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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAAAAAAATCAAGCCTTGGGTGGCCATCGCATCGCCACTGTGCTGATGTACCTCTCTAATGTTGAGAAGGGTGGAGAGACCATCTTCCCCAATGCAGAGgtagtttgcttgtccttcctgtgtttactgtcttaagaatgccagttgtaacaacttcaacattcaatag

Basic information

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

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G520535_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os10g27340.2 (Oryza sativa), 5'ss of exon 5
CAAAAAAAATCAAGCCTTGGGTGGCCATCGCATCGCCACTGTGCTGATGTACCTCTCTAATGTTGAGAAGGGTGGAGAGACCATCTTCCCCAATGCAGAGgtagtttgcttgtccttcctg--tgtttactgtcttaa------gaatgccagttgtaacaacttcaacattcaatag--
|||||| ||||||||  | || || ||||| |||||||||||||| |||||||| ||  | |||| |||||| |||||||||||||| ||  | ||||||||||||| | ||||||   |   | | ||| || |||       | ||  |  ||| |  ||||  |  |||   |    
CAAAAATAATCAAGCTCTTGGAGGACATCGGATCGCCACTGTGCTCATGTACCTTTCAGACGTTGGGAAGGGGGGAGAGACCATCTTTCCAGAAGCAGAGgtagtttacctgtcctctttaactttctacagtgttagccacttggatttcccttgcagtaactcgactattttttttag

upper sequence: GRMZM2G520535_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA19G02110.1 (Glycine max), 5'ss of exon 6
CAAAAAAAATCAAGCCTTGGGTGGCCATCGCATCGCCACTGTGCTGATGTACCTCTCTAATGTTGAGAAGGGTGGAGAGACCATCTTCCCCAATGCAGAGgtagtttgcttgtccttcctgtg-tttactg--------tcttaagaatgccagttgtaacaacttcaacattcaatag----------------------------------------------
||||   |||||||   ||||||||||||| || ||||||||  |||||||  | ||| |||||||||||||||| || || || || |||||||| ||||||      || || |  || || ||  |||        | ||||  |  ||  | |   |  |  |   ||  || ||                                              
CAAAGCTAATCAAGTTATGGGTGGCCATCGGATTGCCACTGTATTGATGTATTTGTCTGATGTTGAGAAGGGTGGGGAAACAATTTTTCCCAATGCCGAGgtaaagattttctcatggctttgattctctgatgtttccttttaaagaaacccctggctccctcccctcaatcaaaaagaataaaagaaaaatgaaatcgtaattaatttgttttgccttttcag
















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:     ACCTCTCTAATGTTGAGAAGGGTGGAGAGACCATCTTCCCCAATGCAGAG                         GGGAAGCTATTACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAAT
genomic: ACCTCTCTAATGTTGAGAAGGGTGGAGAGACCATCTTCCCCAATGCAGAGgtagtttgct ... cattcaatagGGGAAGCTATTACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAAT
EST: gi|71442479|gb|DR823529.1|DR823529
EST:     ACCTCTCTAATGTTGAGAAGGGTGGAGAGACCATCTTCCCCAATGCAGAG                         GGGAAGCTATTACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAAT
genomic: ACCTCTCTAATGTTGAGAAGGGTGGAGAGACCATCTTCCCCAATGCAGAGgtagtttgct ... cattcaatagGGGAAGCTATTACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAAT
EST: gi|31360260|gb|CD444617.1|CD444617
EST:     ACCTCTCTAATGTTGAGAAGGGTGGAGAGACCATCTTCCCCAATGCAGAG                         GGGAAGCTATTACAACCGAAGGACAACACTTGGTCTGATT
genomic: ACCTCTCTAATGTTGAGAAGGGTGGAGAGACCATCTTCCCCAATGCAGAGgtagtttgct ... cattcaatagGGGAAGCTATTACAACCGAAGGACAACACTTGGTCTGATT
EST: gi|60355536|gb|DN222509.1|DN222509
EST:     ACCTCTCTAATGTTGAGAAGGGTGGAGAGACCATCTTCCCCAATGCAGAG                         GGGAAGCTATTACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAAT
genomic: ACCTCTCTAATGTTGAGAAGGGTGGAGAGACCATCTTCCCCAATGCAGAGgtagtttgct ... cattcaatagGGGAAGCTATTACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAAT
EST: gi|211251396|gb|FL479077.1|FL479077
EST:     ACCTCTCTAATGTTGAGAAGGGTGGAGAGACCATCTTCCCCAATGCAGAG                         GGGAAGCTATTACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAAT
genomic: ACCTCTCTAATGTTGAGAAGGGTGGAGAGACCATCTTCCCCAATGCAGAGgtagtttgct ... cattcaatagGGGAAGCTATTACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAAT
EST: gi|211039974|gb|FL073405.1|FL073405
EST:     ACCTCTCTAATGTTGAGAAGGGTGGAGAGACCATCTTCCCCAATGCAGAG                         GGGAAGCTATTACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAAT
genomic: ACCTCTCTAATGTTGAGAAGGGTGGAGAGACCATCTTCCCCAATGCAGAGgtagtttgct ... cattcaatagGGGAAGCTATTACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAAT
EST: gi|149014492|gb|EE044118.2|EE044118
EST:     ACCTCTCTAATGTTGAGAAGGGTGGAGAGACCATCTTCCCCAATGCAGAG                         GGGAAGCTATTACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAAT
genomic: ACCTCTCTAATGTTGAGAAGGGTGGAGAGACCATCTTCCCCAATGCAGAGgtagtttgct ... cattcaatagGGGAAGCTATTACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAAT
EST: gi|71320428|gb|DR796958.1|DR796958
EST:     ACCTCTCTAATGTTGAGAAGGGTGGAGAGACCATCTTCCCCAATGCAGAG                         GGGAAGCTATTACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAAT
genomic: ACCTCTCTAATGTTGAGAAGGGTGGAGAGACCATCTTCCCCAATGCAGAGgtagtttgct ... cattcaatagGGGAAGCTATTACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAAT
EST: gi|148951226|gb|EC896920.2|EC896920
EST:     ACCTCTCTAATGTTGAGAAGGGTGGAGAGACCATCTTCCCCAATGCAGAG                         GGGAAGCTATTACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAAT
genomic: ACCTCTCTAATGTTGAGAAGGGTGGAGAGACCATCTTCCCCAATGCAGAGgtagtttgct ... cattcaatagGGGAAGCTATTACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAAT
EST: gi|76019346|gb|DT946516.1|DT946516
EST:     ACCTCTCTAATGTTGAGAAGGGTGGAGAGACCATCTTCCCCAATGCAGAG                         GGGAAGCTATTACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAAT
genomic: ACCTCTCTAATGTTGAGAAGGGTGGAGAGACCATCTTCCCCAATGCAGAGgtagtttgct ... cattcaatagGGGAAGCTATTACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAAT
EST: gi|60399600|gb|DN232411.1|DN232411
EST:     ACCTCTCTAATGTTGAGAAGGGTGGAGAGACCATCTTCCCCAATGCAGAG                         GGGAAGCTATTACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAAT
genomic: ACCTCTCTAATGTTGAGAAGGGTGGAGAGACCATCTTCCCCAATGCAGAGgtagtttgct ... cattcaatagGGGAAGCTATTACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAAT
EST: gi|71328190|gb|DR800733.1|DR800733
EST:     ACCTCTCTAATGTTGAGAAGGGTGGAGAGACCATCTTCCCCAATGCAGAG                         GGGAAGCTATTACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAAT
genomic: ACCTCTCTAATGTTGAGAAGGGTGGAGAGACCATCTTCCCCAATGCAGAGgtagtttgct ... cattcaatagGGGAAGCTATTACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAAT
EST: gi|71442480|gb|DR823530.1|DR823530
EST:     ACCTCTCTAATGTTGAGAAGGGTGGAGAGACCATCTTCCCCAATGCAGAG                         GGGAAGCTATTACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAAT
genomic: ACCTCTCTAATGTTGAGAAGGGTGGAGAGACCATCTTCCCCAATGCAGAGgtagtttgct ... cattcaatagGGGAAGCTATTACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAAT
EST: gi|31353117|gb|CD437474.1|CD437474
EST:     ACCTCTCTAATGTTGAGAAGGGTGGAGAGACCATCTTCCCCAATGCAGAG                         GGGAAGCTATTACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAAT
genomic: ACCTCTCTAATGTTGAGAAGGGTGGAGAGACCATCTTCCCCAATGCAGAGgtagtttgct ... cattcaatagGGGAAGCTATTACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAAT
EST: gi|78180250|gb|DV550623.1|DV550623
EST:     ACCTCTCTAATGTTGAGAAGGGTGGAGAGACCATCTTCCCCAATGCAGAG                         GGGAAGCTATTACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAAT
genomic: ACCTCTCTAATGTTGAGAAGGGTGGAGAGACCATCTTCCCCAATGCAGAGgtagtttgct ... cattcaatagGGGAAGCTATTACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAAT
EST: gi|76287083|gb|DV026651.1|DV026651
EST:     ACCTCTCTAATGTTGAGAAGGGTGGAGAGACCATCTTCCCCAATGCAGAG                         GGGAAGCTATTACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAAT
genomic: ACCTCTCTAATGTTGAGAAGGGTGGAGAGACCATCTTCCCCAATGCAGAGgtagtttgct ... cattcaatagGGGAAGCTATTACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAAT
EST: gi|71320427|gb|DR796957.1|DR796957
EST:     ACCTCTCTAATGTTGAGAAGGGTGGAGAGACCATCTTCCCCAATGCAGAG                         GGGAAGCTATTACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAAT
genomic: ACCTCTCTAATGTTGAGAAGGGTGGAGAGACCATCTTCCCCAATGCAGAGgtagtttgct ... cattcaatagGGGAAGCTATTACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAAT
EST: gi|32866418|gb|CF006100.1|CF006100
EST:     CTTCCCCAATGCAGAG                         GGGAAGCTATTACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAAT
genomic: CTTCCCCAATGCAGAGgtagtttgct ... cattcaatagGGGAAGCTATTACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAAT
EST: gi|74236045|gb|DT643959.1|DT643959
EST:     ACCTCTCTAATGTTGAGAAGGGTGGAGAGACCATCTTCCCCAATGCAGAG                         GGGAAGCTATTACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAAT
genomic: ACCTCTCTAATGTTGAGAAGGGTGGAGAGACCATCTTCCCCAATGCAGAGgtagtttgct ... cattcaatagGGGAAGCTATTACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAAT

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), 48 (downstream exon)
Score: 279

CAAAAAAAATCAAGCCTTGGGTGGCCATCGCATCGCCACTGTGCTGATGTACCTCTCTAATGTTGAGAAGGGTGGAGAGACCATCTTCCCCAATGCAGAGgtagtttgct ... cattcaatagGGGAAGCTATTACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAATGGATATGCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 161

CAAAAAAAATCAAGCCTTGGGTGGCCATCGCATCGCCACTGTGCTGATGTACCTCTCTAATGTTGAGAAGGGTGGAGAGACCATCTTCCCCAATGCAGAGgtagtttgct ... cattcaatagGGGAAGCTATTACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAATGGATATGCAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 153

CAAAAAAAATCAAGCCTTGGGTGGCCATCGCATCGCCACTGTGCTGATGTACCTCTCTAATGTTGAGAAGGGTGGAGAGACCATCTTCCCCAATGCAGAGgtagtttgct ... cattcaatagGGGAAGCTATTACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAATGGATATGCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 182

CAAAAAAAATCAAGCCTTGGGTGGCCATCGCATCGCCACTGTGCTGATGTACCTCTCTAATGTTGAGAAGGGTGGAGAGACCATCTTCCCCAATGCAGAGgtagtttgct ... cattcaatagGGGAAGCTATTACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAATGGATATGCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAAAAAAATCAAGCCTTGGGTGGCCATCGCATCGCCACTGTGCTGATGTACCTCTCTAATGTTGAGAAGGGTGGAGAGACCATCTTCCCCAATGCAGAGgtagtttgcttgtccttcctgtgtttactgtcttaagaatgccagttgtaacaacttcaacattcaatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA