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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgacaacatacatttcaaaatcagttttatgttatgttggcctctattttccttgtggagttgtgatactgaatcttctcctgcactgtttcccccctagGATGATTCTGAAATAGTTGCCATGATAAAAGAATTATTGGAGACTCGTATTCGACCAGCTGTTCAAGATGACGGCGGTGACATTGAATACCGAGGATTCG

Basic information

species Zea mays
transcript GRMZM2G131249_T03
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G131249_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os05g06330.1 (Oryza sativa), 3'ss of exon 3
tgacaacatacatttcaaaatcagttttatgttatgttggcctctattttccttgtggagttgtgatactgaatcttctcctgcactgtttccc----ccctagGATGATTCTGAAATAGTTGCCATGATAAAAGAATTATTGGAGACTCGTATTCGACCAGCTGTTCAAGATGACGGCGGTGACATTGAATACCGAGGATTCG
| |   |  ||   ||    |  || |  |  ||   |   |  |    ||||  |  |      |  || | | || ||    | | || | |    || ||||||||||| ||||||||||| ||||||||||| ||  |||||||||| ||||||||||||||||||||||| || |||||||||||||| |||||||| |
taatggctcac--ctcgttttgcgtatcttcctaatctcctcaatcccctcctcctcaaacac--accctaagtattttcacatatttttcctctatgccatagGATGATTCAGAAATAGTTGCAATGATAAAAGAGTTGCTGGAGACTCGCATTCGACCAGCTGTTCAAGATGATGGTGGTGACATTGAATATCGAGGATTTG

upper sequence: GRMZM2G131249_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA20G38630.1 (Glycine max), 3'ss of exon 2
--tgacaacatacatt--tcaaaatcagttttatgttatgttggcctctattttccttgtggagttgtgatactgaatcttctcctgcactgtttcccccctagGATGATTCTGAAATAGTTGCCATGATAAAAGAATTATTGGAGACTCGTATTCGACCAGCTGTTCAAGATGACGGCGGTGACATTGAATACCGAGGATTCG
   |||    || | |  || || |  || |||  | |||   |    ||      ||| | ||  |  | ||| |||  |  | |  ||  ||| ||   |||||||||||||||| |||||| ||||| || ||||| || |||||||| |||||||| || || |||||||| ||||| |||||||||||  |||| || |
taagactttgtaaaatggtccaagtttgtcttac-tcatgg-agtacataggaagtttgagaaggcg-aaaactaaatggta-catatacatttttccatatagGATGATTCTGAAACAGTTGCAATGATCAAGGAATTGTTAGAGACTCGAATTCGACCTGCAGTGCAAGATGATGGCGGGGACATTGAATATAGAGGTTTTG

upper sequence: GRMZM2G131249_T03 (Zea mays), 3'ss of exon 3
lower sequence: Vv13s0106g00620.t01 (Vitis vinifera), 3'ss of exon 3
-------tgacaacatacatttcaaaatcagttttatgttatgttggcctctattttccttgtggagttgtgatactgaatcttctcctgcactgtttcccccctagGATGATTCTGAAATAGTTGCCATGATAAAAGAATTATTGGAGACTCGTATTCGACCAGCTGTTCAAGATGACGGCGGTGACATTGAATACCGAGGATTCG
         | ||  |  | ||| ||||   |||| || | |||  ||   ||||  |    |  |  |    ||   || | | || ||   |||| ||     |||||||||||||||  || || ||||| |||||| | ||||||||||||||||||||||| ||||||||||| || || ||||| || || || ||||| |
tggaactccaaaatgtttaattccaaat--attttctgat-tgtctgcagttattc-ctgcataaatctcatgtatataaccatttcttg---tgttgccatgacagGATGATTCTGAAACTGTAGCAATGATCAAAGAACTGTTGGAGACTCGTATTCGACCAGCAGTTCAAGATGATGGTGGGGACATCGAGTATCGGGGATTTG

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|32911598|gb|CF016410.1|CF016410
EST:     TTTTTCTGGACTCAAATGCTGCAGCTTCTATGGACACAGCAATTCACGAG                         GATGATTCTGAAATA
genomic: TTTTTCTGGACTCAAATGCTGCAGCTTCTATGGACACAGCAATTCACGAGgtatctcaac ... tcccccctagGATGATTCTGAAATA
EST: gi|211501968|gb|FL391661.1|FL391661
EST:     TTTTTCTGGACTCAAATGCTGCAGCTTCTATGGACACAGCAATTCACGAG                         GATGATTCTGAAATAGTTGCCATGATAAAAGAATTATTGGGAGACTCGTAN
genomic: TTTTTCTGGACTCAAATGCTGCAGCTTCTATGGACACAGCAATTCACGAGgtatctcaac ... tcccccctagGATGATTCTGAAATAGTTGCCATGATAAAAGAATTATTGG-AGACTCGTA-
EST: gi|67024319|gb|CO453068.1|CO453068
EST:     TTTTTCTGGACTCAAATGCTGCAGCTTCTATGGACACAGCAATTCACGAG                         GATGATTCTGAAATAGTTGCCATGATAAAAGAATTATTGGAGACTCGTATT
genomic: TTTTTCTGGACTCAAATGCTGCAGCTTCTATGGACACAGCAATTCACGAGgtatctcaac ... tcccccctagGATGATTCTGAAATAGTTGCCATGATAAAAGAATTATTGGAGACTCGTATT
EST: gi|211423867|gb|FL405822.1|FL405822
EST:     TTTTTCTGGACTCAAATGCTGCAGCTTCTATGGACACAGCA-TTCACGAA                         GATGATTCTGAAATAGTTGC-ATGATAAAAGAATTATTG
genomic: TTTTTCTGGACTCAAATGCTGCAGCTTCTATGGACACAGCAATTCACGAGgtatctcaac ... tcccccctagGATGATTCTGAAATAGTTGCCATGATAAAAGAATTATTG
EST: gi|89755071|gb|DY685633.1|DY685633
EST:     TTTTTCTGGACTCAAATGCTGCAGCTTCTATGGACACAGCAATTCACGAG                         GATGATTCTGAAATAGTTGCCATGATAAAAGAATTATTGGAGACTCGTATT
genomic: TTTTTCTGGACTCAAATGCTGCAGCTTCTATGGACACAGCAATTCACGAGgtatctcaac ... tcccccctagGATGATTCTGAAATAGTTGCCATGATAAAAGAATTATTGGAGACTCGTATT
EST: gi|38502507|gb|CF972367.1|CF972367
EST:     TTTTTCTGGACTCAAATGCTGCAGCTTCTATGGACACAGCAATTCACGAG                         GATGATTCTGAAATAGTTACCATGATAAAAGAATTATTGGAGACTCGTATT
genomic: TTTTTCTGGACTCAAATGCTGCAGCTTCTATGGACACAGCAATTCACGAGgtatctcaac ... tcccccctagGATGATTCTGAAATAGTTGCCATGATAAAAGAATTATTGGAGACTCGTATT
EST: gi|211150249|gb|FL395020.1|FL395020
EST:     TTTTTCTGGACTCAAATGCTGCAGCTTCTATGGACACAGCAATTCACGAG                         GATGATTCTGAAATAGTTGCCATGATAAAAGAATTATTGGAGACTCGTATT
genomic: TTTTTCTGGACTCAAATGCTGCAGCTTCTATGGACACAGCAATTCACGAGgtatctcaac ... tcccccctagGATGATTCTGAAATAGTTGCCATGATAAAAGAATTATTGGAGACTCGTATT
EST: gi|50338103|gb|CO533229.1|CO533229
EST:     TTTTTCTGGACTCAAATGCTGCAGCTTCTATGGACACAGCAATTCACGAG                         GATGATTCTGAAATAGTTGCCATGATAAAAGAATTATTGGAGACTCGTATT
genomic: TTTTTCTGGACTCAAATGCTGCAGCTTCTATGGACACAGCAATTCACGAGgtatctcaac ... tcccccctagGATGATTCTGAAATAGTTGCCATGATAAAAGAATTATTGGAGACTCGTATT
EST: gi|71436813|gb|DR817863.1|DR817863
EST:     TTTTTCTGGACTCAAATGCTGCAGCTTCTATGGACACAGCAATTCACGAG                         GATGATTCTGAAATAGTTGCCATGATAAAAGAATTATTGGAGACTCGTATT
genomic: TTTTTCTGGACTCAAATGCTGCAGCTTCTATGGACACAGCAATTCACGAGgtatctcaac ... tcccccctagGATGATTCTGAAATAGTTGCCATGATAAAAGAATTATTGGAGACTCGTATT
EST: gi|76012527|gb|DT939697.1|DT939697
EST:     TTTTTCTGGACTCAAATGCTGCAGCTTCTATGGACACAGCAATTCACGAG                         GATGATTCTGAAATAGTTGCCATGATAAAAGAATTATTGGAGACTCGTATT
genomic: TTTTTCTGGACTCAAATGCTGCAGCTTCTATGGACACAGCAATTCACGAGgtatctcaac ... tcccccctagGATGATTCTGAAATAGTTGCCATGATAAAAGAATTATTGGAGACTCGTATT
EST: gi|22472228|gb|BU036708.1|BU036708
EST:     TTTTTCTGGACTCAAATGCTGCAGCTTCTATGGACACAGCAATTCACGAG                         GATGATTCTGAAATA
genomic: TTTTTCTGGACTCAAATGCTGCAGCTTCTATGGACACAGCAATTCACGAGgtatctcaac ... tcccccctagGATGATTCTGAAATA
EST: gi|108953674|gb|EC364835.1|EC364835
EST:     TTTCTGGACTCAAATGCTGCAGCTTCTATGGGACACAGCAAATTCACGAG                         GATGAATTCTTGAAATAGTTGCCATGGATAAAAAGAATTATTGGA
genomic: TTTCTGGACTCAAATGCTGCAGCTTCTATGG-ACACAGCAA-TTCACGAGgtatctcaac ... tcccccctagGATGA-TTCT-GAAATAGTTGCCATG-ATAAAA-GAATTATTGGA
EST: gi|17921487|gb|BM259138.1|BM259138
EST:     TTTTTCTGGACTCAAATGCTGCAGCTTCTATGGACACAGCAATTCACGAG                         GATGATTCTGAAATAGTT
genomic: TTTTTCTGGACTCAAATGCTGCAGCTTCTATGGACACAGCAATTCACGAGgtatctcaac ... tcccccctagGATGATTCTGAAATAGTT
EST: gi|94475082|gb|EB704040.1|EB704040
EST:     TTTTTCTGGACTCAAATGCTGCAGCTTCTATGGACACAGCAATTCACGAG                         GATGATTCTGAAATAGTTGCCATGATAAAAGAATTATTGGAGACTCGTATT
genomic: TTTTTCTGGACTCAAATGCTGCAGCTTCTATGGACACAGCAATTCACGAGgtatctcaac ... tcccccctagGATGATTCTGAAATAGTTGCCATGATAAAAGAATTATTGGAGACTCGTATT
EST: gi|211452112|gb|FL393956.1|FL393956
EST:     TTTTTCTGGACTCAAATGCTGCAGCTTCTATGGACACAGCAATTCACGAG                         GATGATTCTGAAATAGTTGCCATGATAAAAGAATTATTGGAGACTCGTATT
genomic: TTTTTCTGGACTCAAATGCTGCAGCTTCTATGGACACAGCAATTCACGAGgtatctcaac ... tcccccctagGATGATTCTGAAATAGTTGCCATGATAAAAGAATTATTGGAGACTCGTATT
EST: gi|22473172|gb|BU037652.1|BU037652
EST:     TTTTTCTGGACTCAAATGCTGCAGCTTCTATGGACACAGCAATTCACGAG                         GATGATTCTGAAATAGTTGCCATGATAAAAGAATTATTGGAGACTCGTATT
genomic: TTTTTCTGGACTCAAATGCTGCAGCTTCTATGGACACAGCAATTCACGAGgtatctcaac ... tcccccctagGATGATTCTGAAATAGTTGCCATGATAAAAGAATTATTGGAGACTCGTATT
EST: gi|22546273|gb|BU098584.1|BU098584
EST:     TTTTTCTGGACTCAAATGCTGCAGCTTCTATGGACACAGCAATTCACGAG                         GATGATTCTGAAATAGTTGCCATGATAAAAGAATTATTGGAGACTCGTATT
genomic: TTTTTCTGGACTCAAATGCTGCAGCTTCTATGGACACAGCAATTCACGAGgtatctcaac ... tcccccctagGATGATTCTGAAATAGTTGCCATGATAAAAGAATTATTGGAGACTCGTATT
EST: gi|17921814|gb|BM259465.1|BM259465
EST:     TTTTTCTGGACTCAAATGCTGCAGCTTCTATGGACACAGCAATTCACGAG                         GATGATTCTGAAATAGTT
genomic: TTTTTCTGGACTCAAATGCTGCAGCTTCTATGGACACAGCAATTCACGAGgtatctcaac ... tcccccctagGATGATTCTGAAATAGTT
EST: gi|84980471|gb|DW530820.1|DW530820
EST:     TTTTTCTGGACTCAAATGCTGCAGCTTCTATGGACACAGCAATTCACGAG                         GATGATTCTGAAATATTTGCCATGATAAAAGAATTATTGGAGACTCGTATT
genomic: TTTTTCTGGACTCAAATGCTGCAGCTTCTATGGACACAGCAATTCACGAGgtatctcaac ... tcccccctagGATGATTCTGAAATAGTTGCCATGATAAAAGAATTATTGGAGACTCGTATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttccttgtggagttgtgatactgaatcttctcctgcactgtttcccccctagGATGATTCTGAAATAGTTGCCATGATAAAAGAATTATTGGAGACTCGTATTCGACCAGCTGTTCAAGATGACGGCGGTGACATTGAATACCGAGGATTCG
                            tcttctcctgcactgt  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgacaacatacatttcaaaatcagttttatgttatgttggcctctattttccttgtggagttgtgatactgaatcttctcctgcactgtttcccccctagGATGATTCTGAAATAGTTGCCATGATAAAAGAATTATTGGAGACTCGTATTCGACCAGCTGTTCAAGATGACGGCGGTGACATTGAATACCGAGGATTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT