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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcaagctgcacactttaactttactgagaagacatttgcattctaatacttcgtcttgctgtatgctgtttatctaataataaggtgcgtttttgacagGTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAG

Basic information

species Zea mays
transcript GRMZM2G135132_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G135132_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g41590.1 (Oryza sativa), 3'ss of exon 2
-------------------------------------------------tgcaagctgcacactttaactttactgagaag-acatttgcattctaatacttcgtcttgctgtatgctgtttatctaataataaggtgcgttt--ttgacagGTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAG
                                                 |||| | ||           |  | |   ||  | | | | |   |  || ||     | || ||  ||| | |  |||||||    |   |||  ||  |||||||||||||||||| |||||  ||||||||||||||||||| ||||
gtaagtatttatattagtatcacccttaaatattctattgtcattattatgcatg-tgtttgagccgcttccatttttaattatactggtagagttgtagtttcctcttctttaaactgct-acttaataatccactctttttactttgcagGTATGATGAGTTGGCCAGCAAGGGCAATGTTGAATATATTGCCGGAG
















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|211433554|gb|FL254730.1|FL254730
EST:     GACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCCTAT                         GTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAG
genomic: GACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCCTATgtaagtataa ... tttttgacagGTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAG
EST: gi|211433558|gb|FL254734.1|FL254734
EST:     GACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCCTAT                         GTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAG
genomic: GACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCCTATgtaagtataa ... tttttgacagGTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAG
EST: gi|211436159|gb|FL254742.1|FL254742
EST:     GACATCAAGCTGAA-AATGCCATTCTCGCTGAGGAGAAGCACTTGCCTAT                         GTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAG
genomic: GACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCCTATgtaagtataa ... tttttgacagGTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAG
EST: gi|211430963|gb|FL254725.1|FL254725
EST:     GACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCCTAT                         GTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAG
genomic: GACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCCTATgtaagtataa ... tttttgacagGTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAG
EST: gi|87155643|gb|DY400432.1|DY400432
EST:     GACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTTGCCTAT                         GTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAG
genomic: GACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCCTATgtaagtataa ... tttttgacagGTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAG
EST: gi|211430959|gb|FL254721.1|FL254721
EST:     GACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCCTAT                         GTATGATGAGTTGGCTAGCAACAGCAATGNTGAATATATTGCTGGAG
genomic: GACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCCTATgtaagtataa ... tttttgacagGTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAG
EST: gi|211535005|gb|FL000874.1|FL000874
EST:     GACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTTGCCTAT                         GTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAG
genomic: GACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCCTATgtaagtataa ... tttttgacagGTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAG
EST: gi|211430960|gb|FL254722.1|FL254722
EST:     GACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCCTAT                         GTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAG
genomic: GACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCCTATgtaagtataa ... tttttgacagGTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAG
EST: gi|211433562|gb|FL254738.1|FL254738
EST:     GACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCCTAT                         GTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAG
genomic: GACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCCTATgtaagtataa ... tttttgacagGTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAG
EST: gi|211430956|gb|FL254718.1|FL254718
EST:     GACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCCTAT                         GTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAG
genomic: GACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCCTATgtaagtataa ... tttttgacagGTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAG
EST: gi|211433550|gb|FL254726.1|FL254726
EST:     GACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCCTAT                         GTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAG
genomic: GACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCCTATgtaagtataa ... tttttgacagGTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAG
EST: gi|211430955|gb|FL254717.1|FL254717
EST:     GACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCCTAT                         GTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAG
genomic: GACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCCTATgtaagtataa ... tttttgacagGTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAG
EST: gi|26559465|gb|CA831700.1|CA831700
EST:     GACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTTGCCTAT                         GTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAG
genomic: GACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCCTATgtaagtataa ... tttttgacagGTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAG
EST: gi|32916313|gb|CF021125.1|CF021125
EST:     GACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTTGCCTAT                         GTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAG
genomic: GACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCCTATgtaagtataa ... tttttgacagGTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAG
EST: gi|211433561|gb|FL254737.1|FL254737
EST:     GACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCCTAT                         GTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAG
genomic: GACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCCTATgtaagtataa ... tttttgacagGTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAG
EST: gi|211430957|gb|FL254719.1|FL254719
EST:     GACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCCTAT                         GTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAG
genomic: GACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCCTATgtaagtataa ... tttttgacagGTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAG
EST: gi|22546548|gb|BU098859.1|BU098859
EST:     GACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTTGCCTAT                         GTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAG
genomic: GACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCCTATgtaagtataa ... tttttgacagGTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAG
EST: gi|211433560|gb|FL254736.1|FL254736
EST:     GACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCCTAT                         GTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAG
genomic: GACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCCTATgtaagtataa ... tttttgacagGTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAG
EST: gi|211430954|gb|FL254716.1|FL254716
EST:     GACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCCTAT                         GTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAG
genomic: GACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCCTATgtaagtataa ... tttttgacagGTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAG
EST: gi|211433557|gb|FL254733.1|FL254733
EST:     GACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCCTAT                         GTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAG
genomic: GACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCCTATgtaagtataa ... tttttgacagGTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAG
EST: gi|31353988|gb|CD438345.1|CD438345
EST:     GACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTTGCCTAT                         GTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAG
genomic: GACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCCTATgtaagtataa ... tttttgacagGTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAG
EST: gi|211538002|gb|FL000876.1|FL000876
EST:     GACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTTGCCTAT                         GTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAG
genomic: GACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCCTATgtaagtataa ... tttttgacagGTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAG

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), 46 (downstream exon)
Score: 138

GTATGACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCCTATgtaagtataa ... tttttgacagGTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 162

GTATGACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCCTATgtaagtataa ... tttttgacagGTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 235

GTATGACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCCTATgtaagtataa ... tttttgacagGTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 237

GTATGACATCAAGCTGAACAATGCCATTCTCGCTGAGGAGAAGCACTCGCCTATgtaagtataa ... tttttgacagGTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatacttcgtcttgctgtatgctgtttatctaataataaggtgcgtttttgacagGTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAG
                                           cgttttt  CT-rich tract
                      tgtttatctaataata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcaagctgcacactttaactttactgagaagacatttgcattctaatacttcgtcttgctgtatgctgtttatctaataataaggtgcgtttttgacagGTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
tgcaagc
- - - - gcacact
- - - - - - - - - - tttactg
- - - - - - - - - - - - - - - - - - -tgcattc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtatgc