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'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatttccttcccgtgctgtttctgatacctcacctaaatggtttggttcttttttattgtaatctcatagctattcttttgggccccaatacagCTACCATCTAGGTATGGAATTACTTAATCAATCAGATGGAGCTGGTGAAGCATTGTTGAAAATGCTCTGGCATCATCCAGATGCTGTTCTGTGCTGCTCC

Basic information

species Zea mays
transcript GRMZM2G109987_T05
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G109987_T05 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os03g01890.1 (Oryza sativa), 3'ss of exon 16
------------gtaatttccttcccgtgctgt--ttctgatacctcacctaaatgg-tttggttcttttttat------tgtaatctcatagctattcttttgggccccaatacagCTACCATCTAGGTATGGAATTACTTAATCAATCAGATGGAGCTGGTGAAGCATTGTTGAAAATGCTCTGGCATCATCCAGATGCTGTTCTGTGCTGCTCC
            ||| |||| |||| |||| ||  |  |||||  | |    |||   |||| |  ||||  ||      || || || | |   ||  | ||  |||      ||| |||||||||||  | || ||||||| |||||||||||||| ||  |||  ||||||||| ||||| |||||| | | ||||||| || |||||||||| 
gtaagtgtactcgtagtttc-ttcctgtgcagtagtgatgatatttaataagaataaatttgatagttttccatgttggttgcaagctgacaaa-atattattatgccgtcgctcagTTACCATCTAGGGGTAGAGTTACTTAGTCAATCAGATGGAGATGCAGAACAATTGTTGAAGATGCTATGGCATTACCAAGATGCTATTTTGTGCTGCTCA
















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|32827400|gb|CD967078.1|CD967078
EST:     GGCTTCCCTGAAGCTGCCACACTTGCTAGATGGGTTTGCCAGAGTTATCA                         CTACCATCTAGGTATGGAATTACTTA
genomic: GGCTTCCCTGAAGCTGCCACACTTGCTAGATGGGTTTGCCAGAGTTATCAgtaatttcct ... cccaatacagCTACCATCTAGGTATGGAATTACTTA
EST: gi|14244886|gb|BG842824.2|BG842824
EST:     AGCTGCCACACTTGCTAGATGGGTTTGCCAGAGTTATCA                         CTACCATCTAGGTATGGAATTACTTAATCAATCAGATGGAGCTGGTGAAGC
genomic: AGCTGCCACACTTGCTAGATGGGTTTGCCAGAGTTATCAgtaatttcct ... cccaatacagCTACCATCTAGGTATGGAATTACTTAATCAATCAGATGGAGCTGGTGAAGC
EST: gi|30032082|gb|CB833933.1|CB833933
EST:     GGCTTCCCTGAAGCTGCCACACTTGCTAGATGGGTTTGCCAGAGTTATCA                         CTACCATCTAGGTATGGAATTACTTAATCAATCAGATGGAGCTGGTGAAGC
genomic: GGCTTCCCTGAAGCTGCCACACTTGCTAGATGGGTTTGCCAGAGTTATCAgtaatttcct ... cccaatacagCTACCATCTAGGTATGGAATTACTTAATCAATCAGATGGAGCTGGTGAAGC
EST: gi|211351868|gb|FK984283.1|FK984283
EST:     GGCTTCCCTGAAGCTGCCACACTTGCTAGATGGGTTTGCCAGAGTTATCA                         CTACCATCTAGGTATGGAATTACTTAATCAATCAGATGGAGCTGGTGAAGC
genomic: GGCTTCCCTGAAGCTGCCACACTTGCTAGATGGGTTTGCCAGAGTTATCAgtaatttcct ... cccaatacagCTACCATCTAGGTATGGAATTACTTAATCAATCAGATGGAGCTGGTGAAGC
EST: gi|6626571|gb|AW258103.1|AW258103
EST:     GGCTTCCCTGAAGCTGCCACACTTGCTAGATGGGTTTGCCAGAGTTATCA                         CTACCATCTAGGTATGGAATTACTTAATCAATCAGATGGAGCTGGTGAAGC
genomic: GGCTTCCCTGAAGCTGCCACACTTGCTAGATGGGTTTGCCAGAGTTATCAgtaatttcct ... cccaatacagCTACCATCTAGGTATGGAATTACTTAATCAATCAGATGGAGCTGGTGAAGC
EST: gi|101391393|gb|EB817631.1|EB817631
EST:     GGCTTCCCTGAAGCTGCCACACTTGCTAGATGGGTTTGCCAGAGTTATCA                         CTACCATCTAGGTATGGAATTACTTAATCAATCAGATGGAGCTGGTGAAGC
genomic: GGCTTCCCTGAAGCTGCCACACTTGCTAGATGGGTTTGCCAGAGTTATCAgtaatttcct ... cccaatacagCTACCATCTAGGTATGGAATTACTTAATCAATCAGATGGAGCTGGTGAAGC
EST: gi|32832830|gb|CD972508.1|CD972508
EST:     GGCTTCCCTGAAGCTGCCACACTTGCTAGATGGGTTTGCCAGAGTTATCA                         CTACCATCTAGGTATGGAATTACTTAATCAATCAGATGGAGCTGGTGAAGC
genomic: GGCTTCCCTGAAGCTGCCACACTTGCTAGATGGGTTTGCCAGAGTTATCAgtaatttcct ... cccaatacagCTACCATCTAGGTATGGAATTACTTAATCAATCAGATGGAGCTGGTGAAGC
EST: gi|31350140|gb|CD434497.1|CD434497
EST:     GGCTTCCCTGAAGCTGCCACACTTGCTAGATGGGTTTGCCAGAGTTATCA                         CTACCATCTAGGTATGGAATTACTTAATCAATCAGATGGAGCTGGTGAAGC
genomic: GGCTTCCCTGAAGCTGCCACACTTGCTAGATGGGTTTGCCAGAGTTATCAgtaatttcct ... cccaatacagCTACCATCTAGGTATGGAATTACTTAATCAATCAGATGGAGCTGGTGAAGC
EST: gi|32832810|gb|CD972488.1|CD972488
EST:     GGCTTCCCTGAAGCTGCCACACTTGCTAGATGGGTTTGCCAGAGTTATCA                         CTACCATCTAGGTATGGAATTACTTAATCAATCAGATGGAGCTGGTGAAGC
genomic: GGCTTCCCTGAAGCTGCCACACTTGCTAGATGGGTTTGCCAGAGTTATCAgtaatttcct ... cccaatacagCTACCATCTAGGTATGGAATTACTTAATCAATCAGATGGAGCTGGTGAAGC
EST: gi|32835598|gb|CD975276.1|CD975276
EST:     GGCTTCCCTGAAGCTGCCACACTTGCTAGATGGGTTTGCCAGAGTTATCA                         CTACCATCTAGGTATGGAATTACTTAATCAATCAGATGGAGCTGGTGAAGC
genomic: GGCTTCCCTGAAGCTGCCACACTTGCTAGATGGGTTTGCCAGAGTTATCAgtaatttcct ... cccaatacagCTACCATCTAGGTATGGAATTACTTAATCAATCAGATGGAGCTGGTGAAGC
EST: gi|60336823|gb|DN203796.1|DN203796
EST:     GGCTTCCCTGAAGCTGCCACACTTGCTAGATGGGTTTGCCAGAGTTATCA                         CTACCATCTAGGTATGGAATTACTTAATCAATCAGATGGAGCTGGTGAAGC
genomic: GGCTTCCCTGAAGCTGCCACACTTGCTAGATGGGTTTGCCAGAGTTATCAgtaatttcct ... cccaatacagCTACCATCTAGGTATGGAATTACTTAATCAATCAGATGGAGCTGGTGAAGC

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: 47 (upstream exon), 48 (downstream exon)
Score: 119

CTATATCTCCCTCCCAATCTGGTCTAAATGCTGGGCATAGGATGCTTTCTGGCTTCCCTGAAGCTGCCACACTTGCTAGATGGGTTTGCCAGAGTTATCAgtaatttcct ... cccaatacagCTACCATCTAGGTATGGAATTACTTAATCAATCAGATGGAGCTGGTGAAGCATTGTTGAAAATGCTCTGGCATCATCCAGATGCTGTTCTGTGCTGCTCC


Block sizes: 46 (upstream exon), 40 (downstream exon)
Score: 18

CTATATCTCCCTCCCAATCTGGTCTAAATGCTGGGCATAGGATGCTTTCTGGCTTCCCTGAAGCTGCCACACTTGCTAGATGGGTTTGCCAGAGTTATCAgtaatttcct ... cccaatacagCTACCATCTAGGTATGGAATTACTTAATCAATCAGATGGAGCTGGTGAAGCATTGTTGAAAATGCTCTGGCATCATCCAGATGCTGTTCTGTGCTGCTCC


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 35

CTATATCTCCCTCCCAATCTGGTCTAAATGCTGGGCATAGGATGCTTTCTGGCTTCCCTGAAGCTGCCACACTTGCTAGATGGGTTTGCCAGAGTTATCAgtaatttcct ... cccaatacagCTACCATCTAGGTATGGAATTACTTAATCAATCAGATGGAGCTGGTGAAGCATTGTTGAAAATGCTCTGGCATCATCCAGATGCTGTTCTGTGCTGCTCC


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 29

CTATATCTCCCTCCCAATCTGGTCTAAATGCTGGGCATAGGATGCTTTCTGGCTTCCCTGAAGCTGCCACACTTGCTAGATGGGTTTGCCAGAGTTATCAgtaatttcct ... cccaatacagCTACCATCTAGGTATGGAATTACTTAATCAATCAGATGGAGCTGGTGAAGCATTGTTGAAAATGCTCTGGCATCATCCAGATGCTGTTCTGTGCTGCTCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtttggttcttttttattgtaatctcatagctattcttttgggccccaatacagCTACCATCTAGGTATGGAATTACTTAATCAATCAGATGGAGCTGGTGAAGCATTGTTGAAAATGCTCTGGCATCATCCAGATGCTGTTCTGTGCTGCTCC
       ttcttttttattgtaa  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatttccttcccgtgctgtttctgatacctcacctaaatggtttggttcttttttattgtaatctcatagctattcttttgggccccaatacagCTACCATCTAGGTATGGAATTACTTAATCAATCAGATGGAGCTGGTGAAGCATTGTTGAAAATGCTCTGGCATCATCCAGATGCTGTTCTGTGCTGCTCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT