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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcaaccatacccattgtttggattttgttattcatataaactagtaccatagatagatacagaagttggccctcactaacgctggtacccccccaccccaccccacccatcattttggcagGATTTGCTGGCTATTTTGACTCTGTTCTTTATAAGGATGTTCATCTTGGAATCGAGCCAAACACCGCTACACCAAACATGTTCAGCTG

Basic information

species Zea mays
transcript GRMZM2G011456_T02
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G011456_T03 (Zea mays), 3'ss of exon 19
lower sequence: LOC_Os02g04660.2 (Oryza sativa), 3'ss of exon 14
gtatgcaaccatacccattgtttggattttgttattcatataaactagtaccatagatagatacagaagttggccctcactaacgctggtacccccccaccccaccc-cacccatcattttggcagGATTTGCTGGCTATTTTGACTCTGTTCTTTATAAGGATGTTCATCTTGGAATCGAGCCAAACACCGCTACACCAAACATGTTCAGCTG
                  | | | | | |||   |  |  |    |  |||  |     | ||||         | ||  ||    ||| |       || | || |   |||||||||||||||||||||||||| ||||||||  | ||  | ||||| ||||||||||||||||| || |||||||| ||||||||||||||||| |||||
-----------------gtatgtagctattgagttatacttgtgattatactttgctatgttacaaggtagaaacatctatatatttggcagaatttgactctactcattcccatcattttggcagGATTTGCTGGATATTTTGATGCCGTATTGTATAAAGATGTTCATCTTGGAATTGAACCAAACACGGCTACACCAAACATGTTTAGCTG

upper sequence: GRMZM2G011456_T03 (Zea mays), 3'ss of exon 19
lower sequence: AT4G31120.1 (Arabidopsis thaliana), 3'ss of exon 20
gtatgcaaccatacccattgtttggattttgttattcatataaactagtaccatagatagatacagaagttggccctcactaacgctggtacccccccaccccaccccacccatcattttggcagGATTTGCTGGCTATTTTGACTCTGTTCTTTATAAGGATGTTCATCTTGGAATCGAGCCAAACACCGCTACACCAAACATGTTCAGCTG
                        |    || | ||  | ||  |   |    |   |  ||    |  ||    |||  |  |  |  |    |   | |  |  | ||     ||  |   |||||| |||||||||||||| || || |||||||| |||||||||||||| |||||||| |  || || ||||||||||||||||||||
------------------------gtacctgct-tttttctagcccttttttgtttgttaatgtcaattttacatctccatttccgtaat----ctgaaactgaatctact-gcgatcataatagGATTCGCTGGCTATTTTGATTCCGTCCTTTATAAAGATGTTCATCTTGGGATCGAGCCTACAACAGCAACACCAAACATGTTCAGCTG

upper sequence: GRMZM2G011456_T03 (Zea mays), 3'ss of exon 19
lower sequence: AT4G31120.2 (Arabidopsis thaliana), 3'ss of exon 20
gtatgcaaccatacccattgtttggattttgttattcatataaactagtaccatagatagatacagaagttggccctcactaacgctggtacccccccaccccaccccacccatcattttggcagGATTTGCTGGCTATTTTGACTCTGTTCTTTATAAGGATGTTCATCTTGGAATCGAGCCAAACACCGCTACACCAAACATGTTCAGCTG------------
                        |    || | ||  | ||  |   |    |   |  ||    |  ||    |||  |  |  |  |    |   | |  |  | ||     ||  |   |||||| |||||||||||||| || || |||||||| |||||||||||||| |||||||| |  || || ||||||||||||||||||||            
------------------------gtacctgct-tttttctagcccttttttgtttgttaatgtcaattttacatctccatttccgtaat----ctgaaactgaatctact-gcgatcataatagGATTCGCTGGCTATTTTGATTCCGTCCTTTATAAAGATGTTCATCTTGGGATCGAGCCTACAACAGCAACACCAAACATGTTCAGCTGGTAATGGATTAA

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|20803221|gb|BQ294271.1|BQ294271
EST:     CAAGTTGCAATTTGAAATGCTGCCAGACATGGGTTCATGCCTTGTGCACG                         GATTTGCTGGCTATTTTGACTCTGTTCTTTATAAGGATGTTCATCTTGGAA
genomic: CAAGTTGCAATTTGAAATGCTGCCAGACATGGGTTCATGCCTTGTGCACGgtatgcaacc ... attttggcagGATTTGCTGGCTATTTTGACTCTGTTCTTTATAAGGATGTTCATCTTGGAA
EST: gi|40336264|gb|CK370334.1|CK370334
EST:     TGGGTCCATGCCTTGTGCACG                         GATTTGCTGGCTATTTTGACTCTGTTCTTTATAAGGATGTTCATCTTGGAA
genomic: TGGGTTCATGCCTTGTGCACGgtatgcaacc ... attttggcagGATTTGCTGGCTATTTTGACTCTGTTCTTTATAAGGATGTTCATCTTGGAA
EST: gi|5005784|gb|AI711846.1|AI711846
EST:     CAGACATGGGTTCATGCCTTGTGCACG                         GATTTGCTGGCTATTTTGACTCTGTTCTTTATAAGGATGTTCATCTTGGAA
genomic: CAGACATGGGTTCATGCCTTGTGCACGgtatgcaacc ... attttggcagGATTTGCTGGCTATTTTGACTCTGTTCTTTATAAGGATGTTCATCTTGGAA
EST: gi|60345333|gb|DN212306.1|DN212306
EST:     CAAGTTGCAATTTGAAATGCTGCCAGACATGGGTTCATGCCTTGTGCACG                         GATTTGCTGGCTATTTTGACTCTGTTCTTTATAAGGATGTTCATCTTGGAA
genomic: CAAGTTGCAATTTGAAATGCTGCCAGACATGGGTTCATGCCTTGTGCACGgtatgcaacc ... attttggcagGATTTGCTGGCTATTTTGACTCTGTTCTTTATAAGGATGTTCATCTTGGAA
EST: gi|21843268|gb|BQ703849.1|BQ703849
EST:     CAAGTTGCAATTTGAAATGCTGCCAGACATGGGTTCATGCCTTGTGCACG                         GATTTGCTGGCTATTTTGACTCTGNTCTTTATAAGGATGTTCATCTTGGAA
genomic: CAAGTTGCAATTTGAAATGCTGCCAGACATGGGTTCATGCCTTGTGCACGgtatgcaacc ... attttggcagGATTTGCTGGCTATTTTGACTCTGTTCTTTATAAGGATGTTCATCTTGGAA
EST: gi|32944743|gb|CF049562.1|CF049562
EST:     CAAGTTACAATTTGAAATGCTGCCAGACATGGGTTCATGCCATGTGCACG                         GATTTGCTGGCTATTTTGACTCTGTTCTTTATAAGGATGTTCATCTTGGAA
genomic: CAAGTTGCAATTTGAAATGCTGCCAGACATGGGTTCATGCCTTGTGCACGgtatgcaacc ... attttggcagGATTTGCTGGCTATTTTGACTCTGTTCTTTATAAGGATGTTCATCTTGGAA
EST: gi|211483571|gb|FL225316.1|FL225316
EST:     CAAGTTGCAATTTGAAATGCTGCCAGACATGGGTTCATGCCTTGTGCACG                         GATTTGCTGGCTATTTTGACTCTGTTCTTTATAAGGATGTTCATCTTGGAA
genomic: CAAGTTGCAATTTGAAATGCTGCCAGACATGGGTTCATGCCTTGTGCACGgtatgcaacc ... attttggcagGATTTGCTGGCTATTTTGACTCTGTTCTTTATAAGGATGTTCATCTTGGAA
EST: gi|71300981|gb|DR786519.1|DR786519
EST:     CAAGTTGCAATTTGAAATGCTGCCAGACATGGGTTCATGCCTTGTGCACG                         GATTTGCTGGCTATTTTGACTCTGTTCTTTATAAGGATGTTCATCTTGGAA
genomic: CAAGTTGCAATTTGAAATGCTGCCAGACATGGGTTCATGCCTTGTGCACGgtatgcaacc ... attttggcagGATTTGCTGGCTATTTTGACTCTGTTCTTTATAAGGATGTTCATCTTGGAA
EST: gi|211483574|gb|FL225319.1|FL225319
EST:     CAAGTTGCAATTTGAAATGCTGCCAGACATGGGTTCATGCCTTGTGCACG                         GATTTGCTGGCTATTTTGACTCTGTTCTTTATAAGGATGTTCATCTTGGAA
genomic: CAAGTTGCAATTTGAAATGCTGCCAGACATGGGTTCATGCCTTGTGCACGgtatgcaacc ... attttggcagGATTTGCTGGCTATTTTGACTCTGTTCTTTATAAGGATGTTCATCTTGGAA
EST: gi|31558383|gb|CD527595.1|CD527595
EST:     TGCCAGACATGGGTTCATGCCTTGTGCACG                         GATTTGCTGGCTATTTTGACTCTGTTCTTTATAAGGATGTTCATCTTGGAA
genomic: TGCCAGACATGGGTTCATGCCTTGTGCACGgtatgcaacc ... attttggcagGATTTGCTGGCTATTTTGACTCTGTTCTTTATAAGGATGTTCATCTTGGAA
EST: gi|37392891|gb|CF633698.1|CF633698
EST:     TGGGTTCATGCCTTGTGCACG                         GATTTGCTGGCTATTTTGACTCTGTTCTTTATAAGGATGTTCATCTTGGAA
genomic: TGGGTTCATGCCTTGTGCACGgtatgcaacc ... attttggcagGATTTGCTGGCTATTTTGACTCTGTTCTTTATAAGGATGTTCATCTTGGAA
EST: gi|26456816|gb|CA828399.1|CA828399
EST:     CAAGTTGCAATTTGAAATGCTGCCAGACATGGGTTCATGCCTTGTGCACG                         GATTTGCTGGCTATTTTGACTCTGGTCTTTATAAGGATGGTCATCTTGGAA
genomic: CAAGTTGCAATTTGAAATGCTGCCAGACATGGGTTCATGCCTTGTGCACGgtatgcaacc ... attttggcagGATTTGCTGGCTATTTTGACTCTGTTCTTTATAAGGATGTTCATCTTGGAA
EST: gi|87155574|gb|DY400363.1|DY400363
EST:     CAAGTTGCAATTTGAAATGCTGCCAGACATGGGTTCATGCCTTGTGCACG                         GATTTGCTGGCTATTTTGACTCTGTTCTTTATAAGGATGTTCATCTTGGAA
genomic: CAAGTTGCAATTTGAAATGCTGCCAGACATGGGTTCATGCCTTGTGCACGgtatgcaacc ... attttggcagGATTTGCTGGCTATTTTGACTCTGTTCTTTATAAGGATGTTCATCTTGGAA
EST: gi|91876144|gb|EB406101.1|EB406101
EST:     CAAGTTGCAATTTGAAATGCTGCCAGACATGGGTTCATGCCTTGTGCACG                         GATTTGCTGGCTATTTTGACTCTGTTCTTTATAAGGATGTTCATCTTGGAA
genomic: CAAGTTGCAATTTGAAATGCTGCCAGACATGGGTTCATGCCTTGTGCACGgtatgcaacc ... attttggcagGATTTGCTGGCTATTTTGACTCTGTTCTTTATAAGGATGTTCATCTTGGAA
EST: gi|31558384|gb|CD527596.1|CD527596
EST:     CAAGTTGCAATTTGAAATGCTGCCAGACATGGGTTCATGCCTTGTGCACG                         GATTTGCTGGCTATTTTGACTCTGTTCTTTATAAGGATGTTCATCTTGGAA
genomic: CAAGTTGCAATTTGAAATGCTGCCAGACATGGGTTCATGCCTTGTGCACGgtatgcaacc ... attttggcagGATTTGCTGGCTATTTTGACTCTGTTCTTTATAAGGATGTTCATCTTGGAA
EST: gi|33468107|gb|CF245156.1|CF245156
EST:     TGCAATTTGAAATGCTGCCAGACATGGGTTCATGCCTTGTGCACG                         GATTTGCTGGCTATTTTGACTCTGTTCTTTATAAGGATGTTCATCTTGGAA
genomic: TGCAATTTGAAATGCTGCCAGACATGGGTTCATGCCTTGTGCACGgtatgcaacc ... attttggcagGATTTGCTGGCTATTTTGACTCTGTTCTTTATAAGGATGTTCATCTTGGAA
EST: gi|37398225|gb|CF636423.1|CF636423
EST:     CAAGTTGCAATTTGAAATGCTGCCAGACATGGGTTCATGCCTTGTGCACG                         GATTTGCTGGCTATTTTGACTCTGTTCTTTATAAGGATGTTCATCTTGGAA
genomic: CAAGTTGCAATTTGAAATGCTGCCAGACATGGGTTCATGCCTTGTGCACGgtatgcaacc ... attttggcagGATTTGCTGGCTATTTTGACTCTGTTCTTTATAAGGATGTTCATCTTGGAA
EST: gi|26557923|gb|CA830158.1|CA830158
EST:     CAAGTTGCAATTTGAAATGCTGCCAGACATGGGTTCATGCCTTGTGCACG                         GATTTGCTGGCTATTTTGACTCTGTTCTTTATAAGGATGTTCATCTTGGAA
genomic: CAAGTTGCAATTTGAAATGCTGCCAGACATGGGTTCATGCCTTGTGCACGgtatgcaacc ... attttggcagGATTTGCTGGCTATTTTGACTCTGTTCTTTATAAGGATGTTCATCTTGGAA
EST: gi|60397916|gb|DN230732.1|DN230732
EST:     CAAGTTGCAATTTGAAATGCTGCCAGACATGGGTTCATGCCTTGTGCACG                         GAATTGCTGGCTATTTTGACT
genomic: CAAGTTGCAATTTGAAATGCTGCCAGACATGGGTTCATGCCTTGTGCACGgtatgcaacc ... attttggcagGATTTGCTGGCTATTTTGACT
EST: gi|71311076|gb|DR791852.1|DR791852
EST:     CAAGTTGCAATTTGAAATGCTGCCAGACATGGGTTCATGCCTTGTGCACG                         GATTTGCTGGCTATTTTGACTCTGTTCTTTATAAGGATGTTCATCTTGGAA
genomic: CAAGTTGCAATTTGAAATGCTGCCAGACATGGGTTCATGCCTTGTGCACGgtatgcaacc ... attttggcagGATTTGCTGGCTATTTTGACTCTGTTCTTTATAAGGATGTTCATCTTGGAA
EST: gi|91048537|gb|EB158955.1|EB158955
EST:     CAAGTTGCAATTTGAAATGCTGCCAGACATGGGTTCATGCCTTGTGCACG                         GATTTGCTGGCTATTTTGACTCTGTTCTTTATAAGGATGTTCATCTTGGAA
genomic: CAAGTTGCAATTTGAAATGCTGCCAGACATGGGTTCATGCCTTGTGCACGgtatgcaacc ... attttggcagGATTTGCTGGCTATTTTGACTCTGTTCTTTATAAGGATGTTCATCTTGGAA
EST: gi|211352737|gb|FL476231.1|FL476231
EST:     CAAGTTGCAATTTGAAATGCTGCCAGACATGGGTTCATGCCTTGTGCACG                         GATTTGCTGGCTATTTTGACTCTGTTCTTTATAAGGATGTTCATCTTGGAA
genomic: CAAGTTGCAATTTGAAATGCTGCCAGACATGGGTTCATGCCTTGTGCACGgtatgcaacc ... attttggcagGATTTGCTGGCTATTTTGACTCTGTTCTTTATAAGGATGTTCATCTTGGAA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 92

ACTTTCACCCATCCAAATTTCTCACCAAATGCCAGCAACCAAAGGTACACCAAGTTGCAATTTGAAATGCTGCCAGACATGGGTTCATGCCTTGTGCACGgtatgcaacc ... attttggcagGATTTGCTGGCTATTTTGACTCTGTTCTTTATAAGGATGTTCATCTTGGAATCGAGCCAAACACCGCTACACCAAACATGTTCAGCTG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 55

ACTTTCACCCATCCAAATTTCTCACCAAATGCCAGCAACCAAAGGTACACCAAGTTGCAATTTGAAATGCTGCCAGACATGGGTTCATGCCTTGTGCACGgtatgcaacc ... attttggcagGATTTGCTGGCTATTTTGACTCTGTTCTTTATAAGGATGTTCATCTTGGAATCGAGCCAAACACCGCTACACCAAACATGTTCAGCTG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 49

ACTTTCACCCATCCAAATTTCTCACCAAATGCCAGCAACCAAAGGTACACCAAGTTGCAATTTGAAATGCTGCCAGACATGGGTTCATGCCTTGTGCACGgtatgcaacc ... attttggcagGATTTGCTGGCTATTTTGACTCTGTTCTTTATAAGGATGTTCATCTTGGAATCGAGCCAAACACCGCTACACCAAACATGTTCAGCTG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 40

ACTTTCACCCATCCAAATTTCTCACCAAATGCCAGCAACCAAAGGTACACCAAGTTGCAATTTGAAATGCTGCCAGACATGGGTTCATGCCTTGTGCACGgtatgcaacc ... attttggcagGATTTGCTGGCTATTTTGACTCTGTTCTTTATAAGGATGTTCATCTTGGAATCGAGCCAAACACCGCTACACCAAACATGTTCAGCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggccctcactaacgctggtacccccccaccccaccccacccatcattttggcagGATTTGCTGGCTATTTTGACTCTGTTCTTTATAAGGATGTTCATCTTGGAATCGAGCCAAACACCGCTACACCAAACATGTTCAGCTG
       cactaac  putative branch site (score: 40)
                                           tcatttt  putative PPT
                                          atcatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcaaccatacccattgtttggattttgttattcatataaactagtaccatagatagatacagaagttggccctcactaacgctggtacccccccaccccaccccacccatcattttggcagGATTTGCTGGCTATTTTGACTCTGTTCTTTATAAGGATGTTCATCTTGGAATCGAGCCAAACACCGCTACACCAAACATGTTCAGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG