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

GTATGTTGACAGCACCTTTGTAGAAAGAACGAAGGAAGTTGAAGCCAGCAACTCTGATGATGTGGCTAGATCAATTTCAAGAGAGACAATTACAAACACTgtgagttagtagttttccgatgactttacagtttgtcagaaatgcggctgcctattttctgggtgctgtctgtctttctaggctctagaatgttctgctgcaagatgacacttttttgttttgttttgtacattgtgcttgcag

Basic information

species Zea mays
transcript GRMZM5G823750_T02
intron # 6
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|78116573|gb|DV534960.1|DV534960
EST:     ATCAATTTCAAGAGAGACAATTACAAACACT                         ACACCATTTGGAGAAATGATGGAGGATTCACTGGCTTGTATACTGGGTTCT
genomic: ATCAATTTCAAGAGAGACAATTACAAACACTgtgagttagt ... gtgcttgcagACACCATTTGGAGAAATGATGGAGGATTCACTGGCTTGTATACTGGGTTCT
EST: gi|60345643|gb|DN212616.1|DN212616
EST:     ACTCTGATGATGTGGCTAGATCAATTTCAAGAGAGACAATTACAAACACT                         ACACCATTTGGAGAAATGATGGAGGATTCACTGGCTTGTATACTGGGTTCT
genomic: ACTCTGATGATGTGGCTAGATCAATTTCAAGAGAGACAATTACAAACACTgtgagttagt ... gtgcttgcagACACCATTTGGAGAAATGATGGAGGATTCACTGGCTTGTATACTGGGTTCT
EST: gi|60338165|gb|DN205138.1|DN205138
EST:     ACTCTGATGATGTGGCTAGATCAATTTCAAGAGAGACAATTACAAACACT                         ACACCATTTGGAGAAATGATGGAGGATTCACTGGCTTGTATACTGGGTTCT
genomic: ACTCTGATGATGTGGCTAGATCAATTTCAAGAGAGACAATTACAAACACTgtgagttagt ... gtgcttgcagACACCATTTGGAGAAATGATGGAGGATTCACTGGCTTGTATACTGGGTTCT
EST: gi|5791479|gb|AI978271.1|AI978271
EST:     ACTCTGATGATGTGGCTAGATCAATTTCAAGAGAGACAATTACAAACACT                         ACACCATTTGGAGAAATGATGGAGGATTCACTGGCTTGTATACTGGGTTCT
genomic: ACTCTGATGATGTGGCTAGATCAATTTCAAGAGAGACAATTACAAACACTgtgagttagt ... gtgcttgcagACACCATTTGGAGAAATGATGGAGGATTCACTGGCTTGTATACTGGGTTCT
EST: gi|60395120|gb|DN227989.1|DN227989
EST:     ACTCTGATGATGTGGCTAGATCAATTTCAAGAGAGACAATTACAAACACT                         ACACCATTTGGAGAAATGATGGAGGATTCACTGGCTTGTATACTGGGTTCT
genomic: ACTCTGATGATGTGGCTAGATCAATTTCAAGAGAGACAATTACAAACACTgtgagttagt ... gtgcttgcagACACCATTTGGAGAAATGATGGAGGATTCACTGGCTTGTATACTGGGTTCT
EST: gi|76013572|gb|DT940742.1|DT940742
EST:     ACTCTGATGATGTGGCTAGATCAATTTCAAGAGAGACAATTACAAACACT                         ACACCATTTGGAGAAATGATGGAGGATTCACTGGCTTGTATACTGGGTTCT
genomic: ACTCTGATGATGTGGCTAGATCAATTTCAAGAGAGACAATTACAAACACTgtgagttagt ... gtgcttgcagACACCATTTGGAGAAATGATGGAGGATTCACTGGCTTGTATACTGGGTTCT
EST: gi|60342423|gb|DN209396.1|DN209396
EST:     ACTCTGATGATGTGGCTAGATCAATTTCAAGAGAGACAATTACAAACACT                         ACACCATTTGGAGAAATGATGGAGGATTCACTGGCTTGTATACTGGGTTCT
genomic: ACTCTGATGATGTGGCTAGATCAATTTCAAGAGAGACAATTACAAACACTgtgagttagt ... gtgcttgcagACACCATTTGGAGAAATGATGGAGGATTCACTGGCTTGTATACTGGGTTCT
EST: gi|6022643|gb|AW067455.1|AW067455
EST:     ACTCTGATGATGTGGCTAGATCAATTTCAAGAGAGACAATTACAAACACT                         ACACCATTTGGAGAAATGATGGAGGATTCACTGGCTTGNATACTGGGTTCT
genomic: ACTCTGATGATGTGGCTAGATCAATTTCAAGAGAGACAATTACAAACACTgtgagttagt ... gtgcttgcagACACCATTTGGAGAAATGATGGAGGATTCACTGGCTTGTATACTGGGTTCT
EST: gi|76013571|gb|DT940741.1|DT940741
EST:     ACTCTGATGATGTGGCTAGATCAATTTCAAGAGAGACAATTACAAACACT                         ACACCATTTGGAGAAATGATGGAGGATTCACTGGCTTGTATACTGGGTTCT
genomic: ACTCTGATGATGTGGCTAGATCAATTTCAAGAGAGACAATTACAAACACTgtgagttagt ... gtgcttgcagACACCATTTGGAGAAATGATGGAGGATTCACTGGCTTGTATACTGGGTTCT
EST: gi|101385030|gb|EB814560.1|EB814560
EST:     CTCTGATGATGTGGCTAGATCAATTTTCA-GAGAGACAATTACAAACACT                         ACACCATTTGGAGAAATGATGGAGGATTCACTGGCTTGTATACTGGGTTCT
genomic: CTCTGATGATGTGGCTAGATCAATTT-CAAGAGAGACAATTACAAACACTgtgagttagt ... gtgcttgcagACACCATTTGGAGAAATGATGGAGGATTCACTGGCTTGTATACTGGGTTCT
EST: gi|211478590|gb|FL369717.1|FL369717
EST:     ACTCTGATGATGTGGCTAGATCAATTTCAAGAGAGACAATTACAAACACT                         ACACCATTTGGAGAAATGATGGAGGATTCACTGGCTTGTATACTGGGTTCT
genomic: ACTCTGATGATGTGGCTAGATCAATTTCAAGAGAGACAATTACAAACACTgtgagttagt ... gtgcttgcagACACCATTTGGAGAAATGATGGAGGATTCACTGGCTTGTATACTGGGTTCT
EST: gi|116816691|gb|EC859456.1|EC859456
EST:     ACTCTGATGATGTGGCTAGATCAATTTCAAGAGAGACAATTACAAACACT                         ACACCATTTGGAGAAATGATGGAGGATTCACTGGCTTGTATACTGGGTTCT
genomic: ACTCTGATGATGTGGCTAGATCAATTTCAAGAGAGACAATTACAAACACTgtgagttagt ... gtgcttgcagACACCATTTGGAGAAATGATGGAGGATTCACTGGCTTGTATACTGGGTTCT
EST: gi|84980380|gb|DW530729.1|DW530729
EST:     ACTCTGATGATGTGGCTAGATCAATTTCAAGAGAGACAATTACAAACACT                         ACACCATTTGGAGAAATGATGGAGGATTCACTGGCTTGTATACTGGGTTCT
genomic: ACTCTGATGATGTGGCTAGATCAATTTCAAGAGAGACAATTACAAACACTgtgagttagt ... gtgcttgcagACACCATTTGGAGAAATGATGGAGGATTCACTGGCTTGTATACTGGGTTCT
EST: gi|78116157|gb|DV534545.1|DV534545
EST:     ACTCTGATGATGTGGCTAGATCAATTTCAAGAGAGACAATTACAAACACT                         ACACCATTTGGAGAAATGATGGAGGATTCACTGGCTTGTATACTGGGTTCT
genomic: ACTCTGATGATGTGGCTAGATCAATTTCAAGAGAGACAATTACAAACACTgtgagttagt ... gtgcttgcagACACCATTTGGAGAAATGATGGAGGATTCACTGGCTTGTATACTGGGTTCT
EST: gi|6056596|gb|AW091001.1|AW091001
EST:     ACTCTGATGATGTGGCTAGATCAATTTCAAGAGAGACAATTACAAACACT                         ACACCATTTGGAGAAATGATGGAGGATTCAC
genomic: ACTCTGATGATGTGGCTAGATCAATTTCAAGAGAGACAATTACAAACACTgtgagttagt ... gtgcttgcagACACCATTTGGAGAAATGATGGAGGATTCAC
EST: gi|5917410|gb|AW054201.1|AW054201
EST:     ACTCTGATGATGTGGCTAGATCAATTTCAAGAGAGACAATTACAAACACT                         ACACCATTTGGAGAAATGATGGAGGATTCACTGGCTTGTATACTGGGTTCT
genomic: ACTCTGATGATGTGGCTAGATCAATTTCAAGAGAGACAATTACAAACACTgtgagttagt ... gtgcttgcagACACCATTTGGAGAAATGATGGAGGATTCACTGGCTTGTATACTGGGTTCT
EST: gi|76011928|gb|DT939098.1|DT939098
EST:     ACTCTGATGATGTGGCTAGATCAATTTCAAGAGAGACAATTACAAACACT                         ACACCATTTGGAGAAATGATGGAGGATTCACTGGCTTGTATACTGGGTTCT
genomic: ACTCTGATGATGTGGCTAGATCAATTTCAAGAGAGACAATTACAAACACTgtgagttagt ... gtgcttgcagACACCATTTGGAGAAATGATGGAGGATTCACTGGCTTGTATACTGGGTTCT
EST: gi|60351828|gb|DN218801.1|DN218801
EST:     ACTCTGATGATGTGGCTAGATCAATTTCAAGAGAGACAATTACAAACACT                         ACACCATTTGGAGAAATGATGGAGGATTCACTGGCTTGTATACTGGGTTCT
genomic: ACTCTGATGATGTGGCTAGATCAATTTCAAGAGAGACAATTACAAACACTgtgagttagt ... gtgcttgcagACACCATTTGGAGAAATGATGGAGGATTCACTGGCTTGTATACTGGGTTCT
EST: gi|91050221|gb|EB160639.1|EB160639
EST:     ACTCTGATGATGTGGCTAGATCAATTTCAAGAGAGACAATTACAAACACT                         ACACCATTTGGAGAAATGATGGAGGATTCACTGGCTTGTATACTGGGTTCT
genomic: ACTCTGATGATGTGGCTAGATCAATTTCAAGAGAGACAATTACAAACACTgtgagttagt ... gtgcttgcagACACCATTTGGAGAAATGATGGAGGATTCACTGGCTTGTATACTGGGTTCT
EST: gi|211362094|gb|FL443138.1|FL443138
EST:     ACTCTGATGATGTGGCTAGATCAATTTCAAGAGAGACAATTACAAACACT                         ACACCATTTGGAGAAATGATGGAGGATTCACTGGCTTGTATACTGGGTTCT
genomic: ACTCTGATGATGTGGCTAGATCAATTTCAAGAGAGACAATTACAAACACTgtgagttagt ... gtgcttgcagACACCATTTGGAGAAATGATGGAGGATTCACTGGCTTGTATACTGGGTTCT
EST: gi|93011924|gb|EB637444.1|EB637444
EST:     ACTCTGATGATGTGGCTAGATCAATTTCAAGAGAGACAATTACAAACACT                         T
genomic: ACTCTGATGATGTGGCTAGATCAATTTCAAGAGAGACAATTACAAACACTgtgagttagt ... gtgcttgcag-
EST: gi|93011924|gb|EB637444.1|EB637444
EST:     ACTCTGATGATGTGGCTAGATCAATTTCAAGAGAGACAATTACAAACACT                         T
genomic: ACTCTGATGATGTGGCTAGATCAATTTCAAGAGAGACAATTACAAACACTgtgagttagt ... gtgcttgcag-
EST: gi|93011924|gb|EB637444.1|EB637444
EST:     ACTCTGATGATGTGGCTAGATCAATTTCAAGAGAGACAATTACAAACACT                         T
genomic: ACTCTGATGATGTGGCTAGATCAATTTCAAGAGAGACAATTACAAACACTgtgagttagt ... gtgcttgcag-
EST: gi|93011924|gb|EB637444.1|EB637444
EST:     ACTCTGATGATGTGGCTAGATCAATTTCAAGAGAGACAATTACAAACACT                         T
genomic: ACTCTGATGATGTGGCTAGATCAATTTCAAGAGAGACAATTACAAACACTgtgagttagt ... gtgcttgcag-
EST: gi|93011924|gb|EB637444.1|EB637444
EST:     ACTCTGATGATGTGGCTAGATCAATTTCAAGAGAGACAATTACAAACACT                         T
genomic: ACTCTGATGATGTGGCTAGATCAATTTCAAGAGAGACAATTACAAACACTgtgagttagt ... gtgcttgcag-
EST: gi|93011924|gb|EB637444.1|EB637444
EST:     ACTCTGATGATGTGGCTAGATCAATTTCAAGAGAGACAATTACAAACACT                         T
genomic: ACTCTGATGATGTGGCTAGATCAATTTCAAGAGAGACAATTACAAACACTgtgagttagt ... gtgcttgcag-
EST: gi|93011924|gb|EB637444.1|EB637444
EST:     ACTCTGATGATGTGGCTAGATCAATTTCAAGAGAGACAATTACAAACACT                         T
genomic: ACTCTGATGATGTGGCTAGATCAATTTCAAGAGAGACAATTACAAACACTgtgagttagt ... gtgcttgcag-
EST: gi|93011924|gb|EB637444.1|EB637444
EST:     ACTCTGATGATGTGGCTAGATCAATTTCAAGAGAGACAATTACAAACACT                         T
genomic: ACTCTGATGATGTGGCTAGATCAATTTCAAGAGAGACAATTACAAACACTgtgagttagt ... gtgcttgcag-
EST: gi|93011924|gb|EB637444.1|EB637444
EST:     ACTCTGATGATGTGGCTAGATCAATTTCAAGAGAGACAATTACAAACACT                         T
genomic: ACTCTGATGATGTGGCTAGATCAATTTCAAGAGAGACAATTACAAACACTgtgagttagt ... gtgcttgcag-
EST: gi|93011924|gb|EB637444.1|EB637444
EST:     ACTCTGATGATGTGGCTAGATCAATTTCAAGAGAGACAATTACAAACACT                         T
genomic: ACTCTGATGATGTGGCTAGATCAATTTCAAGAGAGACAATTACAAACACTgtgagttagt ... gtgcttgcag-
EST: gi|211084172|gb|FL469478.1|FL469478
EST:     ACTCTGATGATGTGGCTAGATCAATTTCAAGAGAGACAATTACAAACACT                         ACACCATTTGGAGAAATGATGGAGGATTCACTGGCTTGTATACTGGGTTCT
genomic: ACTCTGATGATGTGGCTAGATCAATTTCAAGAGAGACAATTACAAACACTgtgagttagt ... gtgcttgcagACACCATTTGGAGAAATGATGGAGGATTCACTGGCTTGTATACTGGGTTCT
EST: gi|94477438|gb|EB706396.1|EB706396
EST:     ACTCTGATGATGTGGCTAGATCAATTTCAAGAGAGACAATTACAAACACT                         ACACCATTTGGAGAAATGATGGAGGATTCACTGGCTTGTATACTGGGTTCT
genomic: ACTCTGATGATGTGGCTAGATCAATTTCAAGAGAGACAATTACAAACACTgtgagttagt ... gtgcttgcagACACCATTTGGAGAAATGATGGAGGATTCACTGGCTTGTATACTGGGTTCT
EST: gi|76011927|gb|DT939097.1|DT939097
EST:     ACTCTGATGATGTGGCTAGATCAATTTCAAGAGAGACAATTACAAACACT                         ACACCATTTGGAGAAATGATGGAGGATTCACTGGCTTGTATACTGGGTTCT
genomic: ACTCTGATGATGTGGCTAGATCAATTTCAAGAGAGACAATTACAAACACTgtgagttagt ... gtgcttgcagACACCATTTGGAGAAATGATGGAGGATTCACTGGCTTGTATACTGGGTTCT
EST: gi|166433201|gb|EG125169.1|EG125169
EST:     ACTCTGATGATGTGGCTAGATCAATTTCAAGAGAGACAATTACAAACACT                         ACACCATTTGGAGAAATGA
genomic: ACTCTGATGATGTGGCTAGATCAATTTCAAGAGAGACAATTACAAACACTgtgagttagt ... gtgcttgcagACACCATTTGGAGAAATGA
EST: gi|29544924|gb|CB605532.1|CB605532
EST:     ACTCTGATGATGTGGCTAGATCAATTTCAAGAGAGACAATTACAAACACT                         ACACCATTTGGAGAAATGATGGAGGATTCACTGGCTTGTATACTGGGTTCT
genomic: ACTCTGATGATGTGGCTAGATCAATTTCAAGAGAGACAATTACAAACACTgtgagttagt ... gtgcttgcagACACCATTTGGAGAAATGATGGAGGATTCACTGGCTTGTATACTGGGTTCT

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: 39 (upstream exon), 49 (downstream exon)
Score: 39

GTATGTTGACAGCACCTTTGTAGAAAGAACGAAGGAAGTTGAAGCCAGCAACTCTGATGATGTGGCTAGATCAATTTCAAGAGAGACAATTACAAACACTgtgagttagt ... gtgcttgcagACACCATTTGGAGAAATGATGGAGGATTCACTGGCTTGTATACTGGGTTCTCCCGGATGCAACATGGAAAGCAACAATCCCCCAGAAAAGACAGCTAATG


Block sizes: 39 (upstream exon), 49 (downstream exon)
Score: 48

GTATGTTGACAGCACCTTTGTAGAAAGAACGAAGGAAGTTGAAGCCAGCAACTCTGATGATGTGGCTAGATCAATTTCAAGAGAGACAATTACAAACACTgtgagttagt ... gtgcttgcagACACCATTTGGAGAAATGATGGAGGATTCACTGGCTTGTATACTGGGTTCTCCCGGATGCAACATGGAAAGCAACAATCCCCCAGAAAAGACAGCTAATG


Block sizes: 39 (upstream exon), 41 (downstream exon)
Score: 16

GTATGTTGACAGCACCTTTGTAGAAAGAACGAAGGAAGTTGAAGCCAGCAACTCTGATGATGTGGCTAGATCAATTTCAAGAGAGACAATTACAAACACTgtgagttagt ... gtgcttgcagACACCATTTGGAGAAATGATGGAGGATTCACTGGCTTGTATACTGGGTTCTCCCGGATGCAACATGGAAAGCAACAATCCCCCAGAAAAGACAGCTAATG


Block sizes: 39 (upstream exon), 49 (downstream exon)
Score: 66

GTATGTTGACAGCACCTTTGTAGAAAGAACGAAGGAAGTTGAAGCCAGCAACTCTGATGATGTGGCTAGATCAATTTCAAGAGAGACAATTACAAACACTgtgagttagt ... gtgcttgcagACACCATTTGGAGAAATGATGGAGGATTCACTGGCTTGTATACTGGGTTCTCCCGGATGCAACATGGAAAGCAACAATCCCCCAGAAAAGACAGCTAATG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTATGTTGACAGCACCTTTGTAGAAAGAACGAAGGAAGTTGAAGCCAGCAACTCTGATGATGTGGCTAGATCAATTTCAAGAGAGACAATTACAAACACTgtgagttagtagttttccgatgactttacagtttgtcagaaatgcggctgcctattttctgggtgctgtctgtctttctaggctctagaatgttctgctgcaagatgacacttttttgttttgttttgtacattgtgcttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA