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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctctgtatgactgtatgttacctatttgttggcacaaagcttttcacgtgcaatagtgtgtttatatgatattgttttacactttcctattttggttagATCCTTCAAAAGGTGAAAGCAACATATGACCTTCCGATAGTCACTGATGTGCACGAAAGCCACCAG

Basic information

species Zea mays
transcript GRMZM2G168510_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G168510_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os12g10784.1 (Oryza sativa), 3'ss of exon 3
tctctgtatgactgtatgttacctatttgttggcacaaagcttttcacgtgcaatagtgt--gttt--atatgatattgttttacactttcctattttggttagATCCTTCAAAAGGTGAAAGCAACATATGACCTTCCGATAGTCACTGATGTGCACGAAAGCCACCAG
    |||||   ||||| |||  | ||| ||         |||      |  || | |||  ||||   ||    |||  |  |    |   | |  || | |||| ||| |||| |||||||||||||||||| ||||  | |||||||||||||| ||||||||||||
--agtgtatt-ttgtattttat-tgtttattcttttgcctcttcatgtatataacattgttggtttccctactgcattaatgcattactaattttgctgatcagATACTTGAAAAAGTGAAAGCAACATATGACATTCCAGTGGTCACTGATGTGCATGAAAGCCACCAG
















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|61118196|gb|DN559157.1|DN559157
EST:     GTACATCATCAAAATCATTCCGTGGTCCTGGTCTTGAAGAAGGTCTTAAG                         ATCCTTCAAAAGGTGAAAGCAACATATGACCTTCCGATGGTCACTGATGTG
genomic: GTACATCATCAAAATCATTCCGTGGTCCTGGTCTTGAAGAAGGTCTTAAGgtgaggcatg ... ttttggttagATCCTTCAAAAGGTGAAAGCAACATATGACCTTCCGATAGTCACTGATGTG
EST: gi|9952617|gb|BE639305.1|BE639305
EST:     GTACATCATCAAAATCATTCCGTGGTCCTGGTCTTGAAGAAGGTCTTAAG                         ATCCTTCAAAAGGTGAAAGCAACATATGACCTTCCGATAGTCACTGATGTG
genomic: GTACATCATCAAAATCATTCCGTGGTCCTGGTCTTGAAGAAGGTCTTAAGgtgaggcatg ... ttttggttagATCCTTCAAAAGGTGAAAGCAACATATGACCTTCCGATAGTCACTGATGTG
EST: gi|91055907|gb|EB166325.1|EB166325
EST:     GTACATCATCAAAATCATTCCGTGGTCCTGGTCTTGAAGAAGGTCTTAAG                         ATCCTTCAAAAGGTGAAAGCAACATATGACCTTCCGATAGTCACTGATGTG
genomic: GTACATCATCAAAATCATTCCGTGGTCCTGGTCTTGAAGAAGGTCTTAAGgtgaggcatg ... ttttggttagATCCTTCAAAAGGTGAAAGCAACATATGACCTTCCGATAGTCACTGATGTG
EST: gi|50323772|gb|CO518898.1|CO518898
EST:     GTACATCATCAAAATCATTCCGTGGTCCTGGTCTTGAAGAAGGTCTTAAG                         ATCCTTCAAAAGGTGAAAGCAACATATGACCTTCCGATAGTCACTGATGTG
genomic: GTACATCATCAAAATCATTCCGTGGTCCTGGTCTTGAAGAAGGTCTTAAGgtgaggcatg ... ttttggttagATCCTTCAAAAGGTGAAAGCAACATATGACCTTCCGATAGTCACTGATGTG
EST: gi|50323794|gb|CO518920.1|CO518920
EST:     GTACATCATCAAAATCATTCCGTGGTCCTGGTCTTGAAGAAGGTCTTAAG                         ATCCTTCAAAAGGTGAAAGCAACATATGACCTTCCGATAGTCACTGATGTG
genomic: GTACATCATCAAAATCATTCCGTGGTCCTGGTCTTGAAGAAGGTCTTAAGgtgaggcatg ... ttttggttagATCCTTCAAAAGGTGAAAGCAACATATGACCTTCCGATAGTCACTGATGTG
EST: gi|71307284|gb|DR789817.1|DR789817
EST:     GTACATCATCAAAATCATTCCGTGGTCCTGGTCTTGAAGAAGGTCTTAAG                         ATCCTTCAAAAGGTGAAAGCAACATATGACCTTCCGATAGTCACTGATGTG
genomic: GTACATCATCAAAATCATTCCGTGGTCCTGGTCTTGAAGAAGGTCTTAAGgtgaggcatg ... ttttggttagATCCTTCAAAAGGTGAAAGCAACATATGACCTTCCGATAGTCACTGATGTG
EST: gi|9794838|gb|BE553146.1|BE553146
EST:     GTACATCATCAAAATCATTCCGTGGTCCTGGTCTTGAAGAAGGTCTTAAG                         ATCCTTCAAAAGGTGAAAGCAACATATGACCTTCCGATAGTCACTGATGTG
genomic: GTACATCATCAAAATCATTCCGTGGTCCTGGTCTTGAAGAAGGTCTTAAGgtgaggcatg ... ttttggttagATCCTTCAAAAGGTGAAAGCAACATATGACCTTCCGATAGTCACTGATGTG
EST: gi|4887387|gb|AI677486.1|AI677486
EST:     GAAGAAGGTCTTAAG                         ATCCTTCAAAAGGTGAAAGCAACATATGACCTTCCGATAGTCACTGATGTG
genomic: GAAGAAGGTCTTAAGgtgaggcatg ... ttttggttagATCCTTCAAAAGGTGAAAGCAACATATGACCTTCCGATAGTCACTGATGTG
EST: gi|61118194|gb|DN559155.1|DN559155
EST:     GTACATCATCAAAATCATTCCGTGGTCCTGGTCTTGAAGAAGGTCTTAAG                         ATCCTTCAAAAGGTGAAAGCAACATATGACCTTCCGATAGTCACTGATGTG
genomic: GTACATCATCAAAATCATTCCGTGGTCCTGGTCTTGAAGAAGGTCTTAAGgtgaggcatg ... ttttggttagATCCTTCAAAAGGTGAAAGCAACATATGACCTTCCGATAGTCACTGATGTG
EST: gi|211064516|gb|FL339511.1|FL339511
EST:     GTACATCATCAAAATCATTCCGTGGTCCTGGTCTTGAAGAAGGTCTTAAG                         ATCCTTCAAAAGGTGAAAGCAACATATGACCTTCCGATAGTCACTGATGTG
genomic: GTACATCATCAAAATCATTCCGTGGTCCTGGTCTTGAAGAAGGTCTTAAGgtgaggcatg ... ttttggttagATCCTTCAAAAGGTGAAAGCAACATATGACCTTCCGATAGTCACTGATGTG
EST: gi|74236361|gb|DT644275.1|DT644275
EST:     GTACATCATCAAAATCATTCCGTGGTCCTGGTCTTGAAGAAGGTCTTAAG                         ATCCTTCAAAAGGTGAAAGCAACATATGACCTTCCGATAGTCACTGATGTG
genomic: GTACATCATCAAAATCATTCCGTGGTCCTGGTCTTGAAGAAGGTCTTAAGgtgaggcatg ... ttttggttagATCCTTCAAAAGGTGAAAGCAACATATGACCTTCCGATAGTCACTGATGTG
EST: gi|91050684|gb|EB161102.1|EB161102
EST:     GTACATCATCAAAATCATTCCGTGGTCCTGGTCTTGAAGAAGGTCTTAAG                         ATCCTTCAAAAGGTGAAAGCAACATATGACCTTCCGATAGTCACTGATGTG
genomic: GTACATCATCAAAATCATTCCGTGGTCCTGGTCTTGAAGAAGGTCTTAAGgtgaggcatg ... ttttggttagATCCTTCAAAAGGTGAAAGCAACATATGACCTTCCGATAGTCACTGATGTG
EST: gi|21432170|gb|BQ547660.1|BQ547660
EST:     GTACATCATCAAAATCATTCCGTGGTCCTGGTCTTGAAGAAGGTCTTAAG                         ATCCTTCAAAAGGTGAAAGCAACATATGACCTTCCGATAGTCACTGATGTG
genomic: GTACATCATCAAAATCATTCCGTGGTCCTGGTCTTGAAGAAGGTCTTAAGgtgaggcatg ... ttttggttagATCCTTCAAAAGGTGAAAGCAACATATGACCTTCCGATAGTCACTGATGTG
EST: gi|78121994|gb|DV540378.1|DV540378
EST:     GTACATCATCAAAATCATTCCGTGGTCCTGGTCTTGAAGAAGGTCTTAAG                         ATCCTTCAAAAGGTGAAAGCAACATATGACCTTCCGATAGTCACTGATGTG
genomic: GTACATCATCAAAATCATTCCGTGGTCCTGGTCTTGAAGAAGGTCTTAAGgtgaggcatg ... ttttggttagATCCTTCAAAAGGTGAAAGCAACATATGACCTTCCGATAGTCACTGATGTG
EST: gi|211382423|gb|FK948864.1|FK948864
EST:     GTACATCATCAAAATCGTTCCGTGGTCCTGGTCTTGAAGAAGGTCTAAAG                         ATCCTTCAAAAGGTGAAAGCAACATATGACCTTCCGATAGTCACTGATGTG
genomic: GTACATCATCAAAATCATTCCGTGGTCCTGGTCTTGAAGAAGGTCTTAAGgtgaggcatg ... ttttggttagATCCTTCAAAAGGTGAAAGCAACATATGACCTTCCGATAGTCACTGATGTG
EST: gi|31355531|gb|CD439888.1|CD439888
EST:     GTACATCATCAAAATCATTCCGTGGTCCTGGTCTTGTAGAAGGTCTTAAG                         ATCCTTCAAAAGGTGAAAGCAACATATGACCTTCCGATAGTCACTGATGTG
genomic: GTACATCATCAAAATCATTCCGTGGTCCTGGTCTTGAAGAAGGTCTTAAGgtgaggcatg ... ttttggttagATCCTTCAAAAGGTGAAAGCAACATATGACCTTCCGATAGTCACTGATGTG
EST: gi|211382425|gb|FK948866.1|FK948866
EST:     GTACATCATCAAAATCGTTCCGTGGTCCTGGTCTTGAAGAAGGTCTAAAG                         ATCCTTCAAAAGGTGAAAGCAACATATGACCTTCCGATAGTCACTGATGTG
genomic: GTACATCATCAAAATCATTCCGTGGTCCTGGTCTTGAAGAAGGTCTTAAGgtgaggcatg ... ttttggttagATCCTTCAAAAGGTGAAAGCAACATATGACCTTCCGATAGTCACTGATGTG
EST: gi|71449637|gb|DR830687.1|DR830687
EST:     GTACATCATCAAAATCATTCCGTGGTCCTGGTCTTGAAGAAGGTCTTAAG                         ATCCTTCAAAAGGTGAAAGCAACATATGACCTTCCGATAGTCACTGATGTG
genomic: GTACATCATCAAAATCATTCCGTGGTCCTGGTCTTGAAGAAGGTCTTAAGgtgaggcatg ... ttttggttagATCCTTCAAAAGGTGAAAGCAACATATGACCTTCCGATAGTCACTGATGTG
EST: gi|26457480|gb|CA829063.1|CA829063
EST:     GTACATCATCAAAATCATTCCGTGGTCCTGGTCTTGAAGAAGGTCTTAAG                         ATCCTTCAAAAGGTGAAAGCAACATATGACCTTCCGATAGTCACTGATGTG
genomic: GTACATCATCAAAATCATTCCGTGGTCCTGGTCTTGAAGAAGGTCTTAAGgtgaggcatg ... ttttggttagATCCTTCAAAAGGTGAAAGCAACATATGACCTTCCGATAGTCACTGATGTG
EST: gi|91051935|gb|EB162353.1|EB162353
EST:     GTACATCATCAAAATCATTCCGTGGTCCTGGTCTTGAAGAAGGTCTTAAG                         ATCCTTCAAAAGGTGAAAGCAACATATGACCTTCCGATAGTCACTGATGTG
genomic: GTACATCATCAAAATCATTCCGTGGTCCTGGTCTTGAAGAAGGTCTTAAGgtgaggcatg ... ttttggttagATCCTTCAAAAGGTGAAAGCAACATATGACCTTCCGATAGTCACTGATGTG
EST: gi|78110755|gb|DV529153.1|DV529153
EST:     GTACATCATCAAAATCATTCCGTGGTCCTGGTCTTGAAGAAGGTCTTAAG                         ATCCTTCAAAAGGTGAAAGCAACATATGACCTTCCGATAGTCACTGATGTG
genomic: GTACATCATCAAAATCATTCCGTGGTCCTGGTCTTGAAGAAGGTCTTAAGgtgaggcatg ... ttttggttagATCCTTCAAAAGGTGAAAGCAACATATGACCTTCCGATAGTCACTGATGTG
EST: gi|211162593|gb|FL363072.1|FL363072
EST:     GTACATCATCAAAATCGTTCCGTGGTCCTGGTCTTGAAGAAGGTCTAAAG                         ATCCTTCAAAAGGTGAAAGCAACATATGACCTTCCGATAGTCACTGATGTG
genomic: GTACATCATCAAAATCATTCCGTGGTCCTGGTCTTGAAGAAGGTCTTAAGgtgaggcatg ... ttttggttagATCCTTCAAAAGGTGAAAGCAACATATGACCTTCCGATAGTCACTGATGTG
EST: gi|116816629|gb|EC859381.1|EC859381
EST:     GTACATCATCAAAATCGTTCCGTGGTCCTGGTCTTGAAGAAGGTCTCAAG                         ATCCTTCAAAAGGTGAAAGCAACATATGACCTTCCGATAGTCACTGATGTG
genomic: GTACATCATCAAAATCATTCCGTGGTCCTGGTCTTGAAGAAGGTCTTAAGgtgaggcatg ... ttttggttagATCCTTCAAAAGGTGAAAGCAACATATGACCTTCCGATAGTCACTGATGTG
EST: gi|61118195|gb|DN559156.1|DN559156
EST:     GTACATCATCAAAATCATTCCGTGGTCCTGGTCTTGAAGAAGGTCTTAAG                         ATCCTTCAAAAGGTGAAAGCAACATATGACCTTCCGATAGTCACTGATGTG
genomic: GTACATCATCAAAATCATTCCGTGGTCCTGGTCTTGAAGAAGGTCTTAAGgtgaggcatg ... ttttggttagATCCTTCAAAAGGTGAAAGCAACATATGACCTTCCGATAGTCACTGATGTG
EST: gi|31361455|gb|CD445812.1|CD445812
EST:     GTACATCATCAAAATCATTCCGTGGTCCTGGTCTTGAAGAAGGTCTTAAG                         ATCCTTCAAAAGGTGAAAGCAACATATGACCTTCCGATAGTCACTGATGTG
genomic: GTACATCATCAAAATCATTCCGTGGTCCTGGTCTTGAAGAAGGTCTTAAGgtgaggcatg ... ttttggttagATCCTTCAAAAGGTGAAAGCAACATATGACCTTCCGATAGTCACTGATGTG
EST: gi|211382426|gb|FK948867.1|FK948867
EST:     GTACATCATCAAAATCGTTCCGTGGTCCTGGTCTTGAAGAAGGTCTAAAG                         ATCCTTCAAAAGGTGAAAGCAACATATGACCTTCCGATAGTCACTGATGTG
genomic: GTACATCATCAAAATCATTCCGTGGTCCTGGTCTTGAAGAAGGTCTTAAGgtgaggcatg ... ttttggttagATCCTTCAAAAGGTGAAAGCAACATATGACCTTCCGATAGTCACTGATGTG
EST: gi|211215731|gb|FL322482.1|FL322482
EST:     GTACATCATCAAAATCGTTCCGTGGTCCTGGTCTTGAAGAAGGTCTAAAG                         ATCCTTCAAAAGGTGAAAGCAACATATGACCTTCCGATAGTCACTGATGTG
genomic: GTACATCATCAAAATCATTCCGTGGTCCTGGTCTTGAAGAAGGTCTTAAGgtgaggcatg ... ttttggttagATCCTTCAAAAGGTGAAAGCAACATATGACCTTCCGATAGTCACTGATGTG
EST: gi|21626200|gb|BQ621121.1|BQ621121
EST:     GGTCCTGGTCTTGTATAGAAGGTCTTAAG                         ATCCTTCAAAAGGTGAAAGCAACATATGACCTTCCGATAGTCACTGATGTG
genomic: GGTCCTGGTCTTG-A-AGAAGGTCTTAAGgtgaggcatg ... ttttggttagATCCTTCAAAAGGTGAAAGCAACATATGACCTTCCGATAGTCACTGATGTG

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), 49 (downstream exon)
Score: 141

GCTTGGAATTCCGCTCGTGTTCAAGTCCAGCTTTGATAAAGCAAACCGTACATCATCAAAATCATTCCGTGGTCCTGGTCTTGAAGAAGGTCTTAAGgtgaggcatg ... ttttggttagATCCTTCAAAAGGTGAAAGCAACATATGACCTTCCGATAGTCACTGATGTGCACGAAAGCCACCAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 106

GCTTGGAATTCCGCTCGTGTTCAAGTCCAGCTTTGATAAAGCAAACCGTACATCATCAAAATCATTCCGTGGTCCTGGTCTTGAAGAAGGTCTTAAGgtgaggcatg ... ttttggttagATCCTTCAAAAGGTGAAAGCAACATATGACCTTCCGATAGTCACTGATGTGCACGAAAGCCACCAG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 118

GCTTGGAATTCCGCTCGTGTTCAAGTCCAGCTTTGATAAAGCAAACCGTACATCATCAAAATCATTCCGTGGTCCTGGTCTTGAAGAAGGTCTTAAGgtgaggcatg ... ttttggttagATCCTTCAAAAGGTGAAAGCAACATATGACCTTCCGATAGTCACTGATGTGCACGAAAGCCACCAG


Block sizes: 47 (upstream exon), 44 (downstream exon)
Score: 104

GCTTGGAATTCCGCTCGTGTTCAAGTCCAGCTTTGATAAAGCAAACCGTACATCATCAAAATCATTCCGTGGTCCTGGTCTTGAAGAAGGTCTTAAGgtgaggcatg ... ttttggttagATCCTTCAAAAGGTGAAAGCAACATATGACCTTCCGATAGTCACTGATGTGCACGAAAGCCACCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacgtgcaatagtgtgtttatatgatattgttttacactttcctattttggttagATCCTTCAAAAGGTGAAAGCAACATATGACCTTCCGATAGTCACTGATGTGCACGAAAGCCACCAG
                                   cactttcctatttt  CT-rich tract
              tgtttatatgatattg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctctgtatgactgtatgttacctatttgttggcacaaagcttttcacgtgcaatagtgtgtttatatgatattgttttacactttcctattttggttagATCCTTCAAAAGGTGAAAGCAACATATGACCTTCCGATAGTCACTGATGTGCACGAAAGCCACCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- -ctgtatg
- - - - - - - - - - - - -tttgttg
- - - - - - - - - - - - - - - - gcacaaa
- - - - - - - - - - - - - - - - - - - - - - - -cgtgcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtgttt