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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttatattgttccgtttagtgtattttgttttgttacgcaattctatgtggctaagtgttattctgtgccatgctatctagCCTGAGTGGATGGCACCAGAAGTTCTACGAGACGAGCCCTCAAATGAGAAGTCTGATGTTTACAGCTTCGGTGTAATCTTATGGGAGCTTATGACATTGC

Basic information

species Zea mays
transcript GRMZM2G059671_T04
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G059671_T04 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os02g32610.3 (Oryza sativa), 3'ss of exon 13
gtaagtt-atattgt--tccgtttagtgtattttgttttgttacgcaattctatgtggctaagtgttattctgtgccatgctatctagCCTGAGTGGATGGCACCAGAAGTTCTACGAGACGAGCCCTCAAATGAGAAGTCTGATGTTTACAGCTTCGGTGTAATCTTATGGGAGCTTATGACATTGC
||||||| |||||    |   |||  | | ||   |||| ||  || |     ||    |||||| | |||  ||  ||  | ||||||||||||||||||||||||||||| ||||||| ||||| |||||||||||||||||||| |||||||| ||||| ||| |||||||||| ||||||||||
gtaagttcatattaccgttacttttatttgttgattttttttcagctaaatcgtgctagtaagtgct-ttcgatgtaatattctctagCCTGAGTGGATGGCACCAGAAGTTATACGAGATGAGCCATCAAATGAGAAGTCTGATGTCTACAGCTTTGGTGTTATCCTATGGGAGCTCATGACATTGC

upper sequence: GRMZM2G059671_T04 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA13G21480.1 (Glycine max), 3'ss of exon 12
gtaagtt-atattg-----------ttccgtttagtgtattttgt-tttgttacgcaattctatgtggctaagtgtt--attctgtgccatgctatc---tagCCTGAGTGGATGGCACCAGAAGTTCTACGAGACGAGCCCTCAAATGAGAAGTCTGATGTTTACAGCTTCGGTGTAATCTTATGGGAGCTTATGACATTGC
||||||| | ||||           ||| |||| ||   | || | |||   | | || | | | |  |||  | ||  ||| |   || |    ||   ||||||||||||||||| ||||| |||||  | || ||||| || ||||||||||| |||||||||||||| |||||||||||||||||||||   |||||||
gtaagttcacattgactgcagatatttctgttttgtacgtcttatgtttcagaagtaagttt-tataactatatttttaatttttctccttttcctcccttagCCTGAGTGGATGGCTCCAGAGGTTCTTTGTGATGAGCCATCGAATGAGAAGTCCGATGTTTACAGCTTTGGTGTAATCTTATGGGAGCTTGCAACATTGC

upper sequence: GRMZM2G059671_T04 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA19G37570.2 (Glycine max), 3'ss of exon 13
------------gtaagttatattgttccgtttagtgtattttgttttgttacgcaattctatgt-----ggctaagtgttattctgtgccatgctatctagCCTGAGTGGATGGCACCAGAAGTTCTACGAGACGAGCCCTCAAATGAGAAGTCTGATGTTTACAGCTTCGGTGTAATCTTATGGGAGCTTATGACATTGC
              ||    | |     | ||| |  |  |||||||       || || ||| |        |||||   | ||  |    | |||  ||||||||||||||||| ||||||||||| || |||||||| || ||||||||||| |||||||||||||| ||||| ||||| |||||| |    |||||||
gtaagtttactttcaaaacgtgtatcagccttttgaattgtttgtttcagatgccatttttatttttgcaaattaagttgaactcctttttct-ctacttagCCTGAGTGGATGGCTCCAGAAGTTCTTCGTGACGAGCCATCCAATGAGAAGTCAGATGTTTACAGCTTTGGTGTCATCTTGTGGGAGATCGCAACATTGC

upper sequence: GRMZM2G059671_T04 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA03G34890.1 (Glycine max), 3'ss of exon 13
------------gtaagttatattgttccgtttagtgtattttgttttgttacgcaattctat-gtggc----taagtgttattctgtgccatgctatctagCCTGAGTGGATGGCACCAGAAGTTCTACGAGACGAGCCCTCAAATGAGAAGTCTGATGTTTACAGCTTCGGTGTAATCTTATGGGAGCTTATGACATTGC
              ||    | |   | | ||| |  |  |||| ||       || || |||  | ||    |||||   | ||  |    | |||  ||||||||||||||||| ||||||||||| || || ||||| || ||||||||||| |||||||||||||| ||||| ||||| ||||||||    |||||||
gtaagtatactttcaaaacgtgtatcttccttttgaatcgtttgattcagatgtcatttttattattgcaaattaagttgaactcctttttct-ctacttagCCTGAGTGGATGGCTCCAGAAGTTCTTCGTGATGAGCCATCCAATGAGAAGTCAGATGTTTACAGCTTTGGTGTCATCTTGTGGGAGCTCGCAACATTGC

upper sequence: GRMZM2G059671_T04 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA10G07610.1 (Glycine max), 3'ss of exon 14
gtaagtt-atattg--ttccgtttagtgtattttgt------tttgttacgcaattctatgtggctaagtgtt-----attctgtgccatgctatc---tagCCTGAGTGGATGGCACCAGAAGTTCTACGAGACGAGCCCTCAAATGAGAAGTCTGATGTTTACAGCTTCGGTGTAATCTTATGGGAGCTTATGACATTGC
||||||| | ||||  | | | |   | | ||||||      | |||| |  || | | | |  ||| || ||     ||| |   || |    ||   ||||||||||||||||| ||||| ||||| || || ||||| || |||||||||||||||||||||||||| |||||||||||||||||||||   |||||||
gtaagttcacattgactgcagatgtttctgttttgtactacttatgtttcagaagttt-tataactacgtttttattaatttttctccttttcctcccttagCCTGAGTGGATGGCTCCAGAGGTTCTTCGTGATGAGCCATCGAATGAGAAGTCTGATGTTTACAGCTTTGGTGTAATCTTATGGGAGCTTGCAACATTGC

upper sequence: GRMZM2G059671_T04 (Zea mays), 3'ss of exon 12
lower sequence: AT5G03730.1 (Arabidopsis thaliana), 3'ss of exon 12
----------------gtaagttatattgttccgtttagtgta-ttttgttttgttacgcaattctat--gtggctaagtgttattctgtgccatgctatct-agCCTGAGTGGATGGCACCAGAAGTTCTACGAGACGAGCCCTCAAATGAGAAGTCTGATGTTTACAGCTTCGGTGTAATCTTATGGGAGCTTATGACATTGC
                  ||  || |     | |   |  |||  ||| || |    |  | ||| |   |  ||||| |   |||     |  || ||| | |||| |||||||||||||||||||| || ||||| ||||| || ||||| ||||| ||||| ||||||||||| || ||||| |||||||||   |||||||
gtaagttcagtttgtttgaaactaaaacacgctgaacaacgtaactttcttctaggtcctatttccaatggaagctaaata--attactgactttgatatatcagCCCGAGTGGATGGCACCAGAAGTCCTGCGAGATGAGCCGTCTAATGAAAAGTCAGATGTGTACAGCTTCGGGGTCATCTTGTGGGAGCTTGCTACATTGC

upper sequence: GRMZM2G059671_T04 (Zea mays), 3'ss of exon 12
lower sequence: Vv08s0007g03910.t01 (Vitis vinifera), 3'ss of exon 12
----------gtaagttatattgttccgt----ttagtgtattttgttt---tgttacgcaattctatgtggctaa-gtgttattc---tgtgccatgctatctagCCTGAGTGGATGGCACCAGAAGTTCTACGAGACGAGCCCTCAAATGAGAAGTCTGATGTTTACAGCTTCGGTGTAATCTTATGGGAGCTTATGACATTGC
           |||| || || |   |      | |||   || | |||   || || | |    | |||  | ||  |   |||    | |  |||   ||| |||||||||||||||||||||||||||| || || ||| | |||||||| ||||| ||  | || ||||| ||| ||||||| ||||| |||   |||||||
gtaagttttactaagctagatagcaacacaatctcagttccttgtatttaggtgatatggatcattttgtcacaaatataaaatttacatttttcatttcatc-agCCTGAGTGGATGGCACCAGAAGTTCTTCGGGATGAGGCATCAAATGAAAAGTCAGACATATATAGCTTTGGTATAATCTTGTGGGAACTTGCAACATTGC

upper sequence: GRMZM2G059671_T04 (Zea mays), 3'ss of exon 12
lower sequence: Vv13s0074g00430.t01 (Vitis vinifera), 3'ss of exon 12
-------------------------gtaagttatattgttccgtttagtg-tattttgttttgttacgcaat--tctatgtggctaagtgttattctgtgccatgctatctagCCTGAGTGGATGGCACCAGAAGTTCTACGAGACGAGCCCTCAAATGAGAAGTCTGATGTTTACAGCTTCGGTGTAATCTTATGGGAGCTTATGACATTGC
                          |||  |||||  |    |    || ||||          | |  ||    |   | ||||||  |||   |      |  |   ||||||||||||||||||||||||||||| || || ||||| |||||||| ||||| |||||||||||||| ||||||||||| ||||| ||| |||| ||||
gtaagttctattcaaaactgaaaagttaatgtatataatctgttggcatgctattaaaagcgagcaagggatggcttcaattgctaagacttacctttgattttttttgttagCCTGAGTGGATGGCACCAGAAGTTCTCCGTGATGAGCCATCAAATGAAAAGTCAGATGTTTACAGCTTTGGTGTAATCTTGTGGGAACTTGTGACCTTGC

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|20802940|gb|BQ293990.1|BQ293990
EST:     CCAGATTGAAGGCAAACACATTTCTGTCTTCCAAGACTGCAGCAGGGACT                         CCTGAGTGGATGGCACCAGAAGTTCTACGAGACGAGCCCTCAAATGAGAAG
genomic: CCAGATTGAAGGCAAACACATTTCTGTCTTCCAAGACTGCAGCAGGGACTgtaagttata ... tgctatctagCCTGAGTGGATGGCACCAGAAGTTCTACGAGACGAGCCCTCAAATGAGAAG
EST: gi|76284240|gb|DV023808.1|DV023808
EST:     CCAGATTGAAGGCAAACACATTTCTGTCTTCCAAGACTGCAGCAGGGACT                         CCTGAGTGGATGGCACCAGAAGTTCTACGAGACGAGCCCTCAAATGAGAAG
genomic: CCAGATTGAAGGCAAACACATTTCTGTCTTCCAAGACTGCAGCAGGGACTgtaagttata ... tgctatctagCCTGAGTGGATGGCACCAGAAGTTCTACGAGACGAGCCCTCAAATGAGAAG
EST: gi|67042437|gb|CO468692.1|CO468692
EST:     CCAGATTGAAGGCAAACACATTTCTGTCTTCCAAGACTGCAGCAGGGACT                         CCTGAGTGGATGGCACCAGAAGTTCTACGAGACGAGCCCTCAAATGAGAAG
genomic: CCAGATTGAAGGCAAACACATTTCTGTCTTCCAAGACTGCAGCAGGGACTgtaagttata ... tgctatctagCCTGAGTGGATGGCACCAGAAGTTCTACGAGACGAGCCCTCAAATGAGAAG
EST: gi|149096725|gb|EE182499.2|EE182499
EST:     CCAGATTGAAGGCAAACACATTTCTGTCTTCCAAGACTGCAGCAGGGACT                         CCTGAGTGGATGGCACCAGAAGTTCTACGAGACGAGCCCTCAAATGAGAAG
genomic: CCAGATTGAAGGCAAACACATTTCTGTCTTCCAAGACTGCAGCAGGGACTgtaagttata ... tgctatctagCCTGAGTGGATGGCACCAGAAGTTCTACGAGACGAGCCCTCAAATGAGAAG
EST: gi|113703759|gb|EE681263.1|EE681263
EST:     CCAGATTGAAGGCAAACACATTTCTGTCTTCCAAGACTGCAGCAGGGACT                         CCTGAGTGGATGGCACCAGAAGTTCTACGAGACGAGCCCTCAAATGAGAAG
genomic: CCAGATTGAAGGCAAACACATTTCTGTCTTCCAAGACTGCAGCAGGGACTgtaagttata ... tgctatctagCCTGAGTGGATGGCACCAGAAGTTCTACGAGACGAGCCCTCAAATGAGAAG
EST: gi|26456437|gb|CA828020.1|CA828020
EST:     CCAGATTGAAGGCAAACACATTTCTGTCTTCCAAGACTGCAGCAGGGACT                         CCTGAGTGGATGGCACCAGAAGTTCTACGAGACGAGCCCTCAAATGAGAAG
genomic: CCAGATTGAAGGCAAACACATTTCTGTCTTCCAAGACTGCAGCAGGGACTgtaagttata ... tgctatctagCCTGAGTGGATGGCACCAGAAGTTCTACGAGACGAGCCCTCAAATGAGAAG
EST: gi|88757722|gb|DY541863.1|DY541863
EST:     CCAGATTGAAGGCAAACACATTTCTGTCTTCCAAGACTGCAGCAGGGACT                         CCTGAGTGGATGGCACCAGAAGTTTTACGAGACGAGCCCTCAAATGAGAAG
genomic: CCAGATTGAAGGCAAACACATTTCTGTCTTCCAAGACTGCAGCAGGGACTgtaagttata ... tgctatctagCCTGAGTGGATGGCACCAGAAGTTCTACGAGACGAGCCCTCAAATGAGAAG
EST: gi|20336958|gb|BQ172588.1|BQ172588
EST:     CCAGATTGAAGGCAAACACATTTCTGTCTTCCAAGACTGCAGCAGGGACT                         CCTGAGTGGATGGCACCAGAAGTTCTACGAGACGAGCCCTCAAATGAGAAG
genomic: CCAGATTGAAGGCAAACACATTTCTGTCTTCCAAGACTGCAGCAGGGACTgtaagttata ... tgctatctagCCTGAGTGGATGGCACCAGAAGTTCTACGAGACGAGCCCTCAAATGAGAAG
EST: gi|78110653|gb|DV529058.1|DV529058
EST:     GCAGCAGGGACT                         CCTGAGTGGATGGCACCAGAAGTTCTACGAGACGAGCCCTCAAATGAGAAG
genomic: GCAGCAGGGACTgtaagttata ... tgctatctagCCTGAGTGGATGGCACCAGAAGTTCTACGAGACGAGCCCTCAAATGAGAAG
EST: gi|60358265|gb|DN225238.1|DN225238
EST:     CCAGATTGAAGGCAAACACATTTCTGTCTTCCAAGACTGCAGCAGGGACT                         CCTGAGTGGATGGCACCAGAAGTTCTACGAGACGAGCCCTCAAATGAGAAG
genomic: CCAGATTGAAGGCAAACACATTTCTGTCTTCCAAGACTGCAGCAGGGACTgtaagttata ... tgctatctagCCTGAGTGGATGGCACCAGAAGTTCTACGAGACGAGCCCTCAAATGAGAAG
EST: gi|60357002|gb|DN223975.1|DN223975
EST:     CCAGATTGAAGGCAAACACATTTCTGTCTTCCAAGACTGCAGCAGGGACT                         CCTGAGTGGATGGCACCAGAAGTTCTACGAGACGAGCCCTCAAATGAGAAG
genomic: CCAGATTGAAGGCAAACACATTTCTGTCTTCCAAGACTGCAGCAGGGACTgtaagttata ... tgctatctagCCTGAGTGGATGGCACCAGAAGTTCTACGAGACGAGCCCTCAAATGAGAAG
EST: gi|60337361|gb|DN204334.1|DN204334
EST:     CCAGATTGAAGGCAAACACATTTCTGTCTTCCAAGACTGCAGCAGGGACT                         CCTGAGTGGATGGCACCAGAAGTTCTACGAGACGAGCCCTCAAATGAGAAG
genomic: CCAGATTGAAGGCAAACACATTTCTGTCTTCCAAGACTGCAGCAGGGACTgtaagttata ... tgctatctagCCTGAGTGGATGGCACCAGAAGTTCTACGAGACGAGCCCTCAAATGAGAAG
EST: gi|148945985|gb|EC891279.2|EC891279
EST:     GATTGAAGGCAAACACATTTCTGTCTTCCAAGACTGCAGCAGGGACT                         CCTGAGTGGATGGCACCAGAAGTTCTACGAGACGAGCCCTCAAATGAGAAG
genomic: GATTGAAGGCAAACACATTTCTGTCTTCCAAGACTGCAGCAGGGACTgtaagttata ... tgctatctagCCTGAGTGGATGGCACCAGAAGTTCTACGAGACGAGCCCTCAAATGAGAAG
EST: gi|78544160|gb|DV621658.1|DV621658
EST:     GGCAAACACATTTCTGTCTTCCAAGACTGCAGCAGGGACT                         CCTGAGTGGATGGCACCAGAAGTTCTACGAGACGAGCCCTCAAATGAGAAG
genomic: GGCAAACACATTTCTGTCTTCCAAGACTGCAGCAGGGACTgtaagttata ... tgctatctagCCTGAGTGGATGGCACCAGAAGTTCTACGAGACGAGCCCTCAAATGAGAAG
EST: gi|78544345|gb|DV621843.1|DV621843
EST:     CCAGATTGAAGGCAAACACATTTCTGTCTTCCAAGACTGCAGCAGGGACT                         CCTGAGTGGATGGCACCAGAAGTTCTACGAGACGAGCCCTCAAATGAGAAG
genomic: CCAGATTGAAGGCAAACACATTTCTGTCTTCCAAGACTGCAGCAGGGACTgtaagttata ... tgctatctagCCTGAGTGGATGGCACCAGAAGTTCTACGAGACGAGCCCTCAAATGAGAAG

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: 48 (upstream exon), 48 (downstream exon)
Score: 94

GTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTCTGTCTTCCAAGACTGCAGCAGGGACTgtaagttata ... tgctatctagCCTGAGTGGATGGCACCAGAAGTTCTACGAGACGAGCCCTCAAATGAGAAGTCTGATGTTTACAGCTTCGGTGTAATCTTATGGGAGCTTATGACATTGC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 46

GTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTCTGTCTTCCAAGACTGCAGCAGGGACTgtaagttata ... tgctatctagCCTGAGTGGATGGCACCAGAAGTTCTACGAGACGAGCCCTCAAATGAGAAGTCTGATGTTTACAGCTTCGGTGTAATCTTATGGGAGCTTATGACATTGC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 69

GTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTCTGTCTTCCAAGACTGCAGCAGGGACTgtaagttata ... tgctatctagCCTGAGTGGATGGCACCAGAAGTTCTACGAGACGAGCCCTCAAATGAGAAGTCTGATGTTTACAGCTTCGGTGTAATCTTATGGGAGCTTATGACATTGC


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 23

GTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTCTGTCTTCCAAGACTGCAGCAGGGACTgtaagttata ... tgctatctagCCTGAGTGGATGGCACCAGAAGTTCTACGAGACGAGCCCTCAAATGAGAAGTCTGATGTTTACAGCTTCGGTGTAATCTTATGGGAGCTTATGACATTGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttttgttacgcaattctatgtggctaagtgttattctgtgccatgctatctagCCTGAGTGGATGGCACCAGAAGTTCTACGAGACGAGCCCTCAAATGAGAAGTCTGATGTTTACAGCTTCGGTGTAATCTTATGGGAGCTTATGACATTGC
             aattctat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttatattgttccgtttagtgtattttgttttgttacgcaattctatgtggctaagtgttattctgtgccatgctatctagCCTGAGTGGATGGCACCAGAAGTTCTACGAGACGAGCCCTCAAATGAGAAGTCTGATGTTTACAGCTTCGGTGTAATCTTATGGGAGCTTATGACATTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT