTGACTATTAGAGC
genomic: GGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGTTTCGACAAgtaagctctt ... tatcaaacagCGCACTGGAGTTTCTATCAACATGCAAGATTGCAAATCTGACTATTAGAGC
EST: gi|211342143|gb|FL091791.1|FL091791
EST:     GGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGCTTCGACAA                         CGCACTGGAGTTTCTATCAACATG
genomic: GGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGTTTCGACAAgtaagctctt ... tatcaaacagCGCACTGGAGTTTCTATCAACATG
EST: gi|30087498|gb|CB885704.1|CB885704
EST:     GGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGTTTCGACAA                         CGCACTGGAGTTTCTATCAACATGCAAGATTGCAAATCTGACTATTAGAGC
genomic: GGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGTTTCGACAAgtaagctctt ... tatcaaacagCGCACTGGAGTTTCTATCAACATGCAAGATTGCAAATCTGACTATTAGAGC
EST: gi|211342146|gb|FL091794.1|FL091794
EST:     GGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGCTTCGACAA                         CGCACTGGAGTT-CTATCAACATG
genomic: GGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGTTTCGACAAgtaagctctt ... tatcaaacagCGCACTGGAGTTTCTATCAACATG
EST: gi|211344543|gb|FL091811.1|FL091811
EST:     GGCGATATTCCTGATGACACTGTATTGACCTGCTCACGTGGCTTCGACAA                         CGCACTGGAGTTTCTATCAACATGCAAGATTGCAAATCTGACTATTAGAGC
genomic: GGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGTTTCGACAAgtaagctctt ... tatcaaacagCGCACTGGAGTTTCTATCAACATGCAAGATTGCAAATCTGACTATTAGAGC
EST: gi|211344540|gb|FL091808.1|FL091808
EST:     GGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGCTTCGACAA                         CGCACTGGAGTTTCTATC
genomic: GGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGTTTCGACAAgtaagctctt ... tatcaaacagCGCACTGGAGTTTCTATC
EST: gi|37396358|gb|CF635468.1|CF635468
EST:     GGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGTTTCGACAA                         CGCACTGGAGTTTCTATCAACATGCAAGATTGCAAATCTGACTATTAGAGC
genomic: GGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGTTTCGACAAgtaagctctt ... tatcaaacagCGCACTGGAGTTTCTATCAACATGCAAGATTGCAAATCTGACTATTAGAGC
EST: gi|30087497|gb|CB885703.1|CB885703
EST:     GGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGTTTCGACAA                         CGCACTGGAGTTTCTATCAACATGCAAGATTGCAAATCTGACTATTAGAGC
genomic: GGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGTTTCGACAAgtaagctctt ... tatcaaacagCGCACTGGAGTTTCTATCAACATGCAAGATTGCAAATCTGACTATTAGAGC
EST: gi|211120475|gb|FL454283.1|FL454283
EST:     CTGATGACACTGTATTGACCTGCTCACGTGGCTTCGACAA                         CGCACTGGAGTTTCTATCAACATGCAAGATTGCAAATCTGACTATTAGAGC
genomic: CTGATGACACTGTATTGACCTGCTCACGTGGTTTCGACAAgtaagctctt ... tatcaaacagCGCACTGGAGTTTCTATCAACATGCAAGATTGCAAATCTGACTATTAGAGC
EST: gi|211344542|gb|FL091810.1|FL091810
EST:     GGCGATATTCCTGATGACACTGTATTGACCTGCTCACGTGGCTTCGACAA                         CGCACTGGAGT
genomic: GGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGTTTCGACAAgtaagctctt ... tatcaaacagCGCACTGGAGT
EST: gi|29945972|gb|CB815913.1|CB815913
EST:     GGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGTTTCGACAA                         CGCACTGGAGTTTCTATCAACATGCAAGATTGCAAATCTGACTATTAGAGC
genomic: GGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGTTTCGACAAgtaagctctt ... tatcaaacagCGCACTGGAGTTTCTATCAACATGCAAGATTGCAAATCTGACTATTAGAGC
EST: gi|29945970|gb|CB815912.1|CB815912
EST:     GGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGTTTCGACAA                         CGCACTGGAGTTTCTATCAACATGCAAGATTGCAAATCTGACTATTAGAGC
genomic: GGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGTTTCGACAAgtaagctctt ... tatcaaacagCGCACTGGAGTTTCTATCAACATGCAAGATTGCAAATCTGACTATTAGAGC
EST: gi|211342150|gb|FL091798.1|FL091798
EST:     GGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGCTTCGACAA                         CGCACTGGAGTTTCTATCAACATGC
genomic: GGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGTTTCGACAAgtaagctctt ... tatcaaacagCGCACTGGAGTTTCTATCAACATGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttctgtcaatgtctcagtcttacctaggtttccattgattggcctatcaaacagCGCACTGGAGTTTCTATCAACATGCAAGATTGCAAATCTGACTATTAGAGCAGAACTCGGATGCTGCTTGCTGCATCGAGGCGGTAGATTGACCATCCAG
                                  attgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agcaatgaacttgcacactggtacatggttctgtttatcttgctgtttctgtcaatgtctcagtcttacctaggtttccattgattggcctatcaaacagCGCACTGGAGTTTCTATCAACATGCAAGATTGCAAATCTGACTATTAGAGCAGAACTCGGATGCTGCTTGCTGCATCGAGGCGGTAGATTGACCATCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC