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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagctgaattcctgttggttatataaaagcaatttgcaatagttatctctttacgttatttatggtttgtgcgggatgttccttgctattcttatctcagGCCAGGGGTAGCCAATGCTATTGAGGAATTCAAGACTTCAGTCTATGGTGAAAATTATGACCAAGAGGAGGCAGAAGCGGCAGCAGGGAAAGCTTCCCGT

Basic information

species Zea mays
transcript GRMZM2G414496_T08
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G414496_T07 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os07g08729.1 (Oryza sativa), 3'ss of exon 17
-------------aagctgaattcctgttggttatataaaagcaatttgcaatagttatctctttacgttatttatggtttgtgcgggatgttccttgctattcttatctcagGCCAGGGGTAGCCAATGCTATTGAGGAATTCAAGACTTCAGTCTATGGTGAAAATTATGACCAAGAGGAGGCAGAAGCGGCAGCAGGGAAAGCTTCCCGT
              |  | | ||    ||  ||  |||| | |||  | ||| ||| | |||||             | || || ||| |||| | | | | ||||||||||||||||  ||||  || ||| | |||||||| ||| ||||||||||||||||||||||||| |||||||| || || || ||||||| ||| |||     |
tctactacatattcaattcagttttacttttttgcataacaacaacgtacaacagtcacctctt-------------gcttatgtgggttgtttcctaccactcttatctcagGCCAGTAGTAGTTAAAGCTGTCGAGGAATTTAAGGCTTCAGTCTATGGTGAAAATTATGATCAAGAGGAAGCCGAGGCAGCAGCAGCGAAGGCTGGGGCT
















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|32937939|gb|CF042758.1|CF042758
EST:     ATGCCTGATATAAAGGATGAGACCCTGCCTGACGAAGAAGGCTTGTCTAA                         GCCAGGGGTAGCCAATGCTATTGAGGAATTCAAGACTTCAGTCTATGGTGA
genomic: ATGCCTGATATAAAGGATGAGACCCTGCCTGACGAAGAAGGCTTGTCTAAgtacttcttt ... cttatctcagGCCAGGGGTAGCCAATGCTATTGAGGAATTCAAGACTTCAGTCTATGGTGA
EST: gi|211402618|gb|FL252146.1|FL252146
EST:     ATGCCTGATATAAAGGATGAGACCCTGCCTGACGAAGAAGGCTTGTCTAA                         GCCAGGGGTAGCCAATGCTATTGAGGAATTCAAGACTTCAGTCTATGGTGA
genomic: ATGCCTGATATAAAGGATGAGACCCTGCCTGACGAAGAAGGCTTGTCTAAgtacttcttt ... cttatctcagGCCAGGGGTAGCCAATGCTATTGAGGAATTCAAGACTTCAGTCTATGGTGA
EST: gi|33097000|gb|CF056960.1|CF056960
EST:     ATGCCTGATATAAAGGATGAGACCCTGCCTGACGAAGAAGGCTTGTCTAA                         GCCAGGGGTAGCCAATGCTATTGAGGAATTCAAGACCTCAGTCTATGGTGA
genomic: ATGCCTGATATAAAGGATGAGACCCTGCCTGACGAAGAAGGCTTGTCTAAgtacttcttt ... cttatctcagGCCAGGGGTAGCCAATGCTATTGAGGAATTCAAGACTTCAGTCTATGGTGA
EST: gi|71312125|gb|DR792591.1|DR792591
EST:     ATGCCTGATATAAAGGATGAGACCCTGCCTGACGAAGAAGGCTTGTTTAA                         GCCAGGGGTAGCCAATGCTATTGAGGAATTCAAGACTTCAGTCTATGGTGA
genomic: ATGCCTGATATAAAGGATGAGACCCTGCCTGACGAAGAAGGCTTGTCTAAgtacttcttt ... cttatctcagGCCAGGGGTAGCCAATGCTATTGAGGAATTCAAGACTTCAGTCTATGGTGA
EST: gi|14245465|gb|BG874047.1|BG874047
EST:     ATGCCTGATATAAAGGATGAGACCCTGCCTGACGAAGAAGGCTTGTCTAA                         GCCAGGGGTAGCCAATGCTATTGAGGAATTCAAGACTTCAGTCTATGGTGA
genomic: ATGCCTGATATAAAGGATGAGACCCTGCCTGACGAAGAAGGCTTGTCTAAgtacttcttt ... cttatctcagGCCAGGGGTAGCCAATGCTATTGAGGAATTCAAGACTTCAGTCTATGGTGA
EST: gi|71312126|gb|DR792592.1|DR792592
EST:     ATGCCTGATATAAAGGATGAGACCCTGCCTGACGAAGAAGGCTTGTCTAA                         GCCAGGGGTAGCCAATGCTATTGAGGAATTCAAGACTTCAGTCTATGGTGA
genomic: ATGCCTGATATAAAGGATGAGACCCTGCCTGACGAAGAAGGCTTGTCTAAgtacttcttt ... cttatctcagGCCAGGGGTAGCCAATGCTATTGAGGAATTCAAGACTTCAGTCTATGGTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctctttacgttatttatggtttgtgcgggatgttccttgctattcttatctcagGCCAGGGGTAGCCAATGCTATTGAGGAATTCAAGACTTCAGTCTATGGTGAAAATTATGACCAAGAGGAGGCAGAAGCGGCAGCAGGGAAAGCTTCCCGT
                                 ttccttgctattctt  CT-rich tract
          ttatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aagctgaattcctgttggttatataaaagcaatttgcaatagttatctctttacgttatttatggtttgtgcgggatgttccttgctattcttatctcagGCCAGGGGTAGCCAATGCTATTGAGGAATTCAAGACTTCAGTCTATGGTGAAAATTATGACCAAGAGGAGGCAGAAGCGGCAGCAGGGAAAGCTTCCCGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
-agctgaa
- - - - - cctgttg
- - - - - - - - - - - - - - - -atttgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtgcgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tccttgc