Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATGCTATTTGAGCTGCACAATGATGCAACCCAGCGGATTTCACACTGTGGTGTTTTGGAGTTTGTTGCAGAAGAAGGCATGATCATCATGCCCTATTGGgtatgtataaaaggataactcagttcacttgtatcttctgttatatggcgaaagaaatatgtctatacttatttattttatgtattctcacttgtttag

Basic information

species Zea mays
transcript GRMZM2G114220_T02
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G114220_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os04g48770.2 (Oryza sativa), 5'ss of exon 2
TATGCTATTTGAGCTGCACAATGATGCAACCCAGCGGATTTCACACTGTGGTGTTTTGGAGTTTGTTGCAGAAGAAGGCATGATCATCATGCCCTATTGGgtatgta-taaaaggataactcagttcacttgtatcttctgttatatggcgaaagaaatatgtctatacttatttattttatg-tattctcacttgtttag--
|||||| |||||| |||| ||||||||||| |||||||||||||||||||||||  |||| ||||| ||||||||||||||||||||||||||||| |||||||||| ||    |   | |   || |||  ||||| |  ||||||  | ||||||| || |  |  || ||||||  |||  |  | |||  | | |    
TATGCTGTTTGAGTTGCATAATGATGCAACTCAGCGGATTTCACACTGTGGTGTGCTGGAATTTGTGGCAGAAGAAGGCATGATCATCATGCCCTACTGGgtatgtaatatgcagtggattttctttactgatatctgcaattatattcc-aaagaaacatattga--ctgatttatgctataattctttcatatatgtgcag
















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|76909136|gb|DV163240.1|DV163240
EST:     GTGTTTTGGAGTTTGTTGCAGAAGAAGGCATGATCATCATGCCCTATTGG                         ATGATGCAAAACATGCTGCTTCAAGAGGGTGACACTGTCCATGTAAAAAAT
genomic: GTGTTTTGGAGTTTGTTGCAGAAGAAGGCATGATCATCATGCCCTATTGGgtatgtataa ... acttgtttagATGATGCAAAACATGCTGCTTCAAGAGGGTGACACTGTCCATGTAAAAAAT
EST: gi|211395124|gb|FL156801.1|FL156801
EST:     GTGTTTTGGAGTTTGTTGCAGAAGAAGGCATGATCATCATGCCCTATTGG                         ATGATGCAAAACATGCTGCTTNCA-GAGGGTGACACTGGTC-ATGTAAAAA
genomic: GTGTTTTGGAGTTTGTTGCAGAAGAAGGCATGATCATCATGCCCTATTGGgtatgtataa ... acttgtttagATGATGCAAAACATGCTGCTT-CAAGAGGGTGACACTG-TCCATGTAAAAA
EST: gi|91873355|gb|EB403312.1|EB403312
EST:     GTGTTTTGGAGTTTGTTGCAGAAGAAGGCATGATCATCATGCCCTATTGG                         ATGATGCAAAACATGCTGCTTCAAGAGGGTGACACTGTCCATGTAAAAAAT
genomic: GTGTTTTGGAGTTTGTTGCAGAAGAAGGCATGATCATCATGCCCTATTGGgtatgtataa ... acttgtttagATGATGCAAAACATGCTGCTTCAAGAGGGTGACACTGTCCATGTAAAAAAT
EST: gi|14242735|gb|BG840580.2|BG840580
EST:     GTGTTTTGGAGTTTGTTGCAGAAGAAGGCATGATCATCATGCCCTATTGG                         ATGATGCAAAACATGCTGCTTCAAGAGGGTGACACTGTCCATGTAAAAAAT
genomic: GTGTTTTGGAGTTTGTTGCAGAAGAAGGCATGATCATCATGCCCTATTGGgtatgtataa ... acttgtttagATGATGCAAAACATGCTGCTTCAAGAGGGTGACACTGTCCATGTAAAAAAT
EST: gi|32850146|gb|CD989827.1|CD989827
EST:     GTGTTTTGGAGTTTGTTGCAGAAGAAGGCATGATCATCATGCCCTATTGG                         ATGATGCAAAACATGCTGCTTCAAGAGGGTGACACTGTCCATGTAAAAAAT
genomic: GTGTTTTGGAGTTTGTTGCAGAAGAAGGCATGATCATCATGCCCTATTGGgtatgtataa ... acttgtttagATGATGCAAAACATGCTGCTTCAAGAGGGTGACACTGTCCATGTAAAAAAT
EST: gi|71417924|gb|DR804257.1|DR804257
EST:     GTGTTTTGGAGTTTGTTGCAGAAGAAGGCATGATCATCATGCCCTATTGG                         ATGATGCAAAACATGCTGCTTCAAGAGGGTGACACTGTCCATGTAAAAAAT
genomic: GTGTTTTGGAGTTTGTTGCAGAAGAAGGCATGATCATCATGCCCTATTGGgtatgtataa ... acttgtttagATGATGCAAAACATGCTGCTTCAAGAGGGTGACACTGTCCATGTAAAAAAT
EST: gi|50338446|gb|CO533572.1|CO533572
EST:     GTGTTTTGGAGTTTGTTGCAGAAGAAGGCATGATCATCATGCCCTATTGG                         ATGATGCAAAACATGCTGCTTCAAGAGGGTGACACTGTCCATGTA
genomic: GTGTTTTGGAGTTTGTTGCAGAAGAAGGCATGATCATCATGCCCTATTGGgtatgtataa ... acttgtttagATGATGCAAAACATGCTGCTTCAAGAGGGTGACACTGTCCATGTA
EST: gi|211389876|gb|FL156781.1|FL156781
EST:     GTGTTTTGGAGTTTGTTGCAGAAGAAGGCATGATCATCATGCC-TATTGG                         ATGATGCAAAACATGCT
genomic: GTGTTTTGGAGTTTGTTGCAGAAGAAGGCATGATCATCATGCCCTATTGGgtatgtataa ... acttgtttagATGATGCAAAACATGCT
EST: gi|93015584|gb|EB641104.1|EB641104
EST:     GTGTTTTGGAGTTTGTTGCAGAAGAAGGCATGATCATCATGCCCTATTGG                         ATGATGCAAAACATGCTGCTTCAAGAGGGTGACACTGTCCATGTAAAAAAT
genomic: GTGTTTTGGAGTTTGTTGCAGAAGAAGGCATGATCATCATGCCCTATTGGgtatgtataa ... acttgtttagATGATGCAAAACATGCTGCTTCAAGAGGGTGACACTGTCCATGTAAAAAAT
EST: gi|32862738|gb|CF002420.1|CF002420
EST:     GTGTTTTGGAGTTTGTTGCAGAAGAAGGCATGATCATCATGCCCTATTGG                         ATGATGCAAAACATGCTGCTTCAAGAGGGTGACACTGTCCATGTAAAAAAT
genomic: GTGTTTTGGAGTTTGTTGCAGAAGAAGGCATGATCATCATGCCCTATTGGgtatgtataa ... acttgtttagATGATGCAAAACATGCTGCTTCAAGAGGGTGACACTGTCCATGTAAAAAAT
EST: gi|91049005|gb|EB159423.1|EB159423
EST:     GTGTTTTGGAGTTTGTTGCAGAAGAAGGCATGATCATCATGCCCTATTGG                         ATGATGCAAAACATGCTGCTTCAAGAGGGTGACACTGTCCATGTAAAAAAT
genomic: GTGTTTTGGAGTTTGTTGCAGAAGAAGGCATGATCATCATGCCCTATTGGgtatgtataa ... acttgtttagATGATGCAAAACATGCTGCTTCAAGAGGGTGACACTGTCCATGTAAAAAAT
EST: gi|6637070|gb|AW261342.1|AW261342
EST:     GTGTTTTGGAGTTTGTTGCAGAAGAAGGCATGATCATCATGCCCTATTGG                         ATGATGCAAAACATGCTGCTTCAAGAGGGTGACACTGTCCATGTCAAAAAT
genomic: GTGTTTTGGAGTTTGTTGCAGAAGAAGGCATGATCATCATGCCCTATTGGgtatgtataa ... acttgtttagATGATGCAAAACATGCTGCTTCAAGAGGGTGACACTGTCCATGTAAAAAAT
EST: gi|211392499|gb|FL156788.1|FL156788
EST:     GTGTTTTGGAGTTTGTTGCAGAAGAAGGCATGATCATCATGCCCTATTGG                         ATGATGCAAAACATGCTGCTTCAAGAGGGTGACACTGTCCATGTAAAAAAT
genomic: GTGTTTTGGAGTTTGTTGCAGAAGAAGGCATGATCATCATGCCCTATTGGgtatgtataa ... acttgtttagATGATGCAAAACATGCTGCTTCAAGAGGGTGACACTGTCCATGTAAAAAAT
EST: gi|213183590|gb|FM196389.1|FM196389
EST:     GTGTTTTGGAGTTTGTTGCAGAAGAAGGCATGATCATCATGCCCTATTGG                         ATGATGCAAAACATGCTGCTTCAAGAGGGTGACACTGTCCATGTAAAAAAT
genomic: GTGTTTTGGAGTTTGTTGCAGAAGAAGGCATGATCATCATGCCCTATTGGgtatgtataa ... acttgtttagATGATGCAAAACATGCTGCTTCAAGAGGGTGACACTGTCCATGTAAAAAAT
EST: gi|32859779|gb|CD999460.1|CD999460
EST:     GTGTTTTGGAGTTTGTTGCAGAAGAAGGCATGATCATCATGCCCTATTGG                         ATGATGCAAAACATGCTGCTTCAAGAGGGTGACACTGTCCATGTAAAAAAT
genomic: GTGTTTTGGAGTTTGTTGCAGAAGAAGGCATGATCATCATGCCCTATTGGgtatgtataa ... acttgtttagATGATGCAAAACATGCTGCTTCAAGAGGGTGACACTGTCCATGTAAAAAAT

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: 43 (upstream exon), 25 (downstream exon)
Score: 135

TATGCTATTTGAGCTGCACAATGATGCAACCCAGCGGATTTCACACTGTGGTGTTTTGGAGTTTGTTGCAGAAGAAGGCATGATCATCATGCCCTATTGGgtatgtataa ... acttgtttagATGATGCAAAACATGCTGCTTCAAGAGGGTGACACTGTCCATGTAAAAAATGCGACTCTTCCCAAGGGCACATATGTGAAATTGCAACCTCACACAACTG


Block sizes: 33 (upstream exon), 34 (downstream exon)
Score: 133

TATGCTATTTGAGCTGCACAATGATGCAACCCAGCGGATTTCACACTGTGGTGTTTTGGAGTTTGTTGCAGAAGAAGGCATGATCATCATGCCCTATTGGgtatgtataa ... acttgtttagATGATGCAAAACATGCTGCTTCAAGAGGGTGACACTGTCCATGTAAAAAATGCGACTCTTCCCAAGGGCACATATGTGAAATTGCAACCTCACACAACTG


Block sizes: 33 (upstream exon), 41 (downstream exon)
Score: 147

TATGCTATTTGAGCTGCACAATGATGCAACCCAGCGGATTTCACACTGTGGTGTTTTGGAGTTTGTTGCAGAAGAAGGCATGATCATCATGCCCTATTGGgtatgtataa ... acttgtttagATGATGCAAAACATGCTGCTTCAAGAGGGTGACACTGTCCATGTAAAAAATGCGACTCTTCCCAAGGGCACATATGTGAAATTGCAACCTCACACAACTG


Block sizes: 44 (upstream exon), 25 (downstream exon)
Score: 216

TATGCTATTTGAGCTGCACAATGATGCAACCCAGCGGATTTCACACTGTGGTGTTTTGGAGTTTGTTGCAGAAGAAGGCATGATCATCATGCCCTATTGGgtatgtataa ... acttgtttagATGATGCAAAACATGCTGCTTCAAGAGGGTGACACTGTCCATGTAAAAAATGCGACTCTTCCCAAGGGCACATATGTGAAATTGCAACCTCACACAACTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATGCTATTTGAGCTGCACAATGATGCAACCCAGCGGATTTCACACTGTGGTGTTTTGGAGTTTGTTGCAGAAGAAGGCATGATCATCATGCCCTATTGGgtatgtataaaaggataactcagttcacttgtatcttctgttatatggcgaaagaaatatgtctatacttatttattttatgtattctcacttgtttag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG