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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcttacagataattagagatgactccttttatggactagttgcaatgcctgcttttggactatttgcatatatgtgattgtttgttgaattattttgcagCCCTTGAAAGGTTTGAAGAGGGTCCTCCATTCACACTGCAAAGGCTTTGTGAG

Basic information

species Zea mays
transcript GRMZM2G033029_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G033029_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os06g19650.1 (Oryza sativa), 3'ss of exon 5
tcttacagataattagagatgactccttttatggactagttgcaatgcctgcttttggactatttgcatatatgtgattgtttgttgaattat-----tttgcagCCCTTGAAAGGTTTGAAGAGGGTCCTCCATTCACACTGCAAAGGCTTTGTGAG
   ||  | |  ||  | | | | |||||     | |  |  |  ||| |  | | |  | ||   || ||   | |||  || || ||  |      |||||||| ||    ||||| ||||| ||||||||||| |||||||||||||| ||||||
---tagtgttttttctacaggccacctttccatcattcctgacc-tgcattttatcgagc-atacacaaatcactaatttctttttaaaaaaaaaatgtttgcagCTCTCTTGAGGTTCGAAGAAGGTCCTCCATTTACACTGCAAAGGCTATGTGAG
















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|109637336|gb|EC590881.1|EC590881
EST:     TGATGGGCAACAGAGGTCTTTCTCAGAGCTATTTAGTCGGCTAAATGGTG                         CCCTTGAAAGGTTTGAAGAGGGTCCTCCATTCACATTGCAAAGGCTTTGTG
genomic: TGATGGGCAACTGAGGTCTTTCTCAGAGCTATTTAGTCGGCTAAATGGTGgtactgcctt ... tattttgcagCCCTTGAAAGGTTTGAAGAGGGTCCTCCATTCACACTGCAAAGGCTTTGTG
EST: gi|71448188|gb|DR829238.1|DR829238
EST:     TGATGGGCAACTGAGGTCTTTCTCAGAGCTATTTAGTCGGCTAAATGGTG                         CCCTTGAAAGGTTTGAAGAGGGTCCTCCATTCACACTGCAAAGGCTTTGTG
genomic: TGATGGGCAACTGAGGTCTTTCTCAGAGCTATTTAGTCGGCTAAATGGTGgtactgcctt ... tattttgcagCCCTTGAAAGGTTTGAAGAGGGTCCTCCATTCACACTGCAAAGGCTTTGTG
EST: gi|71447828|gb|DR828878.1|DR828878
EST:     TGATGGGCAACTGAGGTCTTTCTCATAGCTATTTAATCGGCTAAATGGGG                         CCCTTGAAAGGTTTGAAGA
genomic: TGATGGGCAACTGAGGTCTTTCTCAGAGCTATTTAGTCGGCTAAATGGTGgtactgcctt ... tattttgcagCCCTTGAAAGGTTTGAAGA
EST: gi|76288811|gb|DV028379.1|DV028379
EST:     TGATGGGCAACTGAGGTCTTTCTCAGAGCTATTTAGTCGGCTAAATGGTG                         CCCTTGAAAGGTTTGAAGAGGGTCCTCCATTCACACTGCAAAGGCTTTGTG
genomic: TGATGGGCAACTGAGGTCTTTCTCAGAGCTATTTAGTCGGCTAAATGGTGgtactgcctt ... tattttgcagCCCTTGAAAGGTTTGAAGAGGGTCCTCCATTCACACTGCAAAGGCTTTGTG
EST: gi|94477260|gb|EB706218.1|EB706218
EST:     TGATGGGCAACTGAGGTCTTTCTCAGAGCTATTTAGTCGGCTAAATGGTG                         CCCTTGAAAGGTTTGAAGAGGGTCCTCCATTCACACTGCAAAGGCTTTGTG
genomic: TGATGGGCAACTGAGGTCTTTCTCAGAGCTATTTAGTCGGCTAAATGGTGgtactgcctt ... tattttgcagCCCTTGAAAGGTTTGAAGAGGGTCCTCCATTCACACTGCAAAGGCTTTGTG
EST: gi|74245108|gb|DT653022.1|DT653022
EST:     TGATGGGCAACTGAGGTCTTTCTCAGAGCTATTTAGTCGGCTAAATGGTG                         CCCTTGAAAGGTTTGAAGAGGGTCCTCCATTCACACTGCAAAGGCTTTGTG
genomic: TGATGGGCAACTGAGGTCTTTCTCAGAGCTATTTAGTCGGCTAAATGGTGgtactgcctt ... tattttgcagCCCTTGAAAGGTTTGAAGAGGGTCCTCCATTCACACTGCAAAGGCTTTGTG
EST: gi|211298933|gb|FL395580.1|FL395580
EST:     TGATGGGCAACTGAGGTCTTTCTCAGAGCTATT-AGTCGGCTAAATGGTG                         CC-TTGAAAGGTTTGAAGAGGGTCCTC-ATTCACACTGCAAAGGCTT-GTG
genomic: TGATGGGCAACTGAGGTCTTTCTCAGAGCTATTTAGTCGGCTAAATGGTGgtactgcctt ... tattttgcagCCCTTGAAAGGTTTGAAGAGGGTCCTCCATTCACACTGCAAAGGCTTTGTG
EST: gi|89759923|gb|DY688582.1|DY688582
EST:     TGATGGGCAACTGAGGTCTTTCTCAGAGCTATTTAGTCGGCTAAATGGTG                         CCCTTGAAAGGTTTGAAGAGGGTCCTCCATTCACACTGCAAAGGCTTTGTG
genomic: TGATGGGCAACTGAGGTCTTTCTCAGAGCTATTTAGTCGGCTAAATGGTGgtactgcctt ... tattttgcagCCCTTGAAAGGTTTGAAGAGGGTCCTCCATTCACACTGCAAAGGCTTTGTG
EST: gi|76294110|gb|DV033678.1|DV033678
EST:     TGATGGGCAACTGAGGTCTTTCTCAGAGCTATTTAGTCGGCTAAATGGTG                         CCCTTGAAAGGTTTGAAGAGGGTCCTCCATTCACACTGCAAAGGCTTTGTG
genomic: TGATGGGCAACTGAGGTCTTTCTCAGAGCTATTTAGTCGGCTAAATGGTGgtactgcctt ... tattttgcagCCCTTGAAAGGTTTGAAGAGGGTCCTCCATTCACACTGCAAAGGCTTTGTG
EST: gi|71447829|gb|DR828879.1|DR828879
EST:     TGATGGGCAACTGAGGTCTTTCTCAGAGCTATTTAGTCGGCTAAATGGTG                         CCCTTGAAAGGTTTGAAGAGGGTCCTCCATTCACACTGCAAAGGCTTTGTG
genomic: TGATGGGCAACTGAGGTCTTTCTCAGAGCTATTTAGTCGGCTAAATGGTGgtactgcctt ... tattttgcagCCCTTGAAAGGTTTGAAGAGGGTCCTCCATTCACACTGCAAAGGCTTTGTG
EST: gi|211303817|gb|FL321312.1|FL321312
EST:     TGATGGGCAACTGAGGTCTTTCTCAGAGCTATTTAGTCGGCTAAATGGTG                         CCCTTGAAAGGTTTGAAGAGGGTCCTCCATTCACACTGCAAAGGCTTTGTG
genomic: TGATGGGCAACTGAGGTCTTTCTCAGAGCTATTTAGTCGGCTAAATGGTGgtactgcctt ... tattttgcagCCCTTGAAAGGTTTGAAGAGGGTCCTCCATTCACACTGCAAAGGCTTTGTG
EST: gi|50333548|gb|CO528674.1|CO528674
EST:     TGATGGGCAACTGAGGTCTTTCTCAGAGCTATTTAGTCGGCTAAATGGTG                         CCCTTGAAAGGTTTGAAGAGGGTCCTCCATTCACACTGCAAAGGCTTTGTG
genomic: TGATGGGCAACTGAGGTCTTTCTCAGAGCTATTTAGTCGGCTAAATGGTGgtactgcctt ... tattttgcagCCCTTGAAAGGTTTGAAGAGGGTCCTCCATTCACACTGCAAAGGCTTTGTG
EST: gi|78106485|gb|DV524903.1|DV524903
EST:     TGATGGGCAACTGAGGTCTTTCTCAGAGCTATTTAGTCGGCTAAATGGTG                         CCCTTGAAAGGTTTGAAGAGGGTCCTCCATTCACACTGCAAAGGCTTTGTG
genomic: TGATGGGCAACTGAGGTCTTTCTCAGAGCTATTTAGTCGGCTAAATGGTGgtactgcctt ... tattttgcagCCCTTGAAAGGTTTGAAGAGGGTCCTCCATTCACACTGCAAAGGCTTTGTG
EST: gi|60349327|gb|DN216300.1|DN216300
EST:     ACTGAGGTCTTTCTCAGAGCTATTTAGTCGGCTAAATGGTG                         CCCTTGAAAGGTTTGAAGAGGGTCCTCCATTCACACTGCAAAGGCTTTGTG
genomic: ACTGAGGTCTTTCTCAGAGCTATTTAGTCGGCTAAATGGTGgtactgcctt ... tattttgcagCCCTTGAAAGGTTTGAAGAGGGTCCTCCATTCACACTGCAAAGGCTTTGTG
EST: gi|211444016|gb|FL185353.1|FL185353
EST:     TGATGGGCAACTGAGGTCTTTCTCAGAGCTATTTAGTCGGCTAAATGGTG                         CC-TTGAAAGGTTTGAAGAGGG
genomic: TGATGGGCAACTGAGGTCTTTCTCAGAGCTATTTAGTCGGCTAAATGGTGgtactgcctt ... tattttgcagCCCTTGAAAGGTTTGAAGAGGG
EST: gi|211357155|gb|FL457836.1|FL457836
EST:     TGATGGGCAACTGAGGTCTTTCTCAGAGCTATTTAGTCGGCTAAATGGTG                         CCCTTGAAAGGTTTGAAGAGGGTCCTCCATTCACACTGCAAAGGCTTTGTG
genomic: TGATGGGCAACTGAGGTCTTTCTCAGAGCTATTTAGTCGGCTAAATGGTGgtactgcctt ... tattttgcagCCCTTGAAAGGTTTGAAGAGGGTCCTCCATTCACACTGCAAAGGCTTTGTG
EST: gi|71331612|gb|DR802650.1|DR802650
EST:     TGATGGGCAACTGAGGTCTTTCTCAGAGCTATTTAGTCGGCTAAATGGTG                         CCCTTGAAAGGTTTGAAGAGGGTCCTCCATTCACACTGCAAAGGCTTTGTG
genomic: TGATGGGCAACTGAGGTCTTTCTCAGAGCTATTTAGTCGGCTAAATGGTGgtactgcctt ... tattttgcagCCCTTGAAAGGTTTGAAGAGGGTCCTCCATTCACACTGCAAAGGCTTTGTG
EST: gi|78106599|gb|DV525017.1|DV525017
EST:     TGATGGGCAACTGAGGTCTTTCTCAGAGCTATTTAGTCGGCTAAATGGTG                         CCCTTGAAAGGTTTGAAGAGGGTCCTCCATTCACACTGCAAAGGCTTTGTG
genomic: TGATGGGCAACTGAGGTCTTTCTCAGAGCTATTTAGTCGGCTAAATGGTGgtactgcctt ... tattttgcagCCCTTGAAAGGTTTGAAGAGGGTCCTCCATTCACACTGCAAAGGCTTTGTG
EST: gi|91877466|gb|EB407423.1|EB407423
EST:     TGATGGGCAACTGAGGTCTTTCTCAGAGCTATTTAGTCCGCTAAATGGTG                         CCCTTGAAAGGTTTGAAGAGGGTCCTCCATTCACACTGCAAAGGCTTTGTG
genomic: TGATGGGCAACTGAGGTCTTTCTCAGAGCTATTTAGTCGGCTAAATGGTGgtactgcctt ... tattttgcagCCCTTGAAAGGTTTGAAGAGGGTCCTCCATTCACACTGCAAAGGCTTTGTG

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: 47 (upstream exon), 49 (downstream exon)
Score: 100

GTCTTGGATGAATATTTTGAGGTTGAAATGGTGAGCCAAAATGATGGGCAACTGAGGTCTTTCTCAGAGCTATTTAGTCGGCTAAATGGTGgtactgcctt ... tattttgcagCCCTTGAAAGGTTTGAAGAGGGTCCTCCATTCACACTGCAAAGGCTTTGTGAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 57

GTCTTGGATGAATATTTTGAGGTTGAAATGGTGAGCCAAAATGATGGGCAACTGAGGTCTTTCTCAGAGCTATTTAGTCGGCTAAATGGTGgtactgcctt ... tattttgcagCCCTTGAAAGGTTTGAAGAGGGTCCTCCATTCACACTGCAAAGGCTTTGTGAG


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

GTCTTGGATGAATATTTTGAGGTTGAAATGGTGAGCCAAAATGATGGGCAACTGAGGTCTTTCTCAGAGCTATTTAGTCGGCTAAATGGTGgtactgcctt ... tattttgcagCCCTTGAAAGGTTTGAAGAGGGTCCTCCATTCACACTGCAAAGGCTTTGTGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 53

GTCTTGGATGAATATTTTGAGGTTGAAATGGTGAGCCAAAATGATGGGCAACTGAGGTCTTTCTCAGAGCTATTTAGTCGGCTAAATGGTGgtactgcctt ... tattttgcagCCCTTGAAAGGTTTGAAGAGGGTCCTCCATTCACACTGCAAAGGCTTTGTGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcctgcttttggactatttgcatatatgtgattgtttgttgaattattttgcagCCCTTGAAAGGTTTGAAGAGGGTCCTCCATTCACACTGCAAAGGCTTTGTGAG
                                            ttatttt  CT-rich tract
                                   tttgttgaattatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcttacagataattagagatgactccttttatggactagttgcaatgcctgcttttggactatttgcatatatgtgattgtttgttgaattattttgcagCCCTTGAAAGGTTTGAAGAGGGTCCTCCATTCACACTGCAAAGGCTTTGTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - -agttgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tttgcat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtttgt