Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGAAGTAGTAACGAGAATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAGgtacctcgaaagcatcaattaaattatgcaaaaacccttttagacttgcattttctttccatttagttgttcaacaaccttaactgtatggttctggtatgctcag

Basic information

species Zea mays
transcript GRMZM2G520535_T01
intron # 4
splice site 5'
intron type U2

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|74236044|gb|DT643958.1|DT643958
EST:     AGTAACGAGAATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAG                         AAAATGGCGAATCCATTCAGATATTACACTACCAGAATGGTGAGAAATATG
genomic: AGTAACGAGAATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAGgtacctcgaa ... gtatgctcagAAAATGGCGAATCCATTCAGATATTACACTACCAGAATGGTGAGAAATATG
EST: gi|31360260|gb|CD444617.1|CD444617
EST:     AGTAACGAGAATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAG                         AAAATGGCGAATCCATTCAGATATTACACTACCAGAATGGTGAGAAATATG
genomic: AGTAACGAGAATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAGgtacctcgaa ... gtatgctcagAAAATGGCGAATCCATTCAGATATTACACTACCAGAATGGTGAGAAATATG
EST: gi|60355536|gb|DN222509.1|DN222509
EST:     AGGAGAGGATATCTGCTTGGACATTTCTTCCACCAG                         AAAATGGCGAATCCATTCAGATATTACACTACCAGAATGGTGAGAAATATG
genomic: AGGAGAGGATATCTGCTTGGACATTTCTTCCACCAGgtacctcgaa ... gtatgctcagAAAATGGCGAATCCATTCAGATATTACACTACCAGAATGGTGAGAAATATG
EST: gi|211451195|gb|FL002405.1|FL002405
EST:     AGTAACGAGAATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAG                         AAAATGGCGAATCCATTCAGATATTACACTA
genomic: AGTAACGAGAATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAGgtacctcgaa ... gtatgctcagAAAATGGCGAATCCATTCAGATATTACACTA
EST: gi|211449078|gb|FL002398.1|FL002398
EST:     AGTAACGAGAATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAG                         AAAATGGCGAATCCATTCAGATATTACACTACCAGAATGGTGAGAAATATG
genomic: AGTAACGAGAATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAGgtacctcgaa ... gtatgctcagAAAATGGCGAATCCATTCAGATATTACACTACCAGAATGGTGAGAAATATG
EST: gi|211449073|gb|FL002393.1|FL002393
EST:     AGTAACGAGAATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAG                         AAAATGGCGAATCCATTCAGATATTACACTACCAGA
genomic: AGTAACGAGAATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAGgtacctcgaa ... gtatgctcagAAAATGGCGAATCCATTCAGATATTACACTACCAGA
EST: gi|7958433|gb|AW862735.1|AW862735
EST:     AGTAACGAGAATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAG                         AAAATGGCGAATCCATTCAGATATTACACTACCAGAATG
genomic: AGTAACGAGAATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAGgtacctcgaa ... gtatgctcagAAAATGGCGAATCCATTCAGATATTACACTACCAGAATG
EST: gi|211446954|gb|FL002385.1|FL002385
EST:     AGTAACGAGAATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAG                         AAAATGGCGAATCCATTCAGATATTACACTACCAGAATGGTGAGAAATATG
genomic: AGTAACGAGAATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAGgtacctcgaa ... gtatgctcagAAAATGGCGAATCCATTCAGATATTACACTACCAGAATGGTGAGAAATATG
EST: gi|211451194|gb|FL002404.1|FL002404
EST:     AGTAACGAGAATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAG                         AAAATGGCGAATCCATTCAGATATTACACTACCAGAATGGTGAGAAATATG
genomic: AGTAACGAGAATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAGgtacctcgaa ... gtatgctcagAAAATGGCGAATCCATTCAGATATTACACTACCAGAATGGTGAGAAATATG
EST: gi|211039974|gb|FL073405.1|FL073405
EST:     AGTAACGAGAATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAG                         AAAATGGCGAATCCATTCAGATATTACACTACCAGAATGGTGAGAAATATG
genomic: AGTAACGAGAATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAGgtacctcgaa ... gtatgctcagAAAATGGCGAATCCATTCAGATATTACACTACCAGAATGGTGAGAAATATG
EST: gi|149014492|gb|EE044118.2|EE044118
EST:     AGTAACGAGAATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAG                         AAAATGGCGAATCCATTCAGATATTACACTACCAGAATGGTGAGAAATATG
genomic: AGTAACGAGAATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAGgtacctcgaa ... gtatgctcagAAAATGGCGAATCCATTCAGATATTACACTACCAGAATGGTGAGAAATATG
EST: gi|7844161|gb|AW787383.1|AW787383
EST:     AGTAACGAGAATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAG                         AAAATGGCGAATCCATTCAGATATTACACTACCAGAATGGTGAGA
genomic: AGTAACGAGAATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAGgtacctcgaa ... gtatgctcagAAAATGGCGAATCCATTCAGATATTACACTACCAGAATGGTGAGA
EST: gi|211446953|gb|FL002384.1|FL002384
EST:     AGTAACGAGAATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAG                         AAAATGGCGAATCCATTCAGATATTACACTACCAGAATGGTGAGAAATATG
genomic: AGTAACGAGAATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAGgtacctcgaa ... gtatgctcagAAAATGGCGAATCCATTCAGATATTACACTACCAGAATGGTGAGAAATATG
EST: gi|71320428|gb|DR796958.1|DR796958
EST:     AGTAACGAGAATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAG                         AAAATGGCGAATCCATTCAGATATTACACTACCAGAATGGTGAGAAATATG
genomic: AGTAACGAGAATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAGgtacctcgaa ... gtatgctcagAAAATGGCGAATCCATTCAGATATTACACTACCAGAATGGTGAGAAATATG
EST: gi|211446956|gb|FL002387.1|FL002387
EST:     AGTAACGAGAATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAG                         AAAATGGCGAATCCATTCAGATATTACACTACCAG
genomic: AGTAACGAGAATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAGgtacctcgaa ... gtatgctcagAAAATGGCGAATCCATTCAGATATTACACTACCAG
EST: gi|211449082|gb|FL002402.1|FL002402
EST:     GTWACGAGAATAGAGGAGAAGGATATCTGCTTGGACATTTCTTCCACCAG                         AAAAATGGCGAATC
genomic: GTAACGAGAATAGAGGAGA-GGATATCTGCTTGGACATTTCTTCCACCAGgtacctcgaa ... gtatgctcagAAAA-TGGCGAATC
EST: gi|211039976|gb|FL073407.1|FL073407
EST:     AGTAACGAAAATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAG                         AAAATGGCGAATCCATTCAGATATTACACTACCAGAATGGTGAGAAATATG
genomic: AGTAACGAGAATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAGgtacctcgaa ... gtatgctcagAAAATGGCGAATCCATTCAGATATTACACTACCAGAATGGTGAGAAATATG
EST: gi|7844162|gb|AW787384.1|AW787384
EST:     AGTAACGAGAATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAG                         AAAATGGCGAATCCATTCAGATATTACACTACCAGAATGGTGAGAAATATG
genomic: AGTAACGAGAATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAGgtacctcgaa ... gtatgctcagAAAATGGCGAATCCATTCAGATATTACACTACCAGAATGGTGAGAAATATG
EST: gi|148951226|gb|EC896920.2|EC896920
EST:     AGTAACGAGAATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAG                         AAAATGGCGAATCCATTCAGATATTACACTACCAGAATGGTGAGAAATATG
genomic: AGTAACGAGAATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAGgtacctcgaa ... gtatgctcagAAAATGGCGAATCCATTCAGATATTACACTACCAGAATGGTGAGAAATATG
EST: gi|211446955|gb|FL002386.1|FL002386
EST:     AGTAACGAAAATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAG                         AAAATGGCGAATCCATTCAGATATTACACTACCAGAATGGTGAGAAATATG
genomic: AGTAACGAGAATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAGgtacctcgaa ... gtatgctcagAAAATGGCGAATCCATTCAGATATTACACTACCAGAATGGTGAGAAATATG
EST: gi|76019346|gb|DT946516.1|DT946516
EST:     AGTAACGAGAATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAG                         AAAATGGCGAATCCATTCAGATATTACACTACCAGAATGGTGAGAAATATG
genomic: AGTAACGAGAATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAGgtacctcgaa ... gtatgctcagAAAATGGCGAATCCATTCAGATATTACACTACCAGAATGGTGAGAAATATG
EST: gi|211449068|gb|FL002388.1|FL002388
EST:     AGTAACGAAAATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAG                         AAAATGGCGAATCCATTCAGATATTACACTACCAGAATGGTGAGAAATATG
genomic: AGTAACGAGAATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAGgtacctcgaa ... gtatgctcagAAAATGGCGAATCCATTCAGATATTACACTACCAGAATGGTGAGAAATATG
EST: gi|71328190|gb|DR800733.1|DR800733
EST:     AGTAACGAGAATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAG                         AAAATGGCGAATCCATTCAGATATTACACTACCAGAATGGTGAGAAATATG
genomic: AGTAACGAGAATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAGgtacctcgaa ... gtatgctcagAAAATGGCGAATCCATTCAGATATTACACTACCAGAATGGTGAGAAATATG
EST: gi|211449072|gb|FL002392.1|FL002392
EST:     AGTAACGAGAATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAG                         AAAATGGCGAATCCATTCAGATATTACACTACCAGAATGGKGAGAAATATG
genomic: AGTAACGAGAATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAGgtacctcgaa ... gtatgctcagAAAATGGCGAATCCATTCAGATATTACACTACCAGAATGGTGAGAAATATG
EST: gi|71442480|gb|DR823530.1|DR823530
EST:     AGTAACGAGAATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAG                         AAAATGGCGAATCCATTCAGATATTACACTACCAGAATGGTGAGAAATATG
genomic: AGTAACGAGAATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAGgtacctcgaa ... gtatgctcagAAAATGGCGAATCCATTCAGATATTACACTACCAGAATGGTGAGAAATATG
EST: gi|31353117|gb|CD437474.1|CD437474
EST:     AGTAACGAGAATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAG                         AAAATGGCGAATCCATTCAGATATTACACTACCAGAATGGTGAGAAATATG
genomic: AGTAACGAGAATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAGgtacctcgaa ... gtatgctcagAAAATGGCGAATCCATTCAGATATTACACTACCAGAATGGTGAGAAATATG
EST: gi|78180250|gb|DV550623.1|DV550623
EST:     AGTAACGAGAATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAG                         AAAATGGCGAATCCATTCAGATATTACACTACCAGAATGGTGAGAAATATG
genomic: AGTAACGAGAATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAGgtacctcgaa ... gtatgctcagAAAATGGCGAATCCATTCAGATATTACACTACCAGAATGGTGAGAAATATG
EST: gi|211039973|gb|FL073404.1|FL073404
EST:     AGTAACGAGAATAGAGGAGAGGATATCTGCTTGGACATTTCTYCCACCAG                         AAAATGGCGAATCCATTCAGATATTACACTACCAGAATGGTGAGAAATATG
genomic: AGTAACGAGAATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAGgtacctcgaa ... gtatgctcagAAAATGGCGAATCCATTCAGATATTACACTACCAGAATGGTGAGAAATATG
EST: gi|211039977|gb|FL073408.1|FL073408
EST:     AGTAACGAAAATAAAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAG                         AAAATGGCGAATCCATTCAGATATTACACTACCAGAATGGCGAGAAATATG
genomic: AGTAACGAGAATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAGgtacctcgaa ... gtatgctcagAAAATGGCGAATCCATTCAGATATTACACTACCAGAATGGTGAGAAATATG
EST: gi|211039972|gb|FL073403.1|FL073403
EST:     AGTAACGAGAATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAG                         AAAATGGCGAATCCATTCAGATATTACACTACCAGAATGGTGAGAAATATG
genomic: AGTAACGAGAATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAGgtacctcgaa ... gtatgctcagAAAATGGCGAATCCATTCAGATATTACACTACCAGAATGGTGAGAAATATG
EST: gi|89250537|gb|DY622323.1|DY622323
EST:     AGTAACGAGAATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAG                         AAAATGGCGAATCCATTCAGATATTACACTACCAGAATGGTGAGAAATATG
genomic: AGTAACGAGAATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAGgtacctcgaa ... gtatgctcagAAAATGGCGAATCCATTCAGATATTACACTACCAGAATGGTGAGAAATATG
EST: gi|76287083|gb|DV026651.1|DV026651
EST:     AGTAACGAGAATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAG                         AAAATGGCGAATCCATTCAGATATTACACTACCAGAATGGTGAGAAATATG
genomic: AGTAACGAGAATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAGgtacctcgaa ... gtatgctcagAAAATGGCGAATCCATTCAGATATTACACTACCAGAATGGTGAGAAATATG
EST: gi|211449075|gb|FL002395.1|FL002395
EST:     AGTAACGAGAATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAG                         AAAATGGCGAATCCATTCAGATATTACACTACCAGAATGGTGA
genomic: AGTAACGAGAATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAGgtacctcgaa ... gtatgctcagAAAATGGCGAATCCATTCAGATATTACACTACCAGAATGGTGA
EST: gi|74236045|gb|DT643959.1|DT643959
EST:     AGTAACGAGAATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAG                         AAAATGGCGAATCCATTCAGATATTACACTACCAGAATGGTGAGAAATATG
genomic: AGTAACGAGAATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAGgtacctcgaa ... gtatgctcagAAAATGGCGAATCCATTCAGATATTACACTACCAGAATGGTGAGAAATATG

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: 338

GATGAAGTAGTAACGAGAATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAGgtacctcgaa ... gtatgctcagAAAATGGCGAATCCATTCAGATATTACACTACCAGAATGGTGAGAAATATGAACCCCACTACGACTACTTCCATGACAAAAAAAATCAAGCCTTGGGTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 257

GATGAAGTAGTAACGAGAATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAGgtacctcgaa ... gtatgctcagAAAATGGCGAATCCATTCAGATATTACACTACCAGAATGGTGAGAAATATGAACCCCACTACGACTACTTCCATGACAAAAAAAATCAAGCCTTGGGTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 246

GATGAAGTAGTAACGAGAATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAGgtacctcgaa ... gtatgctcagAAAATGGCGAATCCATTCAGATATTACACTACCAGAATGGTGAGAAATATGAACCCCACTACGACTACTTCCATGACAAAAAAAATCAAGCCTTGGGTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 316

GATGAAGTAGTAACGAGAATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAGgtacctcgaa ... gtatgctcagAAAATGGCGAATCCATTCAGATATTACACTACCAGAATGGTGAGAAATATGAACCCCACTACGACTACTTCCATGACAAAAAAAATCAAGCCTTGGGTGG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGAAGTAGTAACGAGAATAGAGGAGAGGATATCTGCTTGGACATTTCTTCCACCAGgtacctcgaaagcatcaattaaattatgcaaaaacccttttagacttgcattttctttccatttagttgttcaacaaccttaactgtatggttctggtatgctcag

- - - - - - - - - - AGAGGA
- - - - - - - - - -  GAGGAG
- - - - - - - - - - - AGGAGA
- - - - - - - - - - - - GAGAGG
- - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - GAGGAT