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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgctttggattctgctggtctgaattttttgggggtatttctgtacaaattatacgctaattatgtattctgcatacctctatacagGTTGGGTATGTGACTACCATATGCTTTTCTTGTTTCTTGATCAGATGCGTCATG

Basic information

species Zea mays
transcript GRMZM2G174286_T03
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G174286_T03 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os10g39220.1 (Oryza sativa), 3'ss of exon 8
gtacgctttggattctgctggtctgaattttttgggggtatttctgtacaaattatacgctaattatgtattctgcatacctctatacagGTTGGGTATGTGACTACCATATGCTTTTCTTGTTTCTTGATCAGATGCGTCATG
|||  ||| |  ||    | ||||||| |||  | || || ||    ||||||| || | | |  || | ||    || |||   |  ||||||| ||||||||||| || |||||| ||||||||||||||||||| ||||||
gtatactt-gcttttcattagtctgaaatttg-gaggctagtttacgacaaattttatgtttaacatatgtt----attccttcctgtagGTTGGCTATGTGACTACAATCTGCTTTACTTGTTTCTTGATCAGATGTGTCATG

upper sequence: GRMZM2G174286_T03 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA05G26630.2 (Glycine max), 3'ss of exon 8
------------gtacgctttggattctgctggtctgaattt---tttgggggtatttctgtacaaattatacgctaattatgtattctgcatacctcta-tacagGTTGGGTATGTGACTACCATATGCTTTTCTTGTTTCTTGATCAGATGCGTCATG
             |   ||  | | | |    || |  || |    ||      | | ||   |    | ||| |  | |   | | |   ||   |||| | |||||||| ||||||||||||||||||||||| || ||| | |||||||| || |||
gtctgtattctgttttactaagaaatttttctgtatttatctgctcttcacctcactcctccccttgctttacccagagttaatctacctgatctttctaatgcagGTTGGCTATGTGACTACCATATGCTTTTCATGCTTCCTTATCAGATGTGTTATG

upper sequence: GRMZM2G174286_T03 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA08G09640.1 (Glycine max), 3'ss of exon 8
gtacgctttggattctgctggtctgaattttttgggggtatttc-tgtacaaattatacgctaattatgt-attctgcat-acctctata---cagGTTGGGTATGTGACTACCATATGCTTTTCTTGTTTCTTGATCAGATGCGTCATG
||  | ||||  || | ||     ||| |||||  |  ||| |  | | ||  | |  |  |    | || | ||| | | | || | ||   |||||||| ||||||||||||||||||||||| || ||| | |||||||| || |||
gtctgttttgtgttttactaa---gaaatttttctgtttatcttgtcttcacctcactccttcccaaagttaatctacctgatctttttattgcagGTTGGCTATGTGACTACCATATGCTTTTCATGCTTCCTTATCAGATGTGTTATG

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|18170253|gb|BM340093.1|BM340093
EST:     TGCAGCGTTTTCCTGTAGAATCAAAAGGAAGACGAAAGAAATTGCAGGAG                         GTTGGGTATGTGACTACCATATGCTTTTCTTGTTTCTTGATCAGATGCGTC
genomic: TGCAGCGTTTTCCTGTAGAATCAAAAGGAAGACGAAAGAAATTGCAGGAGgtacgctttg ... ctctatacagGTTGGGTATGTGACTACCATATGCTTTTCTTGTTTCTTGATCAGATGCGTC
EST: gi|93284395|gb|EB676659.1|EB676659
EST:     TGCAGCGTTTTCCTGTAGAATCAAAAGGAAGACGAAAGAAATTGCAGGAG                         GTTGGGTATGTGACTACCATATGCTTTTCTTGTTTCTTGATCAGATGCGTC
genomic: TGCAGCGTTTTCCTGTAGAATCAAAAGGAAGACGAAAGAAATTGCAGGAGgtacgctttg ... ctctatacagGTTGGGTATGTGACTACCATATGCTTTTCTTGTTTCTTGATCAGATGCGTC
EST: gi|149112907|gb|EE295706.2|EE295706
EST:     TGCAGCGTTTTCCTGTAGAATCAAAAGGAAGACGAAAGAAATTGCAGGAG                         GTTGGGTATGTGACTACCATATGCTTTTCTTGTTTCTTGATCAGATGCGTC
genomic: TGCAGCGTTTTCCTGTAGAATCAAAAGGAAGACGAAAGAAATTGCAGGAGgtacgctttg ... ctctatacagGTTGGGTATGTGACTACCATATGCTTTTCTTGTTTCTTGATCAGATGCGTC
EST: gi|88754539|gb|DY538680.1|DY538680
EST:     TGCAGCGTTTTCCTGTAGAATCAAAAGGAAGACGAAAGAAATTGCAGGAG                         GTGGGGTATGTGACTACCATATGCTTTTCTTGTTTCTTGATCAGATGCGTC
genomic: TGCAGCGTTTTCCTGTAGAATCAAAAGGAAGACGAAAGAAATTGCAGGAGgtacgctttg ... ctctatacagGTTGGGTATGTGACTACCATATGCTTTTCTTGTTTCTTGATCAGATGCGTC
EST: gi|5922262|gb|AW055551.1|AW055551
EST:     TGCAGCGTTTTCCTGTAGAATCAAAAGGAAGACGAAAGAAATTGCAGGAG                         GTTGGGTATGTGACTACCATATGCTTTTCTTGTTTCTTGATCAGATGCGTC
genomic: TGCAGCGTTTTCCTGTAGAATCAAAAGGAAGACGAAAGAAATTGCAGGAGgtacgctttg ... ctctatacagGTTGGGTATGTGACTACCATATGCTTTTCTTGTTTCTTGATCAGATGCGTC
EST: gi|24765679|gb|CA400838.1|CA400838
EST:     TGCAGCGTTTTCCTGTAGAATCAAAAGGAAGACGAAAGAAATTGCAGGAG                         GTTGGGTATGTGACTACCATATGCTTTTCTTGTTTCTTGATCAGATGCGTC
genomic: TGCAGCGTTTTCCTGTAGAATCAAAAGGAAGACGAAAGAAATTGCAGGAGgtacgctttg ... ctctatacagGTTGGGTATGTGACTACCATATGCTTTTCTTGTTTCTTGATCAGATGCGTC
EST: gi|71300276|gb|DR786208.1|DR786208
EST:     TGCAGCGTTTTCCTGTAGAATCAAAAGGAAGACGAAAGAAATTGCAGGAG                         GTTGGGTATGTGACTACCATATGCTTTTCTTGTTTCTTGATCAGATGCGTC
genomic: TGCAGCGTTTTCCTGTAGAATCAAAAGGAAGACGAAAGAAATTGCAGGAGgtacgctttg ... ctctatacagGTTGGGTATGTGACTACCATATGCTTTTCTTGTTTCTTGATCAGATGCGTC
EST: gi|28985354|gb|CB350599.1|CB350599
EST:     TGCAGCGTTTTCCTGTAGAATCAAAAGGAAGACGAAAGAAATTGCAGGAG                         GTTGGGTATGTGACTACCATATGCTTTTCTTGTTTCTTGATCAGATGCGTC
genomic: TGCAGCGTTTTCCTGTAGAATCAAAAGGAAGACGAAAGAAATTGCAGGAGgtacgctttg ... ctctatacagGTTGGGTATGTGACTACCATATGCTTTTCTTGTTTCTTGATCAGATGCGTC
EST: gi|88749638|gb|DY533779.1|DY533779
EST:     TGCAGCGTTTTCCTGTAGAATCAAAAGGAAGACGAAAGAAATTGCAGGAG                         GTGGGGTATGTGACTACCATATGC-TTTCTTTGTTTCTTGATCAGATGCGT
genomic: TGCAGCGTTTTCCTGTAGAATCAAAAGGAAGACGAAAGAAATTGCAGGAGgtacgctttg ... ctctatacagGTTGGGTATGTGACTACCATATGCTTTTC-TTGTTTCTTGATCAGATGCGT
EST: gi|78106688|gb|DV525106.1|DV525106
EST:     TGCAGCGTTTTCCTGTAGAATCAAAAGGAAGACGAAAGAAATTGCAGGAG                         GTTGGGTATGTGACTACCATATGCTTTTCTTGTTTCTTGATCAGATGCGTC
genomic: TGCAGCGTTTTCCTGTAGAATCAAAAGGAAGACGAAAGAAATTGCAGGAGgtacgctttg ... ctctatacagGTTGGGTATGTGACTACCATATGCTTTTCTTGTTTCTTGATCAGATGCGTC
EST: gi|5739982|gb|AI947672.1|AI947672
EST:     CTGTAGAATCAAAAGGAAGACGAAAGAAATTGCAGGAG                         GTTGGGTATGTGACTACCATATGCTTTTCTTGTTTCTTGATCAGATGCGTC
genomic: CTGTAGAATCAAAAGGAAGACGAAAGAAATTGCAGGAGgtacgctttg ... ctctatacagGTTGGGTATGTGACTACCATATGCTTTTCTTGTTTCTTGATCAGATGCGTC
EST: gi|6095420|gb|AW120087.1|AW120087
EST:     TGCAGCGTTTTCCTGTAGAATCAAAAGGAAGACGAAAGAAATTGCAGGAG                         GTTGGGTATGTGACTACCATATGCTTTTCTTGTTTCTTGATCAGATGCGTC
genomic: TGCAGCGTTTTCCTGTAGAATCAAAAGGAAGACGAAAGAAATTGCAGGAGgtacgctttg ... ctctatacagGTTGGGTATGTGACTACCATATGCTTTTCTTGTTTCTTGATCAGATGCGTC
EST: gi|45846980|gb|CN070923.1|CN070923
EST:     TGCAGCGTTTTCCTGTAGAATCCAAAGGAAGACGAAAGAAATTGCAGGAG                         GTTGGGTATGTGACTACCATATGCTTTTCTTGTTTCTTGATCAGATGCGTC
genomic: TGCAGCGTTTTCCTGTAGAATCAAAAGGAAGACGAAAGAAATTGCAGGAGgtacgctttg ... ctctatacagGTTGGGTATGTGACTACCATATGCTTTTCTTGTTTCTTGATCAGATGCGTC
EST: gi|101383586|gb|EB813848.1|EB813848
EST:     TGCAGCGTTTTCCTGTAGAATCAAAAGGAAGACGAAAGAAATTGCAGGAG                         GTTGGGTATGTGACTACCATATGCTTTTCTTTTTTCTTGATCAGATGCGTC
genomic: TGCAGCGTTTTCCTGTAGAATCAAAAGGAAGACGAAAGAAATTGCAGGAGgtacgctttg ... ctctatacagGTTGGGTATGTGACTACCATATGCTTTTCTTGTTTCTTGATCAGATGCGTC
EST: gi|18174253|gb|BM349641.1|BM349641
EST:     TGCAGCGTTTTCCTGTAGAATCAAAAGGAAGACGAAAGAAATTGCAGGAG                         GTTGGGTATGTGACTACCATATGCTTTTCTTGTTTCTTGATCAGATGCGTC
genomic: TGCAGCGTTTTCCTGTAGAATCAAAAGGAAGACGAAAGAAATTGCAGGAGgtacgctttg ... ctctatacagGTTGGGTATGTGACTACCATATGCTTTTCTTGTTTCTTGATCAGATGCGTC
EST: gi|67017793|gb|CO446542.1|CO446542
EST:     GCAGCGTTTTCCTGTAGAATCAAAAGGAAGACGAAAGAAATTGCANGGAG                         -TTGGGTATGTGACTACCATATGCTTTTCTTGTTTCTTGATCAGATGCGT
genomic: GCAGCGTTTTCCTGTAGAATCAAAAGGAAGACGAAAGAAATTGCA-GGAGgtacgctttg ... ctctatacagGTTGGGTATGTGACTACCATATGCTTTTCTTGTTTCTTGATCAGATGCGT
EST: gi|67020535|gb|CO449284.1|CO449284
EST:     TGCAGCGTTTTCCTGTAGAATCAAAAGGAAGACGAAAGAAATTGCAGGAG                         GTTGGGTATGTGACTACCATATGCTTTTCTTGTTTCTTGATCAGATGCGTC
genomic: TGCAGCGTTTTCCTGTAGAATCAAAAGGAAGACGAAAGAAATTGCAGGAGgtacgctttg ... ctctatacagGTTGGGTATGTGACTACCATATGCTTTTCTTGTTTCTTGATCAGATGCGTC
EST: gi|211179297|gb|FL465342.1|FL465342
EST:     TGCAGCGTTTTCCTGTAGAATCAAAAGGAAGACGAAAGAAATTGCAGGAG                         GTTGGGTATGTGACTACCATATGCTTTTCTTGTTTCTTGATCAGATGCGTC
genomic: TGCAGCGTTTTCCTGTAGAATCAAAAGGAAGACGAAAGAAATTGCAGGAGgtacgctttg ... ctctatacagGTTGGGTATGTGACTACCATATGCTTTTCTTGTTTCTTGATCAGATGCGTC
EST: gi|37383767|gb|CF628916.1|CF628916
EST:     TGCAGCGTTTTCCTGTAGAATCAAAAGGAAGACGAAAGAAATTGCAGGAG                         GTTGGGTATGTGACTACCATATGCTTTTCTTGTTTCTTGATCAGATGCGTC
genomic: TGCAGCGTTTTCCTGTAGAATCAAAAGGAAGACGAAAGAAATTGCAGGAGgtacgctttg ... ctctatacagGTTGGGTATGTGACTACCATATGCTTTTCTTGTTTCTTGATCAGATGCGTC
EST: gi|211215684|gb|FL434860.1|FL434860
EST:     TGCAGCGTTTTCCTGTAGAATCAAAAGGAAGACGAAAGAAATTGCAGGAG                         GTTGGGTATGTGACTACCATATGCTTTTCTTGTTTCTTGATCAGATGCGTC
genomic: TGCAGCGTTTTCCTGTAGAATCAAAAGGAAGACGAAAGAAATTGCAGGAGgtacgctttg ... ctctatacagGTTGGGTATGTGACTACCATATGCTTTTCTTGTTTCTTGATCAGATGCGTC
EST: gi|31364203|gb|CD448558.1|CD448558
EST:     TGCAGCGTTTTCCTGTAGAATCAAAAGGAAGACGAAAGAAATTGCAGGAG                         GTTGGGTATGTGACTACCATATGCTTTTCTTGTTTCTTGATCACATGCGTC
genomic: TGCAGCGTTTTCCTGTAGAATCAAAAGGAAGACGAAAGAAATTGCAGGAGgtacgctttg ... ctctatacagGTTGGGTATGTGACTACCATATGCTTTTCTTGTTTCTTGATCAGATGCGTC
EST: gi|5757367|gb|AI964654.1|AI964654
EST:     TGCAGCGTTTTCCTGTAGAATCAAAAGGAAGACGAAAGAAATTGCAGGAG                         GTTGGGTATGTGACTACCATATGCTTTTCTTGTTTCTTGATCAGATGCGTC
genomic: TGCAGCGTTTTCCTGTAGAATCAAAAGGAAGACGAAAGAAATTGCAGGAGgtacgctttg ... ctctatacagGTTGGGTATGTGACTACCATATGCTTTTCTTGTTTCTTGATCAGATGCGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gggtatttctgtacaaattatacgctaattatgtattctgcatacctctatacagGTTGGGTATGTGACTACCATATGCTTTTCTTGTTTCTTGATCAGATGCGTCATG
                      cgctaat  putative branch site (score: 3)
                                          tacctct  putative PPT
                         taattatgtattct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgctttggattctgctggtctgaattttttgggggtatttctgtacaaattatacgctaattatgtattctgcatacctctatacagGTTGGGTATGTGACTACCATATGCTTTTCTTGTTTCTTGATCAGATGCGTCATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG