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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGTTGATGAGAAGCTCCTCTATGATACCTTCAGTGCATTTGGAGTGATTGTAACTAATCCTAAGgtgacagttgacacacagcaacttttatcttcatgaatcttgcaaagttatattggtttgctgttttctgctgattatatagcagccaaactggcgaaca...

Basic information

species Zea mays
transcript GRMZM2G102639_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G102639_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os10g31900.1 (Oryza sativa), 5'ss of exon 6
GATGTTGATGAGAAGCTCCTCTATGATACCTTCAGTGCATTTGGAGTGATTGTAACTAATCCTAAGgtgacagttgacacacagcaacttttatcttcatgaatct-tgcaaagttatattggtttgct-gttttctgctgattatatagcagccaaactggcgaaca
|||||||| || |||||||| || |||||||||||||| |||||||||||||| |||||||| |||||  || |  | | | | |   |  |   ||  |     | || ||  |  | |  |    || |  ||  |    ||  ||   ||   |  |  |  |  
GATGTTGACGAAAAGCTCCTGTACGATACCTTCAGTGCGTTTGGAGTGATTGTGACTAATCCCAAGgtatcattcaagaaa-accttttactgcatttgtccgcttatgtaatctgttctgtgcacactaggctttagacacttgcatca-agattacttctcttatg

upper sequence: GRMZM2G102639_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA12G36950.1 (Glycine max), 5'ss of exon 6
GATGTTGATGAGAAGCTCCTCTATGATACCTTCAGTGCATTTGGAGTGATTGTAACTAATCCTAAGgtgacagttgacacacagca-acttttatcttcatgaatcttgca------aagttatattggtttgctgttttctgctgattatatagcagccaaactggcgaaca
||||| || ||||||||| | |||||||| ||||||||||||||||| ||||| |||||||| |||||     |    | | |  | |  | ||  ||||| |   |||        |||| | | |     |||  |  | | || | |||            ||       
GATGTAGACGAGAAGCTCTTGTATGATACTTTCAGTGCATTTGGAGTTATTGTTACTAATCCAAAGgtttttctctttaaatattatatatctaatttcatcatgtttgtgtcacttaagtaacagtatccagctagtagcagttgctaatacttttcatgctttg-------

upper sequence: GRMZM2G102639_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA09G00310.1 (Glycine max), 5'ss of exon 6
GATGTTGATGAGAAGCTCCTCTATGATACCTTCAGTGCATTTGGAGTGATTGTAACTAATCCTAAGgtgacagttgacacacagcaacttttatcttcatgaatcttgcaaagttatattggtt-tgctgttttctgctgattata-tagcagccaa-actggcgaaca
||||| |||||||||||| | ||||| || ||||||||||||||||| ||||| |||||||| |||||     |   || | | |     |||| |   | | |    ||   || |     || ||      | | | | |  ||  ||  || || |||    |   
GATGTAGATGAGAAGCTCTTGTATGACACTTTCAGTGCATTTGGAGTTATTGTTACTAATCCAAAGgtttttctcttcaaatatctttcattatatatctaatttcatcatgtttgtgccacttatgtaacagtatccagctagtagcagttgctaatacttttca---

upper sequence: GRMZM2G102639_T02 (Zea mays), 5'ss of exon 4
lower sequence: AT2G18510.1 (Arabidopsis thaliana), 5'ss of exon 6
GATGTTGATGAGAAGCTCCTCTATGATACCTTCAGTGCATTTGGAGTGATTGTAACTAATCCTAAGgtgacagttgacacacagcaacttttatcttcatgaatcttgcaaagttatattggtttgctgttttctgct-gattatatagcagc-caaactggcgaaca-------------------------------------
||||| |||||||||||| | |||||||| |||||||||||||| |||||||   |||||||||||||   | ||   |       |  ||    ||||||| ||||| |    | |||  || | ||||   |   | |||  || |  ||     |  ||    |                                      
GATGTGGATGAGAAGCTCTTGTATGATACTTTCAGTGCATTTGGTGTGATTGCTTCTAATCCTAAGgtagtattttttatttcattagattgtagttcatgattcttg-atctctttatctgtctcctgtcaccgattcgatagtaaattaggattcatcggtattccactgtggagaataaatgttagaaacttttcatttcag

upper sequence: GRMZM2G102639_T02 (Zea mays), 5'ss of exon 4
lower sequence: Vv04s0023g01470.t01 (Vitis vinifera), 5'ss of exon 6
GATGTTGATGAGAAGCTCCTCTATGATACCTTCAGTGCATTTGGAGTGATTGTAACTAATCCTAAGgtgacagttgacacacagcaacttttatcttcatgaatcttgcaaagttatattggtttgctgttttctgctgattatatagcagccaaactggcgaaca-----
||||| |||||||| || || |||||||| ||||||||||||||||| ||||| || ||||| ||||||||   |    |     |  ||   | ||     |   |  | |  ||||||  | || | | |    |      |  |    |    |   |  ||      
GATGTGGATGAGAAACTTCTGTATGATACTTTCAGTGCATTTGGAGTCATTGTCACAAATCCCAAGgtgacgcct----cttttgattttcccttttttgagaatatatacacatatattt-tctgttatatggaaccagaattggaatctctccccatccccaccctaac

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|26558877|gb|CA831112.1|CA831112
EST:     TCCTCTATGATACCTTCAGTGCATTTGGAGTGATTGTAACTAATCCTAAG                         ATAATGCGAGATCCTGAAACAGGAAATTCTAGAGGCTTTGGCTTTGTGAGC
genomic: TCCTCTATGATACCTTCAGTGCATTTGGAGTGATTGTAACTAATCCTAAGgtgacagttg ... ttgtttgaagATAATGCGAGATCCTGAAACAGGAAATTCTAGAGGCTTTGGCTTTGTGAGC
EST: gi|78090866|gb|DV519240.1|DV519240
EST:     TCCTCTATGATACCTTCAGTGCATTTGGAGTGATTGTAACTAATCCTAAG                         ATAATGCGAGATCCTGAAACAGGAAATTCTAGAGGCTTTGGCTTTGTGAGC
genomic: TCCTCTATGATACCTTCAGTGCATTTGGAGTGATTGTAACTAATCCTAAGgtgacagttg ... ttgtttgaagATAATGCGAGATCCTGAAACAGGAAATTCTAGAGGCTTTGGCTTTGTGAGC
EST: gi|91056510|gb|EB166928.1|EB166928
EST:     TCCTCTATGATACCTTCAGTGCATTTGGAGTGATTGTAACTAATCCTAAG                         ATAATGCGAGATCCTGAAACAGGAAATTCTAGAGGCTTTGGCTTTGTGAGC
genomic: TCCTCTATGATACCTTCAGTGCATTTGGAGTGATTGTAACTAATCCTAAGgtgacagttg ... ttgtttgaagATAATGCGAGATCCTGAAACAGGAAATTCTAGAGGCTTTGGCTTTGTGAGC
EST: gi|148943004|gb|EC888052.2|EC888052
EST:     TCCTCTATGATACCTTCAGTGCATTTGGAGTGATTGTAACTAATCCTAAG                         ATAATGCGAGATCCTGAAACAGGAAATTCTAGAGGCTTTGGCTTTGTGAGC
genomic: TCCTCTATGATACCTTCAGTGCATTTGGAGTGATTGTAACTAATCCTAAGgtgacagttg ... ttgtttgaagATAATGCGAGATCCTGAAACAGGAAATTCTAGAGGCTTTGGCTTTGTGAGC
EST: gi|87157489|gb|DY402278.1|DY402278
EST:     TCCTCTATGATACCTTCAGTGCATTTGGAGTGATTGTAACTAATCCTAAG                         ATAATGCGAGATCCTGAAACAGGAAATTCTAGAGGCTTTGGCTTTGTGAGC
genomic: TCCTCTATGATACCTTCAGTGCATTTGGAGTGATTGTAACTAATCCTAAGgtgacagttg ... ttgtttgaagATAATGCGAGATCCTGAAACAGGAAATTCTAGAGGCTTTGGCTTTGTGAGC
EST: gi|33467168|gb|CF244217.1|CF244217
EST:     TCCTCTATGATACCTTCAGTGCATTTGGAGTGATTGTAACTAATCCTAAG                         ATAATGCGAGATCCTGAAACAGGAAATTCTAGAGGCTTTGGCTTTGTGAGC
genomic: TCCTCTATGATACCTTCAGTGCATTTGGAGTGATTGTAACTAATCCTAAGgtgacagttg ... ttgtttgaagATAATGCGAGATCCTGAAACAGGAAATTCTAGAGGCTTTGGCTTTGTGAGC
EST: gi|148956981|gb|EC902927.2|EC902927
EST:     TCCTCTATGATACCTTCAGTGCATTTGGAGTGATTGTAACTAATCCTAAG                         ATAATGCGAGATCCTGAAACAGGAAATTCTAGAGGCTTTGGCTTTGTGAGC
genomic: TCCTCTATGATACCTTCAGTGCATTTGGAGTGATTGTAACTAATCCTAAGgtgacagttg ... ttgtttgaagATAATGCGAGATCCTGAAACAGGAAATTCTAGAGGCTTTGGCTTTGTGAGC
EST: gi|148933043|gb|EE285938.2|EE285938
EST:     TCCTCTATGATACCTTCAGTGCATTTGGAGTGATTGTAACTAATCCTAAG                         ATAATGCGAGATCCTGAAACAGGAAATTCTAGAGGCTTTGGCTTTGTGAGC
genomic: TCCTCTATGATACCTTCAGTGCATTTGGAGTGATTGTAACTAATCCTAAGgtgacagttg ... ttgtttgaagATAATGCGAGATCCTGAAACAGGAAATTCTAGAGGCTTTGGCTTTGTGAGC
EST: gi|78124664|gb|DV543048.1|DV543048
EST:     TCCTCTATGATACCTTCAGTGCATTTGGAGTGATTGTAACTAATCCTAAG                         ATAATGCGAGATCCTGAAACAGGAAATTCTAGAGGCTCTGGCTTTGTGAGC
genomic: TCCTCTATGATACCTTCAGTGCATTTGGAGTGATTGTAACTAATCCTAAGgtgacagttg ... ttgtttgaagATAATGCGAGATCCTGAAACAGGAAATTCTAGAGGCTTTGGCTTTGTGAGC
EST: gi|50322326|gb|CO517452.1|CO517452
EST:     TCCTCTATGATACCTTCAGTGCATTTGGAGTGATTGTAACTAATCCTAAG                         ATAATGCGAGATCCTGAAACAGGAAATTCTAGAGGCTTTGGCTTTGTGAGC
genomic: TCCTCTATGATACCTTCAGTGCATTTGGAGTGATTGTAACTAATCCTAAGgtgacagttg ... ttgtttgaagATAATGCGAGATCCTGAAACAGGAAATTCTAGAGGCTTTGGCTTTGTGAGC
EST: gi|89762379|gb|DY689990.1|DY689990
EST:     TCCTCTATGATACCTTCAGTGCATTTGGAGTGATTGTAACTAATCCTAAG                         ATAATGCGAGATCCTGAAACAGGAAATTCTAGAGGCTTTGGCTTTGTGAGC
genomic: TCCTCTATGATACCTTCAGTGCATTTGGAGTGATTGTAACTAATCCTAAGgtgacagttg ... ttgtttgaagATAATGCGAGATCCTGAAACAGGAAATTCTAGAGGCTTTGGCTTTGTGAGC
EST: gi|94477767|gb|EB706725.1|EB706725
EST:     TCCTCTATGATACCTTCAGTGCATTTGGAGTGATTGTAACTAATCCTAAG                         ATAATGCGAGATCCTGAAACAGGAAATTCTAGAGGCTTTGGCTTTGTGAGC
genomic: TCCTCTATGATACCTTCAGTGCATTTGGAGTGATTGTAACTAATCCTAAGgtgacagttg ... ttgtttgaagATAATGCGAGATCCTGAAACAGGAAATTCTAGAGGCTTTGGCTTTGTGAGC
EST: gi|76288123|gb|DV027691.1|DV027691
EST:     TCCTCTATGATACCTTCAGTGCATTTGGAGTGATTGTAACTAATCCTAAG                         ATAATGCGAGATCCTGAAACAGGAAATTCTAGAGGCTTTGGCTTTGTGAGC
genomic: TCCTCTATGATACCTTCAGTGCATTTGGAGTGATTGTAACTAATCCTAAGgtgacagttg ... ttgtttgaagATAATGCGAGATCCTGAAACAGGAAATTCTAGAGGCTTTGGCTTTGTGAGC
EST: gi|71425499|gb|DR806709.1|DR806709
EST:     TCCTCTATGATACCTTCAGTGCATTTGGAGTGATTGTAACTAATCCTAAG                         ATAATGCGAGATCCTGAAACAGGAAATTCTAGAGGCTTTGGCTTTGTGAGC
genomic: TCCTCTATGATACCTTCAGTGCATTTGGAGTGATTGTAACTAATCCTAAGgtgacagttg ... ttgtttgaagATAATGCGAGATCCTGAAACAGGAAATTCTAGAGGCTTTGGCTTTGTGAGC
EST: gi|31355533|gb|CD439890.1|CD439890
EST:     TCCTCTATGATACCTTCAGTGCATTTGGAGTGATTGTAACTAATCCTAAG                         ATAATGCGAGATCCTGAAACAGGAAATTCTAGAGGCTTTGGCTTTGTGAGC
genomic: TCCTCTATGATACCTTCAGTGCATTTGGAGTGATTGTAACTAATCCTAAGgtgacagttg ... ttgtttgaagATAATGCGAGATCCTGAAACAGGAAATTCTAGAGGCTTTGGCTTTGTGAGC
EST: gi|76291455|gb|DV031023.1|DV031023
EST:     TCCTCTATGATACCTTCAGTGCATTTGGAGTGATTGTAACTAATCCTAAG                         ATAATGCGAGATCCTGAAACAGGAAATTCTAGAGGCTTTGGCTTTGTGAGC
genomic: TCCTCTATGATACCTTCAGTGCATTTGGAGTGATTGTAACTAATCCTAAGgtgacagttg ... ttgtttgaagATAATGCGAGATCCTGAAACAGGAAATTCTAGAGGCTTTGGCTTTGTGAGC
EST: gi|76015742|gb|DT942912.1|DT942912
EST:     TCCTCTATGATACCTTCAGTGCATTTGGAGTGATTGTAACTAATCCTAAG                         ATAATGCGAGATCCTGAAACAGGAAATTCTAGAGGCTTTGGCTTTGTGAGC
genomic: TCCTCTATGATACCTTCAGTGCATTTGGAGTGATTGTAACTAATCCTAAGgtgacagttg ... ttgtttgaagATAATGCGAGATCCTGAAACAGGAAATTCTAGAGGCTTTGGCTTTGTGAGC
EST: gi|76290093|gb|DV029661.1|DV029661
EST:     TCCTCTATGATACCTTCAGTGCATTTGGAGTGATTGTAACTAATCCTAAG                         ATAATGCGAGATCCTGAAACAGGAAATTCTAGAGGCTTTGGCTTTGTGAGC
genomic: TCCTCTATGATACCTTCAGTGCATTTGGAGTGATTGTAACTAATCCTAAGgtgacagttg ... ttgtttgaagATAATGCGAGATCCTGAAACAGGAAATTCTAGAGGCTTTGGCTTTGTGAGC
EST: gi|166644213|gb|EG227915.1|EG227915
EST:     CTCTATGATACCTTCAGTGCATTTGGAGTGATTGTAACTAATCCTAAG                         ATAATGCGAGATCCTGAAACAGGAAATTCTAG
genomic: CTCTATGATACCTTCAGTGCATTTGGAGTGATTGTAACTAATCCTAAGgtgacagttg ... ttgtttgaagATAATGCGAGATCCTGAAACAGGAAATTCTAG
EST: gi|148961210|gb|EE011925.2|EE011925
EST:     CCTCTATGATACCTTCCGTGCATTTGGGAGTGATTGTAACTAATCCTAAG                         ATAATGCGAGATCCCTGAAACCGGAAA
genomic: CCTCTATGATACCTTCAGTGCATTTGG-AGTGATTGTAACTAATCCTAAGgtgacagttg ... ttgtttgaagATAATGCGAGATCC-TGAAACAGGAAA
EST: gi|78124734|gb|DV543118.1|DV543118
EST:     TCCTCTATGATACCTTCAGTGCATTTGGAGTGATTGTAACTAATCCTAAG                         ATAATGCGAGATCCTGAAACAGGAAATTCTAGAGGCTTTGGCTTTGTGAGC
genomic: TCCTCTATGATACCTTCAGTGCATTTGGAGTGATTGTAACTAATCCTAAGgtgacagttg ... ttgtttgaagATAATGCGAGATCCTGAAACAGGAAATTCTAGAGGCTTTGGCTTTGTGAGC
EST: gi|148938096|gb|EC882358.2|EC882358
EST:     TCCTCTATGATACCTTCAGTGCATTTGGAGTGATTGTAACTAATCCTAAG                         ATAATGCGAGATCCTGAAACAGGAAATTCTAGAGGCTTTGGCTTTGTGAGC
genomic: TCCTCTATGATACCTTCAGTGCATTTGGAGTGATTGTAACTAATCCTAAGgtgacagttg ... ttgtttgaagATAATGCGAGATCCTGAAACAGGAAATTCTAGAGGCTTTGGCTTTGTGAGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGTTGATGAGAAGCTCCTCTATGATACCTTCAGTGCATTTGGAGTGATTGTAACTAATCCTAAGgtgacagttgacacacagcaacttttatcttcatgaatcttgcaaagttatattggtttgctgttttctgctgattatatagcagccaaactggcgaaca

- - - - - - - - - - - - - - - - - - - - TTGGAG