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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatgttttgtccttctgaatttcaataacattgcgctgcccatgtaagatagagcaagatctacgggacgattgtattaaccctttttttatttgccagTTTGGAGAAAATGGGAGCTCTTGACTGGAATAAAATTGTCCATCAAAACCAAGGGTGGCGCCTTATTAGCTGCATCTGGCTCCATGCTGGCCTAATCCAT

Basic information

species Zea mays
transcript GRMZM2G116514_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G116514_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os09g35730.1 (Oryza sativa), 3'ss of exon 1
ttatgttttgtccttctgaatttcaataacattgcgctgcccatgtaagataga-gcaagatctacgggacgattgtattaa---ccctttttttatttgccagTTTGGAGAAAATGGGAGCTCTTGACTGGAATAAAATTGTCCATCAAAACCAAGGGTGGCGCCTTATTAGCTGCATCTGGCTCCATGCTGGCCTAATCCAT
      |        | || | |  || | ||   ||  ||||  |    | || | |  |  |    |  |||  ||||||   | || |||||  ||| ||||||| ||||||||||||||||||||||||| ||| |||| |||||  ||||||| ||||| || |||||||| |||||||||||||||||||||||||||
---gaatgaaaatcccagactctgcatcatatgatgc-acccagctttcttggatgaacaacatgattggtgatcctattaacatctctctttttgattggcagTTTGCAGAAAATGGGAGCTCTTGACTGGAACAAAGTTGTTCATCAGCACCAAGGATGGCGTCTCATTAGCTGTATCTGGCTCCATGCTGGCCTAATCCAT
















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|101386352|gb|EB815195.1|EB815195
EST:     TCCTTCCAGCCGCTCCGCGAGAACCCGCTGCTCGGCCCGTCCTCCTCCAC                         TTTGGAGAAAATGGGAGCTCTTGACTGGAATAAAATTGTCCATCAAAACCA
genomic: TCCTTCCAGCCGCTCCGCGAGAACCCGCTGCTCGGCCCGTCCTCCTCCACgtacgttgtc ... tatttgccagTTTGGAGAAAATGGGAGCTCTTGACTGGAATAAAATTGTCCATCAAAACCA
EST: gi|76286369|gb|DV025937.1|DV025937
EST:     TCCTTCCAGCCGCTCCGCGAGAACCCGCTGCTCGGCCCGTCCTCCTCCAC                         TTTGGAGAAAATGGGAGCTCTTGACTGGAATAAAATTGTCCATCAAAACCA
genomic: TCCTTCCAGCCGCTCCGCGAGAACCCGCTGCTCGGCCCGTCCTCCTCCACgtacgttgtc ... tatttgccagTTTGGAGAAAATGGGAGCTCTTGACTGGAATAAAATTGTCCATCAAAACCA
EST: gi|15100365|gb|BI396156.1|BI396156
EST:     TCCTTCCAGCCGCTCCGCGAGAACCCGCTGCTCGGCCCGTCCTCCTCCAC                         TTTGGAGAAAATGGGAGCTCTTGACTGGAATAAAATTGTCCATCAAAACCA
genomic: TCCTTCCAGCCGCTCCGCGAGAACCCGCTGCTCGGCCCGTCCTCCTCCACgtacgttgtc ... tatttgccagTTTGGAGAAAATGGGAGCTCTTGACTGGAATAAAATTGTCCATCAAAACCA
EST: gi|71319572|gb|DR796532.1|DR796532
EST:     TCCTTCCAGCCGCTCCGCGAGAACCCGCTGCTCGGCCCGTCCTCCTCCAC                         TTTGGAGAAAATGGGAGCTCTTGACTGGAATAAAATTGTCCATCAAAACCA
genomic: TCCTTCCAGCCGCTCCGCGAGAACCCGCTGCTCGGCCCGTCCTCCTCCACgtacgttgtc ... tatttgccagTTTGGAGAAAATGGGAGCTCTTGACTGGAATAAAATTGTCCATCAAAACCA
EST: gi|26457322|gb|CA828905.1|CA828905
EST:     TCCTTCCAGCCGCTCCGCGAGAACCCGCTGCTCGGCCCGTCCTCCTCCAC                         TTTGGAGAAAATGGGAGCTCTTGACTGGAATAAAATTGTCCATCAAAACCA
genomic: TCCTTCCAGCCGCTCCGCGAGAACCCGCTGCTCGGCCCGTCCTCCTCCACgtacgttgtc ... tatttgccagTTTGGAGAAAATGGGAGCTCTTGACTGGAATAAAATTGTCCATCAAAACCA
EST: gi|149072555|gb|EE040236.2|EE040236
EST:     TCCTTCCAGCCGCTCCGCGAGAACCCGCTGCTCGGCCCGTCCTCCTCCAC                         TTTGGAGAAAATGGGAGCTCTTGACTGGAATAAAATTGTCCATCAAAACCA
genomic: TCCTTCCAGCCGCTCCGCGAGAACCCGCTGCTCGGCCCGTCCTCCTCCACgtacgttgtc ... tatttgccagTTTGGAGAAAATGGGAGCTCTTGACTGGAATAAAATTGTCCATCAAAACCA
EST: gi|148967078|gb|EE018245.2|EE018245
EST:     TCCTTCCAGCCGCTCCGCGAGAACCCGCTGCTCGGCCCGTCCTCCTCCAC                         TTTGGAGAAAATGGGAGCTCTTGACTGGAATAAAATTGTCCATCAAAACCA
genomic: TCCTTCCAGCCGCTCCGCGAGAACCCGCTGCTCGGCCCGTCCTCCTCCACgtacgttgtc ... tatttgccagTTTGGAGAAAATGGGAGCTCTTGACTGGAATAAAATTGTCCATCAAAACCA
EST: gi|87155865|gb|DY400654.1|DY400654
EST:     TCCTTCCAGCCGCTCCGCGAGAACCCGCTGCTCGGCCCGTCCTCCTCCAC                         TTTGGAGAAAATGGGAGCTCTTGACTGGAATAAAATTGTCCATCAAAACCA
genomic: TCCTTCCAGCCGCTCCGCGAGAACCCGCTGCTCGGCCCGTCCTCCTCCACgtacgttgtc ... tatttgccagTTTGGAGAAAATGGGAGCTCTTGACTGGAATAAAATTGTCCATCAAAACCA
EST: gi|211304275|gb|FL115012.1|FL115012
EST:     TCCTTCCAGCCGCTCCGCGAGAACCCGCTGCTCGGCCCGTCCTCCTCCAC                         TTTGGAGAAAATGGGAGCTCTTGACTGGAATAAAATTGTCCATCAAAACCA
genomic: TCCTTCCAGCCGCTCCGCGAGAACCCGCTGCTCGGCCCGTCCTCCTCCACgtacgttgtc ... tatttgccagTTTGGAGAAAATGGGAGCTCTTGACTGGAATAAAATTGTCCATCAAAACCA
EST: gi|78075433|gb|DV503867.1|DV503867
EST:     TCCTTCCAGCCGCTCCGCGAGAACCCGCTGCTCGGCCCGTCCTCCTCCAC                         TTTGGAGAAAATGGGAGCTCTTGACTGGAATAAAATTGTCCATCAAAACCA
genomic: TCCTTCCAGCCGCTCCGCGAGAACCCGCTGCTCGGCCCGTCCTCCTCCACgtacgttgtc ... tatttgccagTTTGGAGAAAATGGGAGCTCTTGACTGGAATAAAATTGTCCATCAAAACCA
EST: gi|21390183|gb|BQ528232.1|BQ528232
EST:     TCCTTCCAGCCGCTCCGCGAGAACCCGCTGCTCGGCCCGTCCTCCTCCAC                         TTTGGAGAAAATGGGAGCTCTTGACTGGAATAAAATTGTCCATCAAAACCA
genomic: TCCTTCCAGCCGCTCCGCGAGAACCCGCTGCTCGGCCCGTCCTCCTCCACgtacgttgtc ... tatttgccagTTTGGAGAAAATGGGAGCTCTTGACTGGAATAAAATTGTCCATCAAAACCA
EST: gi|148982101|gb|EE028150.2|EE028150
EST:     TCCTTCCAGCCGCTCCGCGAGAACCCGCTGCTCGGCCCGTCCTCCTCCAC                         TTTGGAGAAAATGGGAGCTCTTGACTGGAATAAAATTGTCCATCAAAACCA
genomic: TCCTTCCAGCCGCTCCGCGAGAACCCGCTGCTCGGCCCGTCCTCCTCCACgtacgttgtc ... tatttgccagTTTGGAGAAAATGGGAGCTCTTGACTGGAATAAAATTGTCCATCAAAACCA
EST: gi|211304280|gb|FL115017.1|FL115017
EST:     TCCTTCCAGCCGCTCCGCGAGAACCCGCTGCTCGGCCCGTCCTCCTCCAC                         TTTGGAGAAAATGGGGAGCTCTTGACTGGAATAAAATTGTCCATCAAAACC
genomic: TCCTTCCAGCCGCTCCGCGAGAACCCGCTGCTCGGCCCGTCCTCCTCCACgtacgttgtc ... tatttgccagTTTGGAGAAAATGGG-AGCTCTTGACTGGAATAAAATTGTCCATCAAAACC
EST: gi|26558680|gb|CA830915.1|CA830915
EST:     TCCTTCCAGCCGCTCCGCGAGAACCCGCTGCTCGGCCCGTCCTCCTCCAC                         TTTGGAGAAAATGGGAGCTCTTGACTGGAATAAAATTGTCCATCAAAACCA
genomic: TCCTTCCAGCCGCTCCGCGAGAACCCGCTGCTCGGCCCGTCCTCCTCCACgtacgttgtc ... tatttgccagTTTGGAGAAAATGGGAGCTCTTGACTGGAATAAAATTGTCCATCAAAACCA
EST: gi|71764176|gb|DR962113.1|DR962113
EST:     TCCTTCCAGCCGCTCCGCGAGAACCCGCTGCTCGGCCCGTCCTCCTCCAC                         TTTGGAGAAAATGGGAGCTCTTGACTGGAATAAAATTGTCCATCAAAACCA
genomic: TCCTTCCAGCCGCTCCGCGAGAACCCGCTGCTCGGCCCGTCCTCCTCCACgtacgttgtc ... tatttgccagTTTGGAGAAAATGGGAGCTCTTGACTGGAATAAAATTGTCCATCAAAACCA
EST: gi|22473298|gb|BU037778.1|BU037778
EST:     TCCTTCCAGCCGCTCCGCGAGAACCCGCTGCTCGGCCCGTCCTCCTCCAC                         TTTGGAGAAAATGGGAGCTCTTGACTGGAATAAAATTGTCCATCAAAACCA
genomic: TCCTTCCAGCCGCTCCGCGAGAACCCGCTGCTCGGCCCGTCCTCCTCCACgtacgttgtc ... tatttgccagTTTGGAGAAAATGGGAGCTCTTGACTGGAATAAAATTGTCCATCAAAACCA
EST: gi|71309285|gb|DR790929.1|DR790929
EST:     TCCTTCCAGCCGCTCCGCGAGAACCCGCTGCTCGGCCCGTCCTCCTCCAC                         TTTGGAGAAAATGGGAGCTCTTGACTGGAATAAAATTGTCCATCAAAACCA
genomic: TCCTTCCAGCCGCTCCGCGAGAACCCGCTGCTCGGCCCGTCCTCCTCCACgtacgttgtc ... tatttgccagTTTGGAGAAAATGGGAGCTCTTGACTGGAATAAAATTGTCCATCAAAACCA
EST: gi|76020121|gb|DT947291.1|DT947291
EST:     TCCTTCCAGCCGCTCCGCGAGAACCCGCTGCTCGGCCCGTCCTCCTCCAC                         TTTGGAGAAAATGGGAGCTCTTGACTGGAATAAAATTGTCCATCAAAACCA
genomic: TCCTTCCAGCCGCTCCGCGAGAACCCGCTGCTCGGCCCGTCCTCCTCCACgtacgttgtc ... tatttgccagTTTGGAGAAAATGGGAGCTCTTGACTGGAATAAAATTGTCCATCAAAACCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taagatagagcaagatctacgggacgattgtattaaccctttttttatttgccagTTTGGAGAAAATGGGAGCTCTTGACTGGAATAAAATTGTCCATCAAAACCAAGGGTGGCGCCTTATTAGCTGCATCTGGCTCCATGCTGGCCTAATCCAT
                              tattaac  putative branch site (score: 1)
                                    ccctttttttatttgc  CT-rich tract
                                       tttttttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttatgttttgtccttctgaatttcaataacattgcgctgcccatgtaagatagagcaagatctacgggacgattgtattaaccctttttttatttgccagTTTGGAGAAAATGGGAGCTCTTGACTGGAATAAAATTGTCCATCAAAACCAAGGGTGGCGCCTTATTAGCTGCATCTGGCTCCATGCTGGCCTAATCCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG