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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCCTTCAAAAGGTGAAAGCAACATATGACCTTCCGATAGTCACTGATGTGCACGAAAGCCACCAGgtaatccattcacagattctactgtgttaacacccaattttgcttgattctgcaccagatcatgtttctgttgtacttttgtactgtaagacatgtttcc...

Basic information

species Zea mays
transcript GRMZM2G168510_T02
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G168510_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os12g10784.1 (Oryza sativa), 5'ss of exon 4
ATCCTTCAAAAGGTGAAAGCAACATATGACCTTCCGATAGTCACTGATGTGCACGAAAGCCACCAGgtaatccattcacagat-tctactgtgttaacacccaattttgcttgattctgcaccagatcatgtttctgttgtactt--ttgtactgtaagacatgtttcc
|| ||| |||| |||||||||||||||||| ||||  | |||||||||||||| ||||||||||||||| ||  ||  ||    | |  |   || |    || |  | ||||  ||      | ||  |  |  | |   ||    || | ||| |  || |  ||  
ATACTTGAAAAAGTGAAAGCAACATATGACATTCCAGTGGTCACTGATGTGCATGAAAGCCACCAGgta-tcagttgtcaatcattttttagattgatttgcattaat-cttgtatccaaggaaaattgtcctgttttgagaccaaattctgctgcattactttcttt-
















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|60351240|gb|DN218213.1|DN218213
EST:     GTCACTGATGTGCACGAAAGCCACCAG                         TGTGAAGCTGTTGGAAGAGTTGCTGACATCATACAGATTCCAGCCTTCCTC
genomic: GTCACTGATGTGCACGAAAGCCACCAGgtaatccatt ... attaaatcagTGTGAAGCTGTTGGAAGAGTTGCTGACATCATACAGATTCCAGCCTTCCTC
EST: gi|61118196|gb|DN559157.1|DN559157
EST:     AAGCAACATATGACCTTCCGATGGTCACTGATGTGCACGAAAGCCACCAG                         TGTGAAGCTGTTGGAAGAGTTGCTGACATCATACAGATTCCAGCCTTCCTC
genomic: AAGCAACATATGACCTTCCGATAGTCACTGATGTGCACGAAAGCCACCAGgtaatccatt ... attaaatcagTGTGAAGCTGTTGGAAGAGTTGCTGACATCATACAGATTCCAGCCTTCCTC
EST: gi|9952617|gb|BE639305.1|BE639305
EST:     AAGCAACATATGACCTTCCGATAGTCACTGATGTGCACGAAAGCCACCAG                         TGTGAAGCTGTTGGAAGAGTTGCTGACATCATACAGATTCCAGCCTTCCTC
genomic: AAGCAACATATGACCTTCCGATAGTCACTGATGTGCACGAAAGCCACCAGgtaatccatt ... attaaatcagTGTGAAGCTGTTGGAAGAGTTGCTGACATCATACAGATTCCAGCCTTCCTC
EST: gi|91055907|gb|EB166325.1|EB166325
EST:     AAGCAACATATGACCTTCCGATAGTCACTGATGTGCACGAAAGCCACCAG                         TGTGAAGCTGTTGGAAGAGTTGCTGACATCATACAGATTCCAGCCTTCCTC
genomic: AAGCAACATATGACCTTCCGATAGTCACTGATGTGCACGAAAGCCACCAGgtaatccatt ... attaaatcagTGTGAAGCTGTTGGAAGAGTTGCTGACATCATACAGATTCCAGCCTTCCTC
EST: gi|50323772|gb|CO518898.1|CO518898
EST:     AAGCAACATATGACCTTCCGATAGTCACTGATGTGCACGAAAGCCACCAG                         TGTGAAGCTGTTGGAAGAGTTGCTGACATCATACAGATTCCAGCCTTCCTC
genomic: AAGCAACATATGACCTTCCGATAGTCACTGATGTGCACGAAAGCCACCAGgtaatccatt ... attaaatcagTGTGAAGCTGTTGGAAGAGTTGCTGACATCATACAGATTCCAGCCTTCCTC
EST: gi|50323794|gb|CO518920.1|CO518920
EST:     AAGCAACATATGACCTTCCGATAGTCACTGATGTGCACGAAAGCCACCAG                         TGTGAAGCTGTTGGAAGAGTTGCTGACATCATACAGATTCCAGCCTTCCTC
genomic: AAGCAACATATGACCTTCCGATAGTCACTGATGTGCACGAAAGCCACCAGgtaatccatt ... attaaatcagTGTGAAGCTGTTGGAAGAGTTGCTGACATCATACAGATTCCAGCCTTCCTC
EST: gi|71307284|gb|DR789817.1|DR789817
EST:     AAGCAACATATGACCTTCCGATAGTCACTGATGTGCACGAAAGCCACCAG                         TGTGAAGCTGTTGGAAGAGTTGCTGACATCATACAGATTCCAGCCTTCCTC
genomic: AAGCAACATATGACCTTCCGATAGTCACTGATGTGCACGAAAGCCACCAGgtaatccatt ... attaaatcagTGTGAAGCTGTTGGAAGAGTTGCTGACATCATACAGATTCCAGCCTTCCTC
EST: gi|9794838|gb|BE553146.1|BE553146
EST:     AAGCAACATATGACCTTCCGATAGTCACTGATGTGCACGAAAGCCACCAG                         TGTGAAGCTGTTGGAAGAGTTGCTGACATCATACAGATTCCAGCCTTCCTC
genomic: AAGCAACATATGACCTTCCGATAGTCACTGATGTGCACGAAAGCCACCAGgtaatccatt ... attaaatcagTGTGAAGCTGTTGGAAGAGTTGCTGACATCATACAGATTCCAGCCTTCCTC
EST: gi|60396848|gb|DN229670.1|DN229670
EST:     AAGCAACATATGACCTTCCGATAGTCACTGATGTGCACGAAAGCCACCAG                         TGTGAAGCTGTTGGAAGAGTTGCTGACATCATACAGATTCCAGCCTTCCTC
genomic: AAGCAACATATGACCTTCCGATAGTCACTGATGTGCACGAAAGCCACCAGgtaatccatt ... attaaatcagTGTGAAGCTGTTGGAAGAGTTGCTGACATCATACAGATTCCAGCCTTCCTC
EST: gi|5325144|gb|AI783335.1|AI783335
EST:     AAGCAACATATGACCTTCCGATAGTCACTGATGTGCACGAAAGCCACCAG                         TGTGAAGCTGTTGGAAGAGTTGCTGACATCATACAGATTCCAGCCTTCCTC
genomic: AAGCAACATATGACCTTCCGATAGTCACTGATGTGCACGAAAGCCACCAGgtaatccatt ... attaaatcagTGTGAAGCTGTTGGAAGAGTTGCTGACATCATACAGATTCCAGCCTTCCTC
EST: gi|4887387|gb|AI677486.1|AI677486
EST:     AAGCAACATATGACCTTCCGATAGTCACTGATGTGCACGAAAGCCACCAG                         TGTGAAGCTGTTGGAAGAGTTGCTGACATCATACAGATTCCAGCCTTCCTC
genomic: AAGCAACATATGACCTTCCGATAGTCACTGATGTGCACGAAAGCCACCAGgtaatccatt ... attaaatcagTGTGAAGCTGTTGGAAGAGTTGCTGACATCATACAGATTCCAGCCTTCCTC
EST: gi|61118194|gb|DN559155.1|DN559155
EST:     AAGCAACATATGACCTTCCGATAGTCACTGATGTGCACGAAAGCCACCAG                         TGTGAAGCTGTTGGAAGAGTTGCTGACATCATACAGATTCCAGCCTTCCTC
genomic: AAGCAACATATGACCTTCCGATAGTCACTGATGTGCACGAAAGCCACCAGgtaatccatt ... attaaatcagTGTGAAGCTGTTGGAAGAGTTGCTGACATCATACAGATTCCAGCCTTCCTC
EST: gi|74236361|gb|DT644275.1|DT644275
EST:     AAGCAACATATGACCTTCCGATAGTCACTGATGTGCACGAAAGCCACCAG                         TGTGAAGCTGTTGGAAGAGTTGCTGACATCATACAGATTCCAGCCTTCCTC
genomic: AAGCAACATATGACCTTCCGATAGTCACTGATGTGCACGAAAGCCACCAGgtaatccatt ... attaaatcagTGTGAAGCTGTTGGAAGAGTTGCTGACATCATACAGATTCCAGCCTTCCTC
EST: gi|5770206|gb|AI973380.1|AI973380
EST:     CACTGATGTGCACGAAAGCCACCAG                         TGTGAAGCTGTTGGAAGAGTTGCTGACATCATACAGATTCCAGCCTTCCTC
genomic: CACTGATGTGCACGAAAGCCACCAGgtaatccatt ... attaaatcagTGTGAAGCTGTTGGAAGAGTTGCTGACATCATACAGATTCCAGCCTTCCTC
EST: gi|91050684|gb|EB161102.1|EB161102
EST:     AAGCAACATATGACCTTCCGATAGTCACTGATGTGCACGAAAGCCACCAG                         TGTGAAGCTGTTGGAAGAGTTGCTGACATCATACAGATTCCAGCCTTCCTC
genomic: AAGCAACATATGACCTTCCGATAGTCACTGATGTGCACGAAAGCCACCAGgtaatccatt ... attaaatcagTGTGAAGCTGTTGGAAGAGTTGCTGACATCATACAGATTCCAGCCTTCCTC
EST: gi|60357398|gb|DN224371.1|DN224371
EST:     AAGCAACATATGACCTTCCGATAGTCACTGATGTGCACGAAAGCCACCAG                         TGTGAAGCTGTTGGAAGAGTTGCTGACATCATACAGATTCCAGCCTTCCTC
genomic: AAGCAACATATGACCTTCCGATAGTCACTGATGTGCACGAAAGCCACCAGgtaatccatt ... attaaatcagTGTGAAGCTGTTGGAAGAGTTGCTGACATCATACAGATTCCAGCCTTCCTC
EST: gi|21432170|gb|BQ547660.1|BQ547660
EST:     AAGCAACATATGACCTTCCGATAGTCACTGATGTGCACGAAAGCCACCAG                         TGTGAAGCTGTTGGAAGAGTTGCTGACATCATACAGATTCCAGCCTTCCTC
genomic: AAGCAACATATGACCTTCCGATAGTCACTGATGTGCACGAAAGCCACCAGgtaatccatt ... attaaatcagTGTGAAGCTGTTGGAAGAGTTGCTGACATCATACAGATTCCAGCCTTCCTC
EST: gi|5847238|gb|AW000317.1|AW000317
EST:     AAGCAACATATGACCTTCCGATAGTCACTGATGTGCACGAAAGCCACCAG                         TGTGAAGCTGTTGGAAGAGTTGCTGACATCATACAGATTCCAGCCTTCCTC
genomic: AAGCAACATATGACCTTCCGATAGTCACTGATGTGCACGAAAGCCACCAGgtaatccatt ... attaaatcagTGTGAAGCTGTTGGAAGAGTTGCTGACATCATACAGATTCCAGCCTTCCTC
EST: gi|78121994|gb|DV540378.1|DV540378
EST:     AAGCAACATATGACCTTCCGATAGTCACTGATGTGCACGAAAGCCACCAG                         TGTGAAGCTGTTGGAAGAGTTGCTGACATCATACAGATTCCAGCCTTCCTC
genomic: AAGCAACATATGACCTTCCGATAGTCACTGATGTGCACGAAAGCCACCAGgtaatccatt ... attaaatcagTGTGAAGCTGTTGGAAGAGTTGCTGACATCATACAGATTCCAGCCTTCCTC
EST: gi|78022942|gb|DV491329.1|DV491329
EST:     AAGC-ACATATGACCTTCCGATAGTCACTGATGTGCACGAAAGCCACCCC                         TGTGAAGCTGTTGGAAGAGTTGCTGACATCATACAGATTCCAGCCTTCCTC
genomic: AAGCAACATATGACCTTCCGATAGTCACTGATGTGCACGAAAGCCACCAGgtaatccatt ... attaaatcagTGTGAAGCTGTTGGAAGAGTTGCTGACATCATACAGATTCCAGCCTTCCTC
EST: gi|211382423|gb|FK948864.1|FK948864
EST:     AAGCAACATATGACCTTCCGATAGTCACTGATGTGCACGAAAGCCACCAG                         TGTGAAGCTGTTGGAAGAGTTGCTGACATCATACAGATTCCAGCCTTCCTC
genomic: AAGCAACATATGACCTTCCGATAGTCACTGATGTGCACGAAAGCCACCAGgtaatccatt ... attaaatcagTGTGAAGCTGTTGGAAGAGTTGCTGACATCATACAGATTCCAGCCTTCCTC
EST: gi|31355531|gb|CD439888.1|CD439888
EST:     AAGCAACATATGACCTTCCGATAGTCACTGATGTGCACGAAAGCCACCAG                         TGTGAAGCTGTTGGAAGAGTTGCTGACATCATACAGATTCCAGCCTTCCTC
genomic: AAGCAACATATGACCTTCCGATAGTCACTGATGTGCACGAAAGCCACCAGgtaatccatt ... attaaatcagTGTGAAGCTGTTGGAAGAGTTGCTGACATCATACAGATTCCAGCCTTCCTC
EST: gi|211382425|gb|FK948866.1|FK948866
EST:     AAGCAACATATGACCTTCCGATAGTCACTGATGTGCACGAAAGCCACCAG                         TGTGAAGCTGTTGGAAGAGTTGCTGACATCATACAGATTCCAGCCTTCCTC
genomic: AAGCAACATATGACCTTCCGATAGTCACTGATGTGCACGAAAGCCACCAGgtaatccatt ... attaaatcagTGTGAAGCTGTTGGAAGAGTTGCTGACATCATACAGATTCCAGCCTTCCTC
EST: gi|6828178|gb|AW331821.1|AW331821
EST:     CGAAAGCCACCAG                         TGTGAAGCTGTTGGAAGAGTTGCTGACATCATACAGATTCCAGCCTTCCTC
genomic: CGAAAGCCACCAGgtaatccatt ... attaaatcagTGTGAAGCTGTTGGAAGAGTTGCTGACATCATACAGATTCCAGCCTTCCTC
EST: gi|71449637|gb|DR830687.1|DR830687
EST:     AAGCAACATATGACCTTCCGATAGTCACTGATGTGCACGAAAGCCACCAG                         TGTGAAGCTGTTGGAAGAGTTGCTGACATCATACAGATTCCAGCCTTCCTC
genomic: AAGCAACATATGACCTTCCGATAGTCACTGATGTGCACGAAAGCCACCAGgtaatccatt ... attaaatcagTGTGAAGCTGTTGGAAGAGTTGCTGACATCATACAGATTCCAGCCTTCCTC
EST: gi|26457480|gb|CA829063.1|CA829063
EST:     AAGCAACATATGACCTTCCGATAGTCACTGATGTGCACGAAAGCCACCAG                         TGTGAAGCTGTTGGAAGAGTTGCTGACATCATACAGATTCCAGCCTTCCTC
genomic: AAGCAACATATGACCTTCCGATAGTCACTGATGTGCACGAAAGCCACCAGgtaatccatt ... attaaatcagTGTGAAGCTGTTGGAAGAGTTGCTGACATCATACAGATTCCAGCCTTCCTC
EST: gi|91051935|gb|EB162353.1|EB162353
EST:     AAGCAACATATGACCTTCCGATAGTCACTGATGTGCACGAAAGCCACCAG                         TGTGAAGCTGTTGGAAGAGTTGCTGACATCATACAGATTCCAGCCTTCCTC
genomic: AAGCAACATATGACCTTCCGATAGTCACTGATGTGCACGAAAGCCACCAGgtaatccatt ... attaaatcagTGTGAAGCTGTTGGAAGAGTTGCTGACATCATACAGATTCCAGCCTTCCTC
EST: gi|211162593|gb|FL363072.1|FL363072
EST:     AAGCAACATATGACCTTCCGATAGTCACTGATGTGCACGAAAGCCACCAG                         TGTGAAGCTGTTGGAAGAGTTGCTGACATCATACAGATTCCAGCCTTCCTC
genomic: AAGCAACATATGACCTTCCGATAGTCACTGATGTGCACGAAAGCCACCAGgtaatccatt ... attaaatcagTGTGAAGCTGTTGGAAGAGTTGCTGACATCATACAGATTCCAGCCTTCCTC
EST: gi|116816629|gb|EC859381.1|EC859381
EST:     AAGCAACATATGACCTTCCGATAGTCACTGATGTGCACGAAAGCCACCAG                         TGTGAAGCTGTTGGAAGAGTTGCTGACATCATACA
genomic: AAGCAACATATGACCTTCCGATAGTCACTGATGTGCACGAAAGCCACCAGgtaatccatt ... attaaatcagTGTGAAGCTGTTGGAAGAGTTGCTGACATCATACA
EST: gi|61118195|gb|DN559156.1|DN559156
EST:     AAGCAACATATGACCTTCCGATAGTCACTGATGTGCACGAAAGCCACCAG                         TGTGAAGCTGTTGGAAGAGTTGCTGACATCATACAGATTCCAGCCTTCCTC
genomic: AAGCAACATATGACCTTCCGATAGTCACTGATGTGCACGAAAGCCACCAGgtaatccatt ... attaaatcagTGTGAAGCTGTTGGAAGAGTTGCTGACATCATACAGATTCCAGCCTTCCTC
EST: gi|31361455|gb|CD445812.1|CD445812
EST:     AAGCAACATATGACCTTCCGATAGTCACTGATGTGCACGAAAGCCACCAG                         TGTGAAGCTGTTGGAAGAGTTGCTGACATCATACAGATTCCAGCCTTCCTC
genomic: AAGCAACATATGACCTTCCGATAGTCACTGATGTGCACGAAAGCCACCAGgtaatccatt ... attaaatcagTGTGAAGCTGTTGGAAGAGTTGCTGACATCATACAGATTCCAGCCTTCCTC
EST: gi|211382426|gb|FK948867.1|FK948867
EST:     AAGCAACATATGACCTTCCGATAGTCACTGATGTGCACGAAAGCCACCAG                         TGTGAAGCTGTTGGAAGAGTTGCTGACATCATACAGATTCCAGCCTTCCTC
genomic: AAGCAACATATGACCTTCCGATAGTCACTGATGTGCACGAAAGCCACCAGgtaatccatt ... attaaatcagTGTGAAGCTGTTGGAAGAGTTGCTGACATCATACAGATTCCAGCCTTCCTC
EST: gi|211215731|gb|FL322482.1|FL322482
EST:     AAGCAACATATGACCTTCCGATAGTCACTGATGTGCACGAAAGCCACCAG                         TGTGAAGCTGTTGGAAGAGTTGCTGACATCATACAGATTCCAGCCTTCCTC
genomic: AAGCAACATATGACCTTCCGATAGTCACTGATGTGCACGAAAGCCACCAGgtaatccatt ... attaaatcagTGTGAAGCTGTTGGAAGAGTTGCTGACATCATACAGATTCCAGCCTTCCTC
EST: gi|21626200|gb|BQ621121.1|BQ621121
EST:     AAGCAACATATGACCTTCCGATAGTCACTGATGTGCACGAAAGCCACCAG                         TGTGAAGCTGTTGGAAG
genomic: AAGCAACATATGACCTTCCGATAGTCACTGATGTGCACGAAAGCCACCAGgtaatccatt ... attaaatcagTGTGAAGCTGTTGGAAG

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: 104

ATCCTTCAAAAGGTGAAAGCAACATATGACCTTCCGATAGTCACTGATGTGCACGAAAGCCACCAGgtaatccatt ... attaaatcagTGTGAAGCTGTTGGAAGAGTTGCTGACATCATACAGATTCCAGCCTTCCTCTGTCGCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 108

ATCCTTCAAAAGGTGAAAGCAACATATGACCTTCCGATAGTCACTGATGTGCACGAAAGCCACCAGgtaatccatt ... attaaatcagTGTGAAGCTGTTGGAAGAGTTGCTGACATCATACAGATTCCAGCCTTCCTCTGTCGCCAG


Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 73

ATCCTTCAAAAGGTGAAAGCAACATATGACCTTCCGATAGTCACTGATGTGCACGAAAGCCACCAGgtaatccatt ... attaaatcagTGTGAAGCTGTTGGAAGAGTTGCTGACATCATACAGATTCCAGCCTTCCTCTGTCGCCAG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 63

ATCCTTCAAAAGGTGAAAGCAACATATGACCTTCCGATAGTCACTGATGTGCACGAAAGCCACCAGgtaatccatt ... attaaatcagTGTGAAGCTGTTGGAAGAGTTGCTGACATCATACAGATTCCAGCCTTCCTCTGTCGCCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCCTTCAAAAGGTGAAAGCAACATATGACCTTCCGATAGTCACTGATGTGCACGAAAGCCACCAGgtaatccattcacagattctactgtgttaacacccaattttgcttgattctgcaccagatcatgtttctgttgtacttttgtactgtaagacatgtttcc

- - - - - - - - AAGCAA